From b2338dbcd6f00de1c4a1b9d830e9a9a79944d255 Mon Sep 17 00:00:00 2001 From: Erick Armingol Date: Wed, 16 Oct 2024 14:56:11 +0100 Subject: [PATCH 01/18] Added download of the DB from github --- sccellfie/__init__.py | 2 +- sccellfie/datasets/__init__.py | 3 +- sccellfie/datasets/database.py | 115 +++++++++++++++++++++ sccellfie/datasets/tests/test_database.py | 116 ++++++++++++++++++++++ 4 files changed, 234 insertions(+), 2 deletions(-) create mode 100644 sccellfie/datasets/database.py create mode 100644 sccellfie/datasets/tests/test_database.py diff --git a/sccellfie/__init__.py b/sccellfie/__init__.py index 599ab8f..1ecff63 100644 --- a/sccellfie/__init__.py +++ b/sccellfie/__init__.py @@ -10,4 +10,4 @@ from . import stats as tl from .expression import aggregation, smoothing, thresholds -__version__ = "0.2.3" \ No newline at end of file +__version__ = "0.3.0" \ No newline at end of file diff --git a/sccellfie/datasets/__init__.py b/sccellfie/datasets/__init__.py index 4034a16..fc6e753 100644 --- a/sccellfie/datasets/__init__.py +++ b/sccellfie/datasets/__init__.py @@ -1 +1,2 @@ -from .gene_info import (retrieve_ensembl2symbol_data) \ No newline at end of file +from .gene_info import (retrieve_ensembl2symbol_data) +from .database import (load_sccellfie_database) \ No newline at end of file diff --git a/sccellfie/datasets/database.py b/sccellfie/datasets/database.py new file mode 100644 index 0000000..f82570f --- /dev/null +++ b/sccellfie/datasets/database.py @@ -0,0 +1,115 @@ +import pandas as pd +import os + + +def load_sccellfie_database(organism='human', task_folder=None, rxn_info_filename=None, task_info_filename=None, + task_by_rxn_filename=None, task_by_gene_filename=None, rxn_by_gene_filename=None, + thresholds_filename=None): + """ + Loads files of the metabolic task database from either a local folder, individual file paths, or predefined URLs. + + Parameters + ---------- + organism : str, optional (default='human') + The organism to retrieve data for. Choose 'human' or 'mouse'. Used when loading from URLs. + + task_folder : str, optional (default=None) + The local folder path containing CellFie data files. If provided, this takes priority. + + rxn_info_filename : str, optional (default=None) + Full path for reaction information JSON file. + + task_info_filename : str, optional (default=None) + Full path for task information CSV file. + + task_by_rxn_filename : str, optional (default=None) + Full path for task by reaction CSV file. + + task_by_gene_filename : str, optional (default=None) + Full path for task by gene CSV file. + + rxn_by_gene_filename : str, optional (default=None) + Full path for reaction by gene CSV file. + + thresholds_filename : str, optional (default=None) + Full path for thresholds CSV file. + + Returns + ------- + data : dict + A dictionary containing the loaded data frames and information. + """ + # Define default URLs for human and mouse data + default_urls = { + 'human': 'https://github.com/earmingol/scCellFie/raw/refs/heads/main/task_data/homo_sapiens/', + 'mouse': 'https://github.com/earmingol/scCellFie/raw/refs/heads/main/task_data/mus_musculus/' + } + + # Define default file names + default_file_names = { + 'human': { + 'rxn_info': 'Rxn-Info-Recon2-2.json', + 'task_info': 'Task-Info.csv', + 'task_by_rxn': 'Task_by_Rxn.csv', + 'task_by_gene': 'Task_by_Gene.csv', + 'rxn_by_gene': 'Rxn_by_Gene.csv', + 'thresholds': 'Thresholds.csv' + }, + 'mouse': { + 'rxn_info': 'Rxn-Info-iMM1415.json', + 'task_info': 'Task-Info.csv', + 'task_by_rxn': 'Task_by_Rxn.csv', + 'task_by_gene': 'Task_by_Gene.csv', + 'rxn_by_gene': 'Rxn_by_Gene.csv', + 'thresholds': 'Thresholds.csv' + } + } + + # Determine the base path and file names + if task_folder: + base_path = task_folder + file_paths = { + 'rxn_info': os.path.join(base_path, default_file_names[organism]['rxn_info']), + 'task_info': os.path.join(base_path, default_file_names[organism]['task_info']), + 'task_by_rxn': os.path.join(base_path, default_file_names[organism]['task_by_rxn']), + 'task_by_gene': os.path.join(base_path, default_file_names[organism]['task_by_gene']), + 'rxn_by_gene': os.path.join(base_path, default_file_names[organism]['rxn_by_gene']), + 'thresholds': os.path.join(base_path, default_file_names[organism]['thresholds']) + } + else: + base_path = default_urls.get(organism.lower()) + if not base_path: + raise ValueError("Invalid organism. Choose 'human' or 'mouse', or provide a custom folder path.") + file_paths = { + 'rxn_info': rxn_info_filename or f"{base_path}/{default_file_names[organism]['rxn_info']}", + 'task_info': task_info_filename or f"{base_path}/{default_file_names[organism]['task_info']}", + 'task_by_rxn': task_by_rxn_filename or f"{base_path}/{default_file_names[organism]['task_by_rxn']}", + 'task_by_gene': task_by_gene_filename or f"{base_path}/{default_file_names[organism]['task_by_gene']}", + 'rxn_by_gene': rxn_by_gene_filename or f"{base_path}/{default_file_names[organism]['rxn_by_gene']}", + 'thresholds': thresholds_filename or f"{base_path}/{default_file_names[organism]['thresholds']}" + } + + # Function to load a file + def load_file(file_key, index_col=None): + full_path = file_paths[file_key] + try: + if full_path.endswith('.json'): + return pd.read_json(full_path) + elif full_path.endswith('.csv'): + return pd.read_csv(full_path, index_col=index_col) + else: + raise ValueError(f"Unsupported file format: {full_path}") + except Exception as e: + print(f"Error loading {full_path}: {str(e)}") + return None + + # Load all files + data = {} + data['rxn_info'] = load_file('rxn_info') + data['task_info'] = load_file('task_info') + data['task_by_rxn'] = load_file('task_by_rxn', index_col='Task') + data['task_by_gene'] = load_file('task_by_gene', index_col='Task') + data['rxn_by_gene'] = load_file('rxn_by_gene', index_col='Reaction') + data['thresholds'] = load_file('thresholds', index_col='symbol') + data['organism'] = organism + return data \ No newline at end of file diff --git a/sccellfie/datasets/tests/test_database.py b/sccellfie/datasets/tests/test_database.py new file mode 100644 index 0000000..cfff517 --- /dev/null +++ b/sccellfie/datasets/tests/test_database.py @@ -0,0 +1,116 @@ +import pytest +import os +import tempfile +import pandas as pd + +from unittest.mock import patch + +from sccellfie.datasets.database import load_sccellfie_database # Replace 'your_module' with the actual module name + +# Mock data for testing +mock_json_data = pd.DataFrame({'col1': [1, 2, 3], 'col2': ['a', 'b', 'c']}) +mock_csv_data = pd.DataFrame({'col1': [4, 5, 6], 'col2': ['d', 'e', 'f']}) + + +@pytest.fixture +def mock_read_json(monkeypatch): + def mock_read(path): + return mock_json_data + + monkeypatch.setattr(pd, 'read_json', mock_read) + + +@pytest.fixture +def mock_read_csv(monkeypatch): + def mock_read(path, index_col=None): + return mock_csv_data + + monkeypatch.setattr(pd, 'read_csv', mock_read) + + +def test_load_sccellfie_database_default_urls(mock_read_json, mock_read_csv): + data = load_sccellfie_database(organism='human') + assert isinstance(data, dict) + assert 'rxn_info' in data + assert 'task_info' in data + assert 'task_by_rxn' in data + assert 'task_by_gene' in data + assert 'rxn_by_gene' in data + assert 'thresholds' in data + assert data['organism'] == 'human' + assert data['rxn_info'].equals(mock_json_data) + assert data['task_info'].equals(mock_csv_data) + + +def test_load_sccellfie_database_local_folder(): + with tempfile.TemporaryDirectory() as tmpdirname: + # Create mock files + pd.DataFrame().to_json(os.path.join(tmpdirname, 'Rxn-Info-Recon2-2.json')) + pd.DataFrame().to_csv(os.path.join(tmpdirname, 'Task-Info.csv')) + pd.DataFrame().to_csv(os.path.join(tmpdirname, 'Task_by_Rxn.csv')) + pd.DataFrame().to_csv(os.path.join(tmpdirname, 'Task_by_Gene.csv')) + pd.DataFrame().to_csv(os.path.join(tmpdirname, 'Rxn_by_Gene.csv')) + pd.DataFrame().to_csv(os.path.join(tmpdirname, 'Thresholds.csv')) + + data = load_sccellfie_database(organism='human', task_folder=tmpdirname) + assert isinstance(data, dict) + assert 'rxn_info' in data + assert 'task_info' in data + assert 'task_by_rxn' in data + assert 'task_by_gene' in data + assert 'rxn_by_gene' in data + assert 'thresholds' in data + assert data['organism'] == 'human' + + +def test_load_sccellfie_database_individual_files(): + with tempfile.TemporaryDirectory() as tmpdirname: + # Create mock files with unique names + rxn_info_path = os.path.join(tmpdirname, 'custom_rxn_info.json') + task_info_path = os.path.join(tmpdirname, 'custom_task_info.csv') + task_by_rxn_path = os.path.join(tmpdirname, 'custom_task_by_rxn.csv') + task_by_gene_path = os.path.join(tmpdirname, 'custom_task_by_gene.csv') + rxn_by_gene_path = os.path.join(tmpdirname, 'custom_rxn_by_gene.csv') + thresholds_path = os.path.join(tmpdirname, 'custom_thresholds.csv') + + pd.DataFrame().to_json(rxn_info_path) + pd.DataFrame().to_csv(task_info_path) + pd.DataFrame().to_csv(task_by_rxn_path) + pd.DataFrame().to_csv(task_by_gene_path) + pd.DataFrame().to_csv(rxn_by_gene_path) + pd.DataFrame().to_csv(thresholds_path) + + data = load_sccellfie_database( + organism='human', + rxn_info_filename=rxn_info_path, + task_info_filename=task_info_path, + task_by_rxn_filename=task_by_rxn_path, + task_by_gene_filename=task_by_gene_path, + rxn_by_gene_filename=rxn_by_gene_path, + thresholds_filename=thresholds_path + ) + assert isinstance(data, dict) + assert 'rxn_info' in data + assert 'task_info' in data + assert 'task_by_rxn' in data + assert 'task_by_gene' in data + assert 'rxn_by_gene' in data + assert 'thresholds' in data + assert data['organism'] == 'human' + + +def test_load_sccellfie_database_invalid_organism(): + with pytest.raises(ValueError): + load_sccellfie_database(organism='invalid') + + +@patch('pandas.read_json') +@patch('pandas.read_csv') +def test_load_sccellfie_database_file_error(mock_read_csv, mock_read_json): + mock_read_json.side_effect = Exception("Mock JSON read error") + mock_read_csv.side_effect = Exception("Mock CSV read error") + + data = load_sccellfie_database(organism='human') + assert isinstance(data, dict) + assert all(value is None for key, value in data.items() if key != 'organism') + assert data['organism'] == 'human' \ No newline at end of file From b9bb76ceb6abf7aedb3d284ecb87741f36453cb3 Mon Sep 17 00:00:00 2001 From: Erick Armingol Date: Fri, 18 Oct 2024 09:39:26 +0100 Subject: [PATCH 02/18] Moved toy data to sccellfie.datasets --- sccellfie/{tests => datasets}/toy_inputs.py | 0 sccellfie/expression/tests/test_aggregation.py | 2 +- sccellfie/expression/tests/test_smoothing.py | 2 +- sccellfie/expression/tests/test_threshold.py | 2 +- sccellfie/external/tests/test_tf_idf.py | 2 +- sccellfie/io/tests/test_load_data.py | 2 +- sccellfie/io/tests/test_save_data.py | 2 +- sccellfie/plotting/tests/test_differential_results.py | 2 +- sccellfie/plotting/tests/test_distributions.py | 2 +- sccellfie/preprocessing/tests/test_prepare_inputs.py | 2 +- sccellfie/spatial/tests/test_assortativity.py | 2 +- sccellfie/spatial/tests/test_hotspots.py | 2 +- sccellfie/spatial/tests/test_knn_network.py | 3 +-- sccellfie/stats/tests/test_differential_analysis.py | 2 +- sccellfie/stats/tests/test_markers_from_task.py | 2 +- sccellfie/tests/test_gene_score.py | 2 +- sccellfie/tests/test_metabolic_task.py | 2 +- sccellfie/tests/test_reaction_activity.py | 2 +- 18 files changed, 17 insertions(+), 18 deletions(-) rename sccellfie/{tests => datasets}/toy_inputs.py (100%) diff --git a/sccellfie/tests/toy_inputs.py b/sccellfie/datasets/toy_inputs.py similarity index 100% rename from sccellfie/tests/toy_inputs.py rename to sccellfie/datasets/toy_inputs.py diff --git a/sccellfie/expression/tests/test_aggregation.py b/sccellfie/expression/tests/test_aggregation.py index 49514ee..44f380d 100644 --- a/sccellfie/expression/tests/test_aggregation.py +++ b/sccellfie/expression/tests/test_aggregation.py @@ -4,7 +4,7 @@ import scipy.sparse as sparse from sccellfie.expression.aggregation import agg_expression_cells, top_mean -from sccellfie.tests.toy_inputs import create_random_adata, create_controlled_adata +from sccellfie.datasets.toy_inputs import create_random_adata, create_controlled_adata @pytest.mark.parametrize("use_raw", [False, True]) diff --git a/sccellfie/expression/tests/test_smoothing.py b/sccellfie/expression/tests/test_smoothing.py index edea429..d69d110 100644 --- a/sccellfie/expression/tests/test_smoothing.py +++ b/sccellfie/expression/tests/test_smoothing.py @@ -3,7 +3,7 @@ from scipy.sparse import csr_matrix from sccellfie.expression.smoothing import get_smoothing_matrix, smooth_expression_knn -from sccellfie.tests.toy_inputs import create_controlled_adata +from sccellfie.datasets.toy_inputs import create_controlled_adata def test_get_smoothing_matrix(): # Create a controlled adata object with known connectivities diff --git a/sccellfie/expression/tests/test_threshold.py b/sccellfie/expression/tests/test_threshold.py index 34aab22..203c8a0 100644 --- a/sccellfie/expression/tests/test_threshold.py +++ b/sccellfie/expression/tests/test_threshold.py @@ -3,7 +3,7 @@ from pandas.testing import assert_frame_equal from sccellfie.expression.thresholds import get_local_mean_threshold, get_global_mean_threshold, get_local_percentile_threshold, get_global_percentile_threshold, get_local_trimean_threshold, get_global_trimean_threshold, set_manual_threshold -from sccellfie.tests.toy_inputs import create_controlled_adata +from sccellfie.datasets.toy_inputs import create_controlled_adata @pytest.mark.parametrize("use_raw, lower_bound, upper_bound, exclude_zeros", diff --git a/sccellfie/external/tests/test_tf_idf.py b/sccellfie/external/tests/test_tf_idf.py index 3b15944..23a92da 100644 --- a/sccellfie/external/tests/test_tf_idf.py +++ b/sccellfie/external/tests/test_tf_idf.py @@ -1,7 +1,7 @@ import pandas as pd from sccellfie.external.tf_idf import quick_markers -from sccellfie.tests.toy_inputs import create_random_adata +from sccellfie.datasets.toy_inputs import create_random_adata def test_output_structure(): diff --git a/sccellfie/io/tests/test_load_data.py b/sccellfie/io/tests/test_load_data.py index a034913..6409c87 100644 --- a/sccellfie/io/tests/test_load_data.py +++ b/sccellfie/io/tests/test_load_data.py @@ -10,7 +10,7 @@ from sccellfie.metabolic_task import compute_mt_score from sccellfie.reaction_activity import compute_reaction_activity from sccellfie.spatial import create_knn_network -from sccellfie.tests.toy_inputs import create_random_adata, create_controlled_adata_with_spatial, create_controlled_gpr_dict, create_global_threshold, create_controlled_task_by_rxn +from sccellfie.datasets.toy_inputs import create_random_adata, create_controlled_adata_with_spatial, create_controlled_gpr_dict, create_global_threshold, create_controlled_task_by_rxn @pytest.mark.parametrize("reactions_filename, mt_filename", [ diff --git a/sccellfie/io/tests/test_save_data.py b/sccellfie/io/tests/test_save_data.py index 900aef4..0130b6a 100644 --- a/sccellfie/io/tests/test_save_data.py +++ b/sccellfie/io/tests/test_save_data.py @@ -4,7 +4,7 @@ from sccellfie.io.save_data import save_adata from sccellfie.spatial import create_knn_network -from sccellfie.tests.toy_inputs import create_random_adata, create_random_adata_with_spatial +from sccellfie.datasets.toy_inputs import create_random_adata, create_random_adata_with_spatial @pytest.mark.parametrize("spatial_data, test_attr", [(True, False), (False, False), (False, True)]) # Test with and without spatial data diff --git a/sccellfie/plotting/tests/test_differential_results.py b/sccellfie/plotting/tests/test_differential_results.py index 1784d85..bf9d7c5 100644 --- a/sccellfie/plotting/tests/test_differential_results.py +++ b/sccellfie/plotting/tests/test_differential_results.py @@ -5,7 +5,7 @@ from matplotlib.axes import Axes from sccellfie.plotting.differential_results import create_volcano_plot, create_comparative_violin -from sccellfie.tests.toy_inputs import create_controlled_adata +from sccellfie.datasets.toy_inputs import create_controlled_adata def test_create_volcano_plot(): # Create a sample DataFrame similar to the output of scanpy_differential_analysis diff --git a/sccellfie/plotting/tests/test_distributions.py b/sccellfie/plotting/tests/test_distributions.py index 827a06f..fed2970 100644 --- a/sccellfie/plotting/tests/test_distributions.py +++ b/sccellfie/plotting/tests/test_distributions.py @@ -3,7 +3,7 @@ import matplotlib.pyplot as plt from sccellfie.plotting.distributions import create_multi_violin_plots -from sccellfie.tests.toy_inputs import create_controlled_adata +from sccellfie.datasets.toy_inputs import create_controlled_adata @pytest.fixture diff --git a/sccellfie/preprocessing/tests/test_prepare_inputs.py b/sccellfie/preprocessing/tests/test_prepare_inputs.py index ee37aa4..3a32918 100644 --- a/sccellfie/preprocessing/tests/test_prepare_inputs.py +++ b/sccellfie/preprocessing/tests/test_prepare_inputs.py @@ -7,7 +7,7 @@ from sccellfie.preprocessing.gpr_rules import clean_gene_names, find_genes_gpr from sccellfie.preprocessing.prepare_inputs import preprocess_inputs, stratified_subsample_adata, normalize_adata, transform_adata_gene_names -from sccellfie.tests.toy_inputs import create_random_adata, create_controlled_adata, create_controlled_gpr_dict, create_controlled_task_by_rxn, create_controlled_task_by_gene, create_controlled_rxn_by_gene +from sccellfie.datasets.toy_inputs import create_random_adata, create_controlled_adata, create_controlled_gpr_dict, create_controlled_task_by_rxn, create_controlled_task_by_gene, create_controlled_rxn_by_gene def test_preprocess_inputs(): diff --git a/sccellfie/spatial/tests/test_assortativity.py b/sccellfie/spatial/tests/test_assortativity.py index d7df385..3b41c56 100644 --- a/sccellfie/spatial/tests/test_assortativity.py +++ b/sccellfie/spatial/tests/test_assortativity.py @@ -4,7 +4,7 @@ from sccellfie.spatial.assortativity import compute_var_assortativity, compute_assortativity from sccellfie.spatial.knn_network import create_knn_network -from sccellfie.tests.toy_inputs import create_random_adata_with_spatial +from sccellfie.datasets.toy_inputs import create_random_adata_with_spatial @pytest.mark.parametrize("use_raw", [False, True]) diff --git a/sccellfie/spatial/tests/test_hotspots.py b/sccellfie/spatial/tests/test_hotspots.py index beb74c5..10e169c 100644 --- a/sccellfie/spatial/tests/test_hotspots.py +++ b/sccellfie/spatial/tests/test_hotspots.py @@ -2,7 +2,7 @@ import pandas as pd from sccellfie.spatial.hotspots import obtain_hotspots, summarize_hotspots, compute_hotspots -from sccellfie.tests.toy_inputs import create_random_adata_with_spatial +from sccellfie.datasets.toy_inputs import create_random_adata_with_spatial @pytest.mark.parametrize("use_raw", [False, True]) def test_obtain_hotspots(use_raw): diff --git a/sccellfie/spatial/tests/test_knn_network.py b/sccellfie/spatial/tests/test_knn_network.py index 3c3cd79..8f5eced 100644 --- a/sccellfie/spatial/tests/test_knn_network.py +++ b/sccellfie/spatial/tests/test_knn_network.py @@ -1,6 +1,5 @@ -import networkx as nx from sccellfie.spatial.knn_network import find_spatial_neighbors, create_knn_network -from sccellfie.tests.toy_inputs import create_controlled_adata_with_spatial +from sccellfie.datasets.toy_inputs import create_controlled_adata_with_spatial def test_find_spatial_neighbors(): # Create mock data with spatial coordinates diff --git a/sccellfie/stats/tests/test_differential_analysis.py b/sccellfie/stats/tests/test_differential_analysis.py index 1b712a6..bd8a3f0 100644 --- a/sccellfie/stats/tests/test_differential_analysis.py +++ b/sccellfie/stats/tests/test_differential_analysis.py @@ -7,7 +7,7 @@ from sccellfie.plotting.differential_results import create_volcano_plot from sccellfie.stats.differential_analysis import cohens_d, scanpy_differential_analysis -from sccellfie.tests.toy_inputs import create_random_adata +from sccellfie.datasets.toy_inputs import create_random_adata def test_cohens_d(): diff --git a/sccellfie/stats/tests/test_markers_from_task.py b/sccellfie/stats/tests/test_markers_from_task.py index 0ae96c9..99e228c 100644 --- a/sccellfie/stats/tests/test_markers_from_task.py +++ b/sccellfie/stats/tests/test_markers_from_task.py @@ -6,7 +6,7 @@ from sccellfie.gene_score import compute_gene_scores from sccellfie.reaction_activity import compute_reaction_activity from sccellfie.metabolic_task import compute_mt_score -from sccellfie.tests.toy_inputs import create_controlled_adata, create_controlled_task_by_rxn, create_controlled_gpr_dict, create_global_threshold +from sccellfie.datasets.toy_inputs import create_controlled_adata, create_controlled_task_by_rxn, create_controlled_gpr_dict, create_global_threshold @pytest.mark.parametrize("groupby, group, min_activity", diff --git a/sccellfie/tests/test_gene_score.py b/sccellfie/tests/test_gene_score.py index 010ece3..be373e2 100644 --- a/sccellfie/tests/test_gene_score.py +++ b/sccellfie/tests/test_gene_score.py @@ -8,7 +8,7 @@ from sccellfie.gene_score import gene_score, compute_gene_scores, compute_gpr_gene_score from sccellfie.tests import PCOUNT -from sccellfie.tests.toy_inputs import create_controlled_adata +from sccellfie.datasets.toy_inputs import create_controlled_adata def test_gene_score(): diff --git a/sccellfie/tests/test_metabolic_task.py b/sccellfie/tests/test_metabolic_task.py index d88a406..f56ef28 100644 --- a/sccellfie/tests/test_metabolic_task.py +++ b/sccellfie/tests/test_metabolic_task.py @@ -5,7 +5,7 @@ from sccellfie.reaction_activity import compute_reaction_activity from sccellfie.metabolic_task import compute_mt_score from sccellfie.tests import PCOUNT -from sccellfie.tests.toy_inputs import create_controlled_adata, create_controlled_gpr_dict, create_global_threshold, create_controlled_task_by_rxn +from sccellfie.datasets.toy_inputs import create_controlled_adata, create_controlled_gpr_dict, create_global_threshold, create_controlled_task_by_rxn @pytest.mark.parametrize("use_specificity", [True, False]) diff --git a/sccellfie/tests/test_reaction_activity.py b/sccellfie/tests/test_reaction_activity.py index 9d82db2..1fbfe1d 100644 --- a/sccellfie/tests/test_reaction_activity.py +++ b/sccellfie/tests/test_reaction_activity.py @@ -5,7 +5,7 @@ from sccellfie.gene_score import compute_gene_scores from sccellfie.reaction_activity import compute_reaction_activity from sccellfie.tests import PCOUNT -from sccellfie.tests.toy_inputs import create_controlled_adata, create_controlled_gpr_dict, create_global_threshold +from sccellfie.datasets.toy_inputs import create_controlled_adata, create_controlled_gpr_dict, create_global_threshold @pytest.mark.parametrize("use_specificity", [True, False]) From 175f3a9f9583b41d4c6fa72c8fccd49fc21b1d27 Mon Sep 17 00:00:00 2001 From: Erick Armingol Date: Fri, 18 Oct 2024 09:40:49 +0100 Subject: [PATCH 03/18] Added desc to progress bar in smooth_expression_knn --- sccellfie/expression/smoothing.py | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/sccellfie/expression/smoothing.py b/sccellfie/expression/smoothing.py index fa3d3ca..814e098 100644 --- a/sccellfie/expression/smoothing.py +++ b/sccellfie/expression/smoothing.py @@ -134,7 +134,7 @@ def smooth_expression_knn(adata, key_added='smoothed_X', neighbors_key='neighbor smoothed_matrix = np.zeros(X.shape) # Iterate over chunks of cells - for i in tqdm(range(n_chunks), disable=disable_pbar): + for i in tqdm(range(n_chunks), disable=disable_pbar, desc='Smoothing Expression'): start_idx = i * chunk_size end_idx = min((i + 1) * chunk_size, n_cells) From 670b645264f59c7259f7ab0dd08c66409e3fb174 Mon Sep 17 00:00:00 2001 From: Erick Armingol Date: Fri, 18 Oct 2024 15:16:02 +0100 Subject: [PATCH 04/18] Implemented one-command pipeline --- sccellfie/sccellfie_pipeline.py | 411 +++++++++++++++++++++ sccellfie/tests/test_sccellfie_pipeline.py | 155 ++++++++ 2 files changed, 566 insertions(+) create mode 100644 sccellfie/sccellfie_pipeline.py create mode 100644 sccellfie/tests/test_sccellfie_pipeline.py diff --git a/sccellfie/sccellfie_pipeline.py b/sccellfie/sccellfie_pipeline.py new file mode 100644 index 0000000..e808133 --- /dev/null +++ b/sccellfie/sccellfie_pipeline.py @@ -0,0 +1,411 @@ +import pandas as pd +import scanpy as sc +from tqdm import tqdm + +from sccellfie.datasets.database import load_sccellfie_database +from sccellfie.io.save_data import save_adata +from sccellfie.preprocessing.prepare_inputs import normalize_adata, preprocess_inputs, transform_adata_gene_names, CORRECT_GENES +from sccellfie.expression.smoothing import smooth_expression_knn +from sccellfie.gene_score import compute_gene_scores +from sccellfie.reaction_activity import compute_reaction_activity +from sccellfie.metabolic_task import compute_mt_score + + +def run_sccellfie_pipeline(adata, organism='human', sccellfie_data_folder=None, sccellfie_db=None, n_counts_col='n_counts', + process_by_group=False, groupby=None, neighbors_key='neighbors', + n_neighbors=10, batch_key=None, threshold_key='sccellfie_threshold', smooth_cells=True, + alpha=0.33, chunk_size=5000, disable_pbar=False, save_folder=None, save_filename=None, verbose=True): + """ + Runs the complete scCellFie pipeline on the given AnnData object, processing by cell type if specified. + + Parameters: + ----------- + adata : AnnData + Annotated data matrix containing the expression data and nearest neighbor graph. + The .X matrix must contain raw counts. If neighbors are not present, they will be computed. + + organism : str, optional (default='human') + Organism for the analysis. Options are 'human' or 'mouse'. + + sccellfie_data_folder : str, optional (default=None) + Path to the folder containing the files of the scCellFie database + (reactions, GPR rules, metabolic tasks, etc.). + + scceellfie_db : dict, optional (default=None) + Dictionary containing the scCellFie database information. + If this information is provided, the sccellfie_data_folder will be ignored. + This dictionary must contain the keys 'rxn_info', 'task_by_gene', 'rxn_by_gene', 'task_by_rxn', 'thresholds', and + 'organism'. + Examples of dataframes can be found at + https://github.com/earmingol/scCellFie/raw/refs/heads/main/task_data/homo_sapiens/ + + n_counts_col : str, optional (default='n_counts') + Column name in adata.obs containing the total counts per cell. + If None or not present, the total counts will be computed. + + process_by_group : bool, optional (default=False) + Whether to process data by groups (e.g., cell types). This is intended to be + memory efficient for huge datasets. Results will be not outputted and will be + saved to the disk instead. If True, `groupby` must be specified, as well as `save_folder`. + + groupby : str, optional (default=None) + Column name in adata.obs for the groups to process. Required if process_by_group is True. + + neighbors_key : str, optional (default='neighbors') + Key in adata.uns for neighbor data. If not present, neighbors will be computed. + + n_neighbors : int, optional (default=10) + Number of neighbors to find (if `neighbors_key` is not present). This number of neighbors + will be used in the KNN smoothing too, if `smooth_cells` is True. + + batch_key : str, optional (default=None) + Column name in adata.obs for batch information. If present, Harmony will be used to + integrate the data before computing neighbors (when neighbors are not present in the AnnData object). + + threshold_key : str, optional (default='sccellfie_threshold') + Key for the threshold to use in gene score computation. + This key is present in the threshold file of the scCellFie (or custom) database. + + smooth_cells : bool, optional (default=True) + Whether to perform a smoothing for the expression values based on the nearest neighbors. + If True, KNN smoothing will be performed. + + alpha : float, optional (default: 0.33) + The weight or fraction of the smoothed expression to use in the final expression matrix. + The final expression matrix is computed as (1 - alpha) * X + alpha * (S @ X), where X is the + original expression matrix and S is the smoothed matrix. + + chunk_size : int, optional (default=5000) + Size of chunks for smoothing the expression of large datasets. + This is used to split the data into smaller parts to reduce memory usage. + + disable_pbar : bool, optional (default=False) + Whether to disable the progress bar. + + save_folder : str, optional (default=None) + Folder to save results. The AnnData object is saved to folder/save_filename.h5ad. + The scCellFie attributes are saved to: + - reactions: folder/save_filename_reactions.h5ad. + - metabolic_tasks: folder/save_filename_metabolic_tasks.h5ad. + If process_by_group is True, file names will include cell type name as in + save_filename_celltype.h5ad. + + save_filename : str, optional (default=None) + Filename to save results. If None, the filename will be 'sccellfie'. + + verbose : bool, optional (default=True) + Whether to print messages during the processing. + + Returns: + -------- + preprocessed_db : dict + Complete preprocessed database including the processed AnnData object and scCellFie attributes/results, + normally stored as preprocessed_db['adata'], preprocessed_db['adata'].reactions, + and preprocessed_db['adata'].metabolic_tasks. THIS IS OUTPUT ONLY IF `process_by_group` is False. + """ + if verbose: + print("\n==== scCellFie Pipeline: Initializing ====") + print(f"Loading scCellFie database for organism: {organism}") + else: + disable_pbar = True + + # Load scCellFie database + if sccellfie_db is None: + sccellfie_db = load_sccellfie_database(organism=organism, task_folder=sccellfie_data_folder) + + # Check for ENSEMBL IDs and prepare transformation if necessary + ensembl_ids = all([g.startswith('ENS') for g in adata.var_names]) + + # Default filename + if save_filename is None: + save_filename = 'sccellfie' + + if process_by_group: + if groupby is None: + raise ValueError("groupby must be specified when process_by_group is True") + if save_folder is None: + raise ValueError("save_folder must be specified when process_by_group is True") + + if verbose: + print(f"\n==== scCellFie Pipeline: Processing by groups ====") + print(f"Using column: {groupby}") + + preprocessed_db = None + met_genes = None + first_group = True + + for celltype, df in tqdm(adata.obs.groupby(groupby), desc='Processing groups', disable=disable_pbar): + adata_tmp = adata[df.index, :].copy() + + if first_group: + preprocessed_db = process_chunk(adata=adata_tmp, + sccellfie_db=sccellfie_db, + n_counts_col=n_counts_col, + smooth_cells=smooth_cells, + alpha=alpha, + chunk_size=chunk_size, + threshold_key=threshold_key, + disable_pbar=True, + neighbors_key=neighbors_key, + n_neighbors=n_neighbors, + batch_key=batch_key, + ensembl_ids=ensembl_ids, + organism=organism, + verbose=False, + first_group=True) + met_genes = list(preprocessed_db['adata'].var_names) + first_group = False + else: + preprocessed_db = process_chunk(adata=adata_tmp, + sccellfie_db=sccellfie_db, + n_counts_col=n_counts_col, + smooth_cells=smooth_cells, + alpha=alpha, + chunk_size=chunk_size, + threshold_key=threshold_key, + disable_pbar=True, + neighbors_key=neighbors_key, + n_neighbors=n_neighbors, + batch_key=batch_key, + ensembl_ids=ensembl_ids, + organism=organism, + verbose=False, + first_group=False, + preprocessed_db=preprocessed_db, + met_genes=met_genes) + + # Save results if requested + if save_folder: + save_adata(adata=preprocessed_db['adata'], + folder=save_folder, + filename=save_filename + '_' + celltype.replace(' ', '_'), + verbose=False) + if verbose: + print("\n==== scCellFie Pipeline: Processing completed successfully ====") + else: + if verbose: + print("\n==== scCellFie Pipeline: Processing entire dataset ====") + preprocessed_db = process_chunk(adata=adata, + sccellfie_db=sccellfie_db, + n_counts_col=n_counts_col, + smooth_cells=smooth_cells, + alpha=alpha, + chunk_size=chunk_size, + threshold_key=threshold_key, + disable_pbar=disable_pbar, + neighbors_key=neighbors_key, + n_neighbors=n_neighbors, + batch_key=batch_key, + ensembl_ids=ensembl_ids, + organism=organism, + verbose=verbose, + first_group=True) + + # Save results if requested + if save_folder: + if verbose: + print("\n==== scCellFie Pipeline: Saving results ====") + save_adata(adata=preprocessed_db['adata'], + folder=save_folder, + filename=save_filename) + if verbose: + print("\n==== scCellFie Pipeline: Processing completed successfully ====") + return preprocessed_db + + +def process_chunk(adata, sccellfie_db, n_counts_col, smooth_cells, alpha, chunk_size, threshold_key, disable_pbar, + neighbors_key, n_neighbors, batch_key, ensembl_ids, organism, first_group=True, preprocessed_db=None, + met_genes=None, verbose=True, ): + """ + Processes a chunk of data (either a cell type or the entire dataset). + + Parameters + ---------- + adata : AnnData object + Annotated data matrix containing the expression data and nearest neighbor graph. + + sccellfie_db : dict + Dictionary containing the scCellFie database information. + Keys are 'rxn_info', 'task_by_gene', 'rxn_by_gene', 'task_by_rxn', and 'thresholds'. + + n_counts_col : str + Column name in adata.obs containing the total counts per cell. + + smooth_cells : bool + Whether to perform a smoothing for the expression values based on the nearest neighbors. + + alpha : float + Smoothing factor for KNN smoothing. + + chunk_size : int + Size of chunks for processing large datasets. + + threshold_key : str + Key for the threshold to use in gene score computation. + + disable_pbar : bool + Whether to disable the progress bar. + + neighbors_key : str + Key in adata.uns for neighbor data. + + n_neighbors : int + Number of neighbors to find (if `neighbors_key` is not present). + + batch_key : str or None + Column name in adata.obs for batch information. + This is used for Harmony integration if neighbors are not present. + + ensembl_ids : bool + + organism : str + Organism for the analysis. Options are 'human' or 'mouse'. + + first_group : bool, optional (default=True) + Whether this is the first group to process. + + preprocessed_db : dict, optional (default=None) + Dictionary containing the processed data from previous groups. + + met_genes : list, optional (default=None) + List of genes to filter for subsequent groups. + + verbose : bool, optional (default=True) + Whether to print messages during the processing. + + Returns + ------- + preprocessed_db : dict + Complete preprocessed database including the processed AnnData object and scCellFie attributes/results, + normally stored as preprocessed_db['adata'], preprocessed_db['adata'].reactions, + and preprocessed_db['adata'].metabolic_tasks. + """ + if verbose: + print("\n---- scCellFie Step: Preprocessing data ----") + + # Ensure adata is in memory + if adata.isbacked: + adata = adata.to_memory() + + # Preprocessing + adata.layers['counts'] = adata.X.copy() + normalize_adata(adata, n_counts_key=n_counts_col) + + # Transform gene names if necessary + if ensembl_ids: + transform_adata_gene_names(adata=adata, organism=organism, copy=False, drop_unmapped=True) + + # Check for presence of neighbors + if neighbors_key not in adata.uns.keys(): + if verbose: + print("\n---- scCellFie Step: Computing neighbors ----") + compute_neighbors(adata=adata, batch_key=batch_key, n_neighbors=n_neighbors, verbose=verbose) + + if first_group: + if verbose: + print("\n---- scCellFie Step: Preparing inputs ----") + # Prepare scCellFie inputs and filter reactions, tasks and genes + preprocessed_db = dict() + preprocessed_db['adata'], preprocessed_db['gpr_rules'], preprocessed_db['task_by_gene'], preprocessed_db[ + 'rxn_by_gene'], preprocessed_db['task_by_rxn'] = preprocess_inputs( + adata=adata, + gpr_info=sccellfie_db['rxn_info'], + task_by_gene=sccellfie_db['task_by_gene'], + rxn_by_gene=sccellfie_db['rxn_by_gene'], + task_by_rxn=sccellfie_db['task_by_rxn'], + verbose=verbose + ) + + for k, v in sccellfie_db.items(): + if k not in preprocessed_db.keys(): + preprocessed_db[k] = v + else: + correction_dict = CORRECT_GENES[organism] + correction_dict = {k: v for k, v in correction_dict.items() if v in met_genes} + adata.var.index = [correction_dict[g] if g in correction_dict.keys() else g for g in adata.var.index] + # Filter genes for subsequent groups + adata = adata[:, met_genes] + preprocessed_db['adata'] = adata + + # Smoothing of gene expression + if smooth_cells: + if verbose: + print("\n---- scCellFie Step: Smoothing gene expression ----") + smooth_expression_knn(adata=preprocessed_db['adata'], + alpha=alpha, + mode='adjacency', + neighbors_key=neighbors_key, + chunk_size=chunk_size if preprocessed_db['adata'].shape[0] > 30000 else None, + disable_pbar=disable_pbar) + preprocessed_db['adata'].X = preprocessed_db['adata'].layers['smoothed_X'] + + # Compute gene scores + if verbose: + print("\n---- scCellFie Step: Computing gene scores ----") + + compute_gene_scores(adata=preprocessed_db['adata'], + thresholds=preprocessed_db['thresholds'][[threshold_key]]) + + # Compute reaction activity + if verbose: + print("\n---- scCellFie Step: Computing reaction activity ----") + compute_reaction_activity(adata=preprocessed_db['adata'], + gpr_dict=preprocessed_db['gpr_rules'], + use_specificity=True, + disable_pbar=disable_pbar) + + # Compute metabolic task activity + if verbose: + print("\n---- scCellFie Step: Computing metabolic task activity ----") + compute_mt_score(adata=preprocessed_db['adata'], + task_by_rxn=preprocessed_db['task_by_rxn'], + verbose=verbose) + + return preprocessed_db + + +def compute_neighbors(adata, batch_key, n_neighbors=10, verbose=True): + """ + Computes neighbors for the AnnData object. In addition, + finds the UMAP embeddings from these neighbors if not present. + + Parameters + ---------- + adata : AnnData object + Annotated data matrix containing the expression data. + + batch_key : str or None + Column name in adata.obs for batch information. + This is used for Harmony integration if neighbors are not present. + + n_neighbors : int, optional (default=10) + Number of neighbors to find. + + verbose : bool, optional (default=True) + Whether to print messages during the processing. + + Returns + ------- + None + The neighbors are stored in adata.uns['neighbors']. + UMAP embeddings are stored in adata.obsm['X_umap'] if not present. + """ + bdata = adata.copy() + if 'normalization' not in bdata.uns.keys(): + sc.pp.normalize_total(bdata, target_sum=1e4) + sc.pp.log1p(bdata) + sc.pp.highly_variable_genes(bdata, n_top_genes=2000, flavor='seurat_v3', batch_key=batch_key) + sc.tl.pca(bdata) + adata.obsm['X_pca'] = bdata.obsm['X_pca'] + if batch_key: + try: + sc.external.pp.harmony_integrate(bdata, batch_key, verbose) + rep = 'X_pca_harmony' + adata.obsm[rep] = bdata.obsm[rep] + except: + rep = 'X_pca' + else: + rep = 'X_pca' + sc.pp.neighbors(adata, use_rep=rep, n_neighbors=n_neighbors) + if 'X_umap' not in adata.obsm.keys(): + sc.tl.umap(adata) \ No newline at end of file diff --git a/sccellfie/tests/test_sccellfie_pipeline.py b/sccellfie/tests/test_sccellfie_pipeline.py new file mode 100644 index 0000000..1d50fa8 --- /dev/null +++ b/sccellfie/tests/test_sccellfie_pipeline.py @@ -0,0 +1,155 @@ +import pytest +import numpy as np +import pandas as pd +from anndata import AnnData +from scipy.sparse import csr_matrix + +from sccellfie.sccellfie_pipeline import run_sccellfie_pipeline, process_chunk, compute_neighbors +from sccellfie.datasets.toy_inputs import (create_random_adata, create_controlled_adata, create_controlled_gpr_dict, + create_controlled_task_by_rxn, create_controlled_rxn_by_gene, create_controlled_task_by_gene, + create_global_threshold) + + +def add_toy_neighbors(adata, n_neighbors=10): + """ + Add a toy neighbor object to the AnnData object, mimicking scanpy's format. + """ + n_obs = adata.n_obs + + # Create toy connectivities and distances matrices + connectivities = csr_matrix((np.ones(n_obs * n_neighbors), + (np.repeat(np.arange(n_obs), n_neighbors), + np.random.choice(n_obs, n_obs * n_neighbors))), + shape=(n_obs, n_obs)) + + distances = csr_matrix((np.random.rand(n_obs * n_neighbors), + (np.repeat(np.arange(n_obs), n_neighbors), + np.random.choice(n_obs, n_obs * n_neighbors))), + shape=(n_obs, n_obs)) + + # Create the neighbors dictionary + adata.uns['neighbors'] = { + 'params': { + 'n_neighbors': n_neighbors, + 'method': 'umap' + }, + 'connectivities_key': 'connectivities', + 'distances_key': 'distances' + } + + # Add matrices to obsp + adata.obsp['connectivities'] = connectivities + adata.obsp['distances'] = distances + + # Add toy PCA and UMAP + adata.obsm['X_pca'] = np.random.rand(n_obs, 50) # 50 PCA components + adata.obsm['X_umap'] = np.random.rand(n_obs, 2) # 2D UMAP + +@pytest.fixture +def random_adata_with_neighbors(): + adata = create_random_adata(n_obs=100, n_vars=3, n_clusters=5) + add_toy_neighbors(adata) + return adata + +@pytest.fixture +def controlled_adata_with_neighbors(): + adata = create_controlled_adata() + add_toy_neighbors(adata) + return adata + +@pytest.fixture +def controlled_gpr_dict(): + gpr_dict = create_controlled_gpr_dict() + # Convert to DataFrame + return pd.DataFrame([{'Reaction': k, 'GPR-symbol': v.to_string()} for k, v in gpr_dict.items()]) + +@pytest.fixture +def controlled_task_by_rxn(): + return create_controlled_task_by_rxn() + +@pytest.fixture +def controlled_rxn_by_gene(): + return create_controlled_rxn_by_gene() + +@pytest.fixture +def controlled_task_by_gene(): + return create_controlled_task_by_gene() + + +@pytest.fixture +def global_threshold(): + df = create_global_threshold(threshold=0.5, n_vars=3) + df.index.name = 'symbol' + return df + + +@pytest.fixture +def sccellfie_db(controlled_gpr_dict, controlled_task_by_rxn, controlled_rxn_by_gene, controlled_task_by_gene, + global_threshold): + db = { + 'rxn_info': controlled_gpr_dict, + 'task_by_rxn': controlled_task_by_rxn, + 'rxn_by_gene': controlled_rxn_by_gene, + 'task_by_gene': controlled_task_by_gene, + 'thresholds': global_threshold + } + return db + + +def test_run_sccellfie_pipeline(random_adata_with_neighbors, sccellfie_db, tmp_path, monkeypatch): + + result = run_sccellfie_pipeline( + adata=random_adata_with_neighbors, + organism='human', + sccellfie_data_folder=None, + sccellfie_db=sccellfie_db, + n_counts_col='total_counts', + process_by_group=False, + groupby=None, + neighbors_key='neighbors', + n_neighbors=10, + batch_key=None, + threshold_key='global', + smooth_cells=True, + alpha=0.33, + chunk_size=5000, + disable_pbar=True, + save_folder=str(tmp_path), + save_filename='test_output', + verbose=True # Set to True to see more output + ) + + assert isinstance(result, dict) + assert 'adata' in result + assert isinstance(result['adata'], AnnData) + assert 'gene_scores' in result['adata'].layers + assert hasattr(result['adata'], 'reactions') + assert hasattr(result['adata'], 'metabolic_tasks') + +def test_run_sccellfie_pipeline_with_groups(random_adata_with_neighbors, sccellfie_db, tmp_path, monkeypatch): + random_adata_with_neighbors.obs['group'] = np.random.choice(['A', 'B', 'C'], size=random_adata_with_neighbors.n_obs) + + run_sccellfie_pipeline( + adata=random_adata_with_neighbors, + organism='human', + sccellfie_data_folder=None, + sccellfie_db=sccellfie_db, + n_counts_col='total_counts', # Changed from 'n_counts' to match the fixture + process_by_group=True, + groupby='group', + neighbors_key='neighbors', + n_neighbors=10, + batch_key=None, + threshold_key='global', + smooth_cells=True, + alpha=0.33, + chunk_size=5000, + disable_pbar=True, + save_folder=str(tmp_path), + save_filename='test_output_group', + verbose=False + ) + + # Check if files were created for each group + for group in ['A', 'B', 'C']: + assert (tmp_path / f"test_output_group_{group}.h5ad").exists() \ No newline at end of file From 4d1e085d6211972d9cde816496ebb91ba8c45c48 Mon Sep 17 00:00:00 2001 From: Erick Armingol Date: Fri, 18 Oct 2024 15:16:09 +0100 Subject: [PATCH 05/18] Minor changes --- sccellfie/datasets/database.py | 3 +++ sccellfie/preprocessing/prepare_inputs.py | 4 ++-- 2 files changed, 5 insertions(+), 2 deletions(-) diff --git a/sccellfie/datasets/database.py b/sccellfie/datasets/database.py index f82570f..5a06789 100644 --- a/sccellfie/datasets/database.py +++ b/sccellfie/datasets/database.py @@ -38,6 +38,9 @@ def load_sccellfie_database(organism='human', task_folder=None, rxn_info_filenam ------- data : dict A dictionary containing the loaded data frames and information. + Keys are 'rxn_info', 'task_info', 'task_by_rxn', 'task_by_gene', 'rxn_by_gene', + 'thresholds', and 'organism'. + Examples of dataframes can be found at https://github.com/earmingol/scCellFie/raw/refs/heads/main/task_data/homo_sapiens/ """ # Define default URLs for human and mouse data default_urls = { diff --git a/sccellfie/preprocessing/prepare_inputs.py b/sccellfie/preprocessing/prepare_inputs.py index d969377..89f705b 100644 --- a/sccellfie/preprocessing/prepare_inputs.py +++ b/sccellfie/preprocessing/prepare_inputs.py @@ -2,7 +2,6 @@ import warnings import numpy as np import pandas as pd -import scanpy as sc from scipy import sparse @@ -255,8 +254,9 @@ def normalize_adata(adata, target_sum=10_000, n_counts_key='n_counts', copy=Fals # Check if total counts are already calculated if n_counts_key not in adata.obs.columns: warnings.warn(f"{n_counts_key} not found in adata.obs. Calculating total counts.", UserWarning) - sc.pp.calculate_qc_metrics(adata, layer=None, inplace=True) n_counts_key = 'total_counts' # scanpy uses 'total_counts' as the key + # Calculate total counts from the raw expression matrix + adata.obs[n_counts_key] = adata.X.sum(axis=1) # Input data X_view = adata.X From 306bc887d97a74bbda39b7e2bd47b7a1eb50c26c Mon Sep 17 00:00:00 2001 From: Erick Armingol Date: Fri, 18 Oct 2024 15:18:28 +0100 Subject: [PATCH 06/18] Minor changes --- sccellfie/sccellfie_pipeline.py | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/sccellfie/sccellfie_pipeline.py b/sccellfie/sccellfie_pipeline.py index e808133..77a538f 100644 --- a/sccellfie/sccellfie_pipeline.py +++ b/sccellfie/sccellfie_pipeline.py @@ -12,9 +12,9 @@ def run_sccellfie_pipeline(adata, organism='human', sccellfie_data_folder=None, sccellfie_db=None, n_counts_col='n_counts', - process_by_group=False, groupby=None, neighbors_key='neighbors', - n_neighbors=10, batch_key=None, threshold_key='sccellfie_threshold', smooth_cells=True, - alpha=0.33, chunk_size=5000, disable_pbar=False, save_folder=None, save_filename=None, verbose=True): + process_by_group=False, groupby=None, neighbors_key='neighbors',n_neighbors=10, batch_key=None, + threshold_key='sccellfie_threshold', smooth_cells=True, alpha=0.33, chunk_size=5000, + disable_pbar=False, save_folder=None, save_filename=None, verbose=True): """ Runs the complete scCellFie pipeline on the given AnnData object, processing by cell type if specified. From 267f7cc227abafc6bdf705f910a8ce84abce6145 Mon Sep 17 00:00:00 2001 From: Erick Armingol Date: Fri, 18 Oct 2024 15:18:50 +0100 Subject: [PATCH 07/18] Minor changes --- sccellfie/sccellfie_pipeline.py | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/sccellfie/sccellfie_pipeline.py b/sccellfie/sccellfie_pipeline.py index 77a538f..89f7482 100644 --- a/sccellfie/sccellfie_pipeline.py +++ b/sccellfie/sccellfie_pipeline.py @@ -31,7 +31,7 @@ def run_sccellfie_pipeline(adata, organism='human', sccellfie_data_folder=None, Path to the folder containing the files of the scCellFie database (reactions, GPR rules, metabolic tasks, etc.). - scceellfie_db : dict, optional (default=None) + sccellfie_db : dict, optional (default=None) Dictionary containing the scCellFie database information. If this information is provided, the sccellfie_data_folder will be ignored. This dictionary must contain the keys 'rxn_info', 'task_by_gene', 'rxn_by_gene', 'task_by_rxn', 'thresholds', and From 03c046f1d6dc6d0fa95d9418dfeca27a4e1f0ab4 Mon Sep 17 00:00:00 2001 From: Erick Armingol Date: Mon, 21 Oct 2024 11:30:04 +0100 Subject: [PATCH 08/18] Added import --- sccellfie/__init__.py | 1 + 1 file changed, 1 insertion(+) diff --git a/sccellfie/__init__.py b/sccellfie/__init__.py index 1ecff63..87419af 100644 --- a/sccellfie/__init__.py +++ b/sccellfie/__init__.py @@ -9,5 +9,6 @@ from . import spatial from . import stats as tl from .expression import aggregation, smoothing, thresholds +from .sccellfie_pipeline import run_sccellfie_pipeline __version__ = "0.3.0" \ No newline at end of file From 0504701d3e193578bcb07e222d3b182d4b639855 Mon Sep 17 00:00:00 2001 From: Erick Armingol Date: Mon, 21 Oct 2024 11:31:19 +0100 Subject: [PATCH 09/18] Fixed organism in DB retrieve --- sccellfie/sccellfie_pipeline.py | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/sccellfie/sccellfie_pipeline.py b/sccellfie/sccellfie_pipeline.py index 89f7482..282cee4 100644 --- a/sccellfie/sccellfie_pipeline.py +++ b/sccellfie/sccellfie_pipeline.py @@ -1,4 +1,3 @@ -import pandas as pd import scanpy as sc from tqdm import tqdm @@ -313,6 +312,7 @@ def process_chunk(adata, sccellfie_db, n_counts_col, smooth_cells, alpha, chunk_ task_by_gene=sccellfie_db['task_by_gene'], rxn_by_gene=sccellfie_db['rxn_by_gene'], task_by_rxn=sccellfie_db['task_by_rxn'], + correction_organism=organism, verbose=verbose ) From 9885742d8306d1224b46132045d1953e6efa3ee0 Mon Sep 17 00:00:00 2001 From: Erick Armingol Date: Mon, 21 Oct 2024 11:31:34 +0100 Subject: [PATCH 10/18] Removed duplicated gene names (symbols) --- task_data/mus_musculus/Thresholds.csv | 6070 ++++++++++++------------- 1 file changed, 3026 insertions(+), 3044 deletions(-) diff --git a/task_data/mus_musculus/Thresholds.csv b/task_data/mus_musculus/Thresholds.csv index ee6a8ac..d0693fe 100644 --- a/task_data/mus_musculus/Thresholds.csv +++ b/task_data/mus_musculus/Thresholds.csv @@ -1,3044 +1,3026 @@ -symbol,ensembl_id,sccellfie_threshold -A4galt,ENSMUSG00000047878,2.493392887492253 -A4gnt,ENSMUSG00000037953,0.911013001 -Aaas,ENSMUSG00000036678,1.4732659157184338 -Aacs,ENSMUSG00000029482,1.6024100680695001 -Aadac,ENSMUSG00000027761,3.344482 -Aadat,ENSMUSG00000057228,2.7170193739054325 -Aanat,ENSMUSG00000020804,0.9635438620868174 -Aars1,ENSMUSG00000031960,1.671185458666224 -Aasdh,ENSMUSG00000055923,1.524130379 -Aasdhppt,ENSMUSG00000025894,1.4335514259856958 -Aass,ENSMUSG00000029695,3.344482 -Abat,ENSMUSG00000057880,2.3246732534021923 -Abca1,ENSMUSG00000015243,3.344482 -Abca3,ENSMUSG00000024130,1.8007487561630797 -Abca4,ENSMUSG00000028125,3.344482 -Abca8b,ENSMUSG00000020620,2.108122441120302 -Abcb11,ENSMUSG00000027048,1.2151442631102662 -Abcb1a,ENSMUSG00000040584,3.344482 -Abcb4,ENSMUSG00000042476,1.8220185592748934 -Abcb6,ENSMUSG00000026198,1.1349997866408914 -Abcc1,ENSMUSG00000023088,1.895718888899544 -Abcc2,ENSMUSG00000025194,3.344482 -Abcc3,ENSMUSG00000020865,2.1579377630548238 -Abcc4,ENSMUSG00000032849,2.1886798779446996 -Abcc5,ENSMUSG00000022822,2.488818973701028 -Abcc8,ENSMUSG00000040136,1.9271080611662599 -Abcc9,ENSMUSG00000030249,3.344482 -Abcd1,ENSMUSG00000031378,1.5600565940206272 -Abcd2,ENSMUSG00000055782,2.1316676283701215 -Abcd3,ENSMUSG00000028127,1.990164489456006 -Abcg1,ENSMUSG00000024030,1.993303267 -Abcg2,ENSMUSG00000029802,2.9950175558036243 -Abcg5,ENSMUSG00000040505,1.2467202689811088 -Abcg8,ENSMUSG00000024254,2.5575202735034366 -Abhd12,ENSMUSG00000032046,2.8068071413213214 -Abhd5,ENSMUSG00000032540,1.5589556981912547 -Abhd6,ENSMUSG00000025277,1.8312641064061985 -Abo,ENSMUSG00000015787,2.219849799742359 -Abtb2,ENSMUSG00000032724,3.0510382894398735 -Acaa1a,ENSMUSG00000036138,1.9356197855257542 -Acaa1b,ENSMUSG00000010651,3.344482 -Acaa2,ENSMUSG00000036880,2.936154326 -Acaca,ENSMUSG00000020532,2.6540202940700937 -Acacb,ENSMUSG00000042010,3.325717806535034 -Acad10,ENSMUSG00000029456,1.4951315064650201 -Acad11,ENSMUSG00000090150,1.3093587427395226 -Acad8,ENSMUSG00000031969,1.5397177659834533 -Acad9,ENSMUSG00000027710,1.385365609 -Acadl,ENSMUSG00000026003,2.708503541 -Acadm,ENSMUSG00000062908,2.394512925734221 -Acads,ENSMUSG00000029545,1.8295301138857376 -Acadsb,ENSMUSG00000030861,1.8640347107643689 -Acadvl,ENSMUSG00000018574,1.9721392382558143 -Acat1,ENSMUSG00000032047,2.433795289250083 -Acat2,ENSMUSG00000023832,1.6746590635583005 -Acat3,ENSMUSG00000062480,1.241797510152411 -Ace,ENSMUSG00000020681,3.344482 -Ace2,ENSMUSG00000015405,2.895483201250083 -Acer1,ENSMUSG00000045019,3.3311655615979814 -Acer2,ENSMUSG00000038007,2.105213610927909 -Acer3,ENSMUSG00000030760,2.4036035590017555 -Ache,ENSMUSG00000023328,1.7812703348553156 -Acly,ENSMUSG00000020917,1.985437295651586 -Acmsd,ENSMUSG00000026348,3.344482 -Aco1,ENSMUSG00000028405,1.668212545013903 -Aco2,ENSMUSG00000022477,2.4300180366236255 -Acod1,ENSMUSG00000022126,3.344482 -Acot1,ENSMUSG00000072949,2.2155406800801707 -Acot10,ENSMUSG00000047565,0.842318 -Acot11,ENSMUSG00000034853,2.5290109327687684 -Acot12,ENSMUSG00000021620,3.190195235200414 -Acot13,ENSMUSG00000006717,1.9600505395805523 -Acot2,ENSMUSG00000021226,1.4340840742043461 -Acot4,ENSMUSG00000052392,1.5842046356557693 -Acot6,ENSMUSG00000043487,1.3743051094252106 -Acot7,ENSMUSG00000028937,2.6643992565419823 -Acot8,ENSMUSG00000017307,1.5024461418187505 -Acot9,ENSMUSG00000025287,1.7191930330927379 -Acox1,ENSMUSG00000020777,2.213645579754853 -Acox2,ENSMUSG00000021751,2.868271682008475 -Acox3,ENSMUSG00000029098,1.6774009145308513 -Acp1,ENSMUSG00000044573,2.4875091475587583 -Acp2,ENSMUSG00000002103,1.5255737812606516 -Acp3,ENSMUSG00000032561,2.289930647886205 -Acp4,ENSMUSG00000012777,1.2796637880673216 -Acp5,ENSMUSG00000001348,3.203776197562731 -Acp6,ENSMUSG00000028093,1.5776153361805516 -Acp7,ENSMUSG00000037469,1.0544056016689054 -Acsbg1,ENSMUSG00000032281,3.344482 -Acsbg2,ENSMUSG00000024207,0.842318 -Acsf2,ENSMUSG00000076435,1.9474523003243982 -Acsf3,ENSMUSG00000015016,1.2043424782809096 -Acsl1,ENSMUSG00000018796,3.0232426792114295 -Acsl3,ENSMUSG00000032883,2.554544383137604 -Acsl4,ENSMUSG00000031278,1.7576607591198166 -Acsl5,ENSMUSG00000024981,1.5029685862780477 -Acsl6,ENSMUSG00000020333,1.9279610072282864 -Acsm1,ENSMUSG00000033533,3.344482 -Acsm2,ENSMUSG00000030945,3.344482 -Acsm3,ENSMUSG00000030935,2.6348612430940395 -Acsm4,ENSMUSG00000047026,1.33512682 -Acsm5,ENSMUSG00000030972,3.344482 -Acss1,ENSMUSG00000027452,2.7747987986169895 -Acss2,ENSMUSG00000027605,2.1278958096376868 -Acss3,ENSMUSG00000035948,3.344482 -Acy1,ENSMUSG00000023262,1.542926194670968 -Acy3,ENSMUSG00000024866,3.344482 -Acyp1,ENSMUSG00000008822,1.5141427842206865 -Acyp2,ENSMUSG00000060923,2.5149426886904482 -Ada,ENSMUSG00000017697,2.306594796174025 -Adcy1,ENSMUSG00000020431,3.344482 -Adcy10,ENSMUSG00000026567,2.017293373679025 -Adcy2,ENSMUSG00000021536,3.344482 -Adcy3,ENSMUSG00000020654,1.5757428228681818 -Adcy4,ENSMUSG00000022220,2.9786447034080963 -Adcy5,ENSMUSG00000022840,1.7325477960197968 -Adcy6,ENSMUSG00000022994,1.4418516306313696 -Adcy7,ENSMUSG00000031659,2.7164138147323613 -Adcy8,ENSMUSG00000022376,2.6874206406114425 -Adcy9,ENSMUSG00000005580,2.5381335658491224 -Adh1,ENSMUSG00000074207,3.344482 -Adh4,ENSMUSG00000037797,1.7025125870597293 -Adh5,ENSMUSG00000028138,2.225565370553679 -Adh6b,ENSMUSG00000074206,2.2642598551930297 -Adh7,ENSMUSG00000055301,3.344482 -Adhfe1,ENSMUSG00000025911,3.175705693 -Adi1,ENSMUSG00000020629,1.4179602125348334 -Adk,ENSMUSG00000039197,2.8493771914148844 -Ado,ENSMUSG00000057134,1.4561946492502074 -Adpgk,ENSMUSG00000025236,1.9944689001587184 -Adprh,ENSMUSG00000002844,1.940166460892654 -Adprm,ENSMUSG00000020910,1.4169289072904323 -Adsl,ENSMUSG00000022407,1.5535138160916224 -Adss1,ENSMUSG00000011148,2.097464765669147 -Adss2,ENSMUSG00000015961,1.7309688914948604 -Afmid,ENSMUSG00000017718,1.4672457927966178 -Aga,ENSMUSG00000031521,1.7973743563661917 -Agk,ENSMUSG00000029916,1.6472316886788358 -Agl,ENSMUSG00000033400,2.1783884117420826 -Agmat,ENSMUSG00000040706,1.093267910628829 -Agpat1,ENSMUSG00000034254,1.3030740027759942 -Agpat2,ENSMUSG00000026922,1.8654043016285298 -Agpat3,ENSMUSG00000001211,2.207174988649289 -Agpat4,ENSMUSG00000023827,2.132984100028107 -Agpat5,ENSMUSG00000031467,1.898719552522997 -Agps,ENSMUSG00000042410,2.127782655826071 -Agxt,ENSMUSG00000026272,3.344482 -Agxt2,ENSMUSG00000089678,2.7098166274561697 -Ahctf1,ENSMUSG00000026491,1.8854068167348856 -Ahcy,ENSMUSG00000027597,1.4304489786623018 -Ahcyl1,ENSMUSG00000027893,2.355884200372854 -Ahcyl2,ENSMUSG00000029772,3.1436077584631383 -Aicda,ENSMUSG00000040627,2.2733262688517963 -Ak1,ENSMUSG00000026817,1.6552102856886786 -Ak2,ENSMUSG00000028792,1.9810426291675354 -Ak3,ENSMUSG00000024782,1.7692001622316043 -Ak4,ENSMUSG00000028527,1.7666119320084874 -Ak5,ENSMUSG00000039058,3.315782743369602 -Ak6,ENSMUSG00000078941,1.5456314409433685 -Ak7,ENSMUSG00000041323,1.8582431875494827 -Ak8,ENSMUSG00000026807,1.2952747116173309 -Ak9,ENSMUSG00000091415,2.021324638388686 -Akp3,ENSMUSG00000036500,1.184113649 -Akr1a1,ENSMUSG00000028692,3.344482 -Akr1b1,ENSMUSG00000001642,1.8209487068651335 -Akr1b8,ENSMUSG00000029762,2.381004338804934 -Akr1c20,ENSMUSG00000054757,0.9704282064457618 -Akr1c21,ENSMUSG00000021207,3.344482 -Akr1c6,ENSMUSG00000021210,3.344482 -Akr1d1,ENSMUSG00000038641,2.968374183 -Akr7a5,ENSMUSG00000028743,1.9372026973999883 -Alad,ENSMUSG00000028393,1.9372704281603723 -Alas1,ENSMUSG00000032786,1.926071979639027 -Alas2,ENSMUSG00000025270,3.344482 -Alb,ENSMUSG00000029368,3.344482 -Aldh18a1,ENSMUSG00000025007,1.239167331141088 -Aldh1a1,ENSMUSG00000053279,3.344482 -Aldh1a2,ENSMUSG00000013584,3.344482 -Aldh1a3,ENSMUSG00000015134,2.8628296366951593 -Aldh1b1,ENSMUSG00000035561,1.8366713776493566 -Aldh1l1,ENSMUSG00000030088,2.6972231758731806 -Aldh1l2,ENSMUSG00000020256,1.9008138834514945 -Aldh2,ENSMUSG00000029455,3.344482 -Aldh3a1,ENSMUSG00000019102,3.344482 -Aldh3a2,ENSMUSG00000010025,1.5115938840090772 -Aldh3b1,ENSMUSG00000024885,2.2298420268235426 -Aldh3b2,ENSMUSG00000075296,1.4979160201273467 -Aldh3b3,ENSMUSG00000037263,2.519129851855534 -Aldh4a1,ENSMUSG00000028737,1.990343887 -Aldh5a1,ENSMUSG00000035936,1.3382227659297032 -Aldh6a1,ENSMUSG00000021238,2.1056114048072416 -Aldh7a1,ENSMUSG00000053644,1.7158398394583607 -Aldh8a1,ENSMUSG00000037542,3.344482 -Aldh9a1,ENSMUSG00000026687,1.9505364173861535 -Aldoa,ENSMUSG00000030695,3.344482 -Aldoa,ENSMUSG00000114515,3.344482 -Aldoa,ENSMUSG00000030695,3.344482 -Aldoa,ENSMUSG00000114515,3.344482 -Aldob,ENSMUSG00000028307,3.344482 -Aldoc,ENSMUSG00000017390,3.344482 -Alg1,ENSMUSG00000039427,1.4498923858832091 -Alg10b,ENSMUSG00000075470,1.2380674846301551 -Alg11,ENSMUSG00000063362,1.3670290181832565 -Alg12,ENSMUSG00000035845,1.2375648214564876 -Alg13,ENSMUSG00000041718,1.517630908 -Alg14,ENSMUSG00000039887,1.5737077397469923 -Alg2,ENSMUSG00000039740,1.8181784039018734 -Alg3,ENSMUSG00000033809,1.3268721871919353 -Alg5,ENSMUSG00000036632,1.6410858493072509 -Alg6,ENSMUSG00000073792,1.4391064481984523 -Alg8,ENSMUSG00000035704,1.324971355120779 -Alg9,ENSMUSG00000032059,1.3604542251726321 -Allc,ENSMUSG00000020636,0.842318 -Alox12,ENSMUSG00000000320,2.5326285989998074 -Alox12b,ENSMUSG00000032807,1.04101869 -Alox15,ENSMUSG00000018924,3.344482 -Alox5,ENSMUSG00000025701,3.0926009246749495 -Alox8,ENSMUSG00000020891,1.0493719458628383 -Aloxe3,ENSMUSG00000020892,1.2572368845944273 -Alpi,ENSMUSG00000079440,3.344482 -Alpl,ENSMUSG00000028766,3.344482 -Alppl2,ENSMUSG00000026246,0.842318 -Amacr,ENSMUSG00000022244,1.7785922389644389 -Amd1,ENSMUSG00000075232,1.8597779168000785 -Amd2,ENSMUSG00000063953,1.271478831510859 -Amdhd1,ENSMUSG00000015890,1.0888806228049346 -Amdhd2,ENSMUSG00000036820,1.5123148756150118 -Amfr,ENSMUSG00000031751,1.8587109295437514 -Amn,ENSMUSG00000021278,1.923233760263462 -Ampd1,ENSMUSG00000070385,3.344482 -Ampd2,ENSMUSG00000027889,1.4434795096008517 -Ampd3,ENSMUSG00000005686,1.9340841284136627 -Amt,ENSMUSG00000032607,1.792588949596855 -Amy1,ENSMUSG00000074264,1.9999352595019002 -Amy2a4,ENSMUSG00000096770,0.842318 -Amy2b,ENSMUSG00000083079,3.344482 -Anapc11,ENSMUSG00000025135,2.446161956067994 -Anpep,ENSMUSG00000039062,2.5394134851928953 -Anxa3,ENSMUSG00000029484,3.344482 -Aoah,ENSMUSG00000021322,3.344482 -Aoc1,ENSMUSG00000029811,3.344482 -Aoc2,ENSMUSG00000078651,1.1911506567018595 -Aoc3,ENSMUSG00000019326,2.4345171076434564 -Aox1,ENSMUSG00000063558,3.344482 -Ap1b1,ENSMUSG00000009090,1.6948068249122485 -Ap1g1,ENSMUSG00000031731,1.917222543 -Ap1m1,ENSMUSG00000003033,1.7182446437674903 -Ap1s1,ENSMUSG00000004849,2.249419403807594 -Ap1s2,ENSMUSG00000031367,2.444224556 -Ap3b2,ENSMUSG00000062444,1.7791407258215466 -Ap3d1,ENSMUSG00000020198,1.783368781961466 -Ap3m1,ENSMUSG00000021824,1.6838676892275306 -Ap3m2,ENSMUSG00000031539,1.7434663287673131 -Ap3s2,ENSMUSG00000063801,1.6197673357379507 -Apip,ENSMUSG00000010911,1.4472628406044412 -Apob,ENSMUSG00000020609,3.344482 -Apobec4,ENSMUSG00000055547,1.2002127642068314 -Apoc1,ENSMUSG00000040564,3.344482 -Apoc2,ENSMUSG00000002992,3.344482 -Apoc3,ENSMUSG00000032081,3.344482 -Apoe,ENSMUSG00000002985,3.344482 -Aprt,ENSMUSG00000006589,2.2401883349712732 -Aqp1,ENSMUSG00000004655,3.344482 -Aqp2,ENSMUSG00000023013,3.344482 -Aqp3,ENSMUSG00000028435,3.344482 -Aqp4,ENSMUSG00000024411,3.344482 -Aqp5,ENSMUSG00000044217,3.344482 -Aqp6,ENSMUSG00000043144,3.344482 -Aqp7,ENSMUSG00000028427,3.344482 -Aqp8,ENSMUSG00000030762,3.344482 -Aqp9,ENSMUSG00000032204,3.344482 -Arcn1,ENSMUSG00000032096,1.8945743136475295 -Arf1,ENSMUSG00000048076,3.344482 -Arg1,ENSMUSG00000019987,2.888689364713269 -Arg2,ENSMUSG00000021125,1.941522624 -Arid4b,ENSMUSG00000039219,2.883081640309198 -Arsa,ENSMUSG00000022620,1.2887597755790023 -Arsb,ENSMUSG00000042082,2.2178675947187245 -Art1,ENSMUSG00000030996,3.344482 -Art3,ENSMUSG00000034842,3.344482 -Art4,ENSMUSG00000030217,2.4377003734541804 -Art5,ENSMUSG00000070424,3.058765585689938 -As3mt,ENSMUSG00000003559,1.757896716968345 -Asah1,ENSMUSG00000031591,2.0928384811446503 -Asah2,ENSMUSG00000024887,1.651484864 -Asb12,ENSMUSG00000031204,0.9428751258689342 -Ash1l,ENSMUSG00000028053,3.344482 -Asl,ENSMUSG00000025533,1.8728840311025388 -Asmt,ENSMUSG00000093806,2.010632401 -Asns,ENSMUSG00000029752,1.7730079823365699 -Aspa,ENSMUSG00000020774,3.344482 -Aspg,ENSMUSG00000037686,1.6142120754341336 -Asph,ENSMUSG00000028207,2.958570160199946 -Asrgl1,ENSMUSG00000024654,2.1838093588883987 -Ass1,ENSMUSG00000076441,3.344482 -Ate1,ENSMUSG00000030850,2.2318819245364474 -Atg5lrt,ENSMUSG00000096486,0.842318 -Atg9b,ENSMUSG00000038295,1.1227601942174292 -Atic,ENSMUSG00000026192,1.45076658 -Atp10a,ENSMUSG00000025324,2.830014862804007 -Atp11a,ENSMUSG00000031441,2.086403009332147 -Atp11c,ENSMUSG00000062949,2.4304318289709124 -Atp12a,ENSMUSG00000022229,1.8302062133815478 -Atp1a1,ENSMUSG00000033161,3.344482 -Atp1a2,ENSMUSG00000007097,3.344482 -Atp1a3,ENSMUSG00000040907,3.344482 -Atp1a4,ENSMUSG00000007107,1.024869123754464 -Atp1b1,ENSMUSG00000026576,3.344482 -Atp1b2,ENSMUSG00000041329,3.344482 -Atp1b3,ENSMUSG00000032412,2.542737870437815 -Atp1b4,ENSMUSG00000016327,3.344482 -Atp2a1,ENSMUSG00000030730,3.344482 -Atp2a2,ENSMUSG00000029467,3.344482 -Atp2a3,ENSMUSG00000020788,2.6823263507058566 -Atp2b1,ENSMUSG00000019943,3.344482 -Atp2b2,ENSMUSG00000030302,3.344482 -Atp2b3,ENSMUSG00000031376,2.3462990603701366 -Atp2b4,ENSMUSG00000026463,2.829320326894627 -Atp2c1,ENSMUSG00000032570,2.719216028265468 -Atp2c2,ENSMUSG00000034112,1.302008392907049 -Atp4a,ENSMUSG00000005553,1.747254452019611 -Atp4b,ENSMUSG00000031449,1.363743700636838 -Atp5f1a,ENSMUSG00000025428,3.344482 -Atp5f1b,ENSMUSG00000025393,3.344482 -Atp5f1c,ENSMUSG00000025781,3.344482 -Atp5f1d,ENSMUSG00000003072,3.344482 -Atp5f1e,ENSMUSG00000016252,3.344482 -Atp5mc1,ENSMUSG00000006057,3.344482 -Atp5mc2,ENSMUSG00000062683,3.344482 -Atp5mc3,ENSMUSG00000018770,3.344482 -Atp5me,ENSMUSG00000050856,3.344482 -Atp5mf,ENSMUSG00000038690,3.344482 -Atp5mg,ENSMUSG00000038717,3.344482 -Atp5mj,ENSMUSG00000021290,3.344482 -Atp5mk,ENSMUSG00000071528,3.344482 -Atp5pb,ENSMUSG00000000563,3.344482 -Atp5pd,ENSMUSG00000034566,3.344482 -Atp5pf,ENSMUSG00000022890,3.344482 -Atp5po,ENSMUSG00000116933,2.941225738267674 -Atp5po,ENSMUSG00000022956,2.941225738267674 -Atp5po,ENSMUSG00000116933,3.344482 -Atp5po,ENSMUSG00000022956,3.344482 -Atp6ap1,ENSMUSG00000019087,2.778059218778064 -Atp6v0a1,ENSMUSG00000019302,3.344482 -Atp6v0a2,ENSMUSG00000038023,1.5605429389574716 -Atp6v0a4,ENSMUSG00000038600,3.344482 -Atp6v0b,ENSMUSG00000033379,3.344482 -Atp6v0c,ENSMUSG00000024121,3.344482 -Atp6v0d1,ENSMUSG00000013160,2.5039492222736457 -Atp6v0d2,ENSMUSG00000028238,3.344482 -Atp6v0e,ENSMUSG00000015575,3.029397846305327 -Atp6v1a,ENSMUSG00000052459,3.344482 -Atp6v1b1,ENSMUSG00000006269,3.344482 -Atp6v1b2,ENSMUSG00000006273,3.344482 -Atp6v1c1,ENSMUSG00000022295,2.6779283928298714 -Atp6v1c2,ENSMUSG00000020566,2.226392169916526 -Atp6v1d,ENSMUSG00000021114,2.674178617560047 -Atp6v1e1,ENSMUSG00000019210,3.344482 -Atp6v1e2,ENSMUSG00000053375,1.3572776299372793 -Atp6v1f,ENSMUSG00000004285,3.344482 -Atp6v1g1,ENSMUSG00000039105,3.344482 -Atp6v1g2,ENSMUSG00000024403,3.344482 -Atp6v1g3,ENSMUSG00000026394,3.344482 -Atp6v1h,ENSMUSG00000033793,2.309422664170805 -Atp8a1,ENSMUSG00000037685,3.344482 -Atp8b1,ENSMUSG00000039529,1.8031089678591623 -Atp8b2,ENSMUSG00000060671,1.3433250643478805 -Atxn3,ENSMUSG00000021189,1.5411992365731106 -Auh,ENSMUSG00000021460,1.9725186792682936 -Awat1,ENSMUSG00000015665,1.6652730489106238 -Awat2,ENSMUSG00000031220,1.6188190883354776 -Azin2,ENSMUSG00000028789,1.425771576723598 -B3galnt1,ENSMUSG00000043300,1.5410461905936987 -B3galnt2,ENSMUSG00000039242,1.602292987056182 -B3galt1,ENSMUSG00000034780,3.344482 -B3galt2,ENSMUSG00000033849,2.667729347388957 -B3galt4,ENSMUSG00000067370,1.2712830976529164 -B3galt5,ENSMUSG00000074892,1.8783282041657356 -B3galt6,ENSMUSG00000050796,1.2730039145915792 -B3gat1,ENSMUSG00000045994,1.7851847352671606 -B3gat2,ENSMUSG00000026156,2.411895334787274 -B3gat3,ENSMUSG00000071649,1.8523975256820913 -B3glct,ENSMUSG00000051950,1.5584210673525762 -B3gnt2,ENSMUSG00000051650,1.9391701307852078 -B3gnt3,ENSMUSG00000031803,1.400346988929206 -B3gnt4,ENSMUSG00000029431,1.1656584029255097 -B3gnt5,ENSMUSG00000022686,1.7448045676020576 -B3gnt6,ENSMUSG00000074004,1.1914462520281768 -B3gnt7,ENSMUSG00000079445,1.553627694883845 -B3gnt8,ENSMUSG00000059479,1.8878905948987024 -B3gnt9,ENSMUSG00000069920,1.5535422972381059 -B3gntl1,ENSMUSG00000046605,1.6897305494029327 -B4galnt1,ENSMUSG00000006731,1.6594523225089777 -B4galnt2,ENSMUSG00000013418,2.0328215450533786 -B4galnt3,ENSMUSG00000041372,1.0686582936202518 -B4galnt4,ENSMUSG00000055629,1.2014476505369918 -B4galt1,ENSMUSG00000028413,2.7798074365582957 -B4galt2,ENSMUSG00000028541,1.2556676401197757 -B4galt3,ENSMUSG00000052423,1.4304582126761751 -B4galt4,ENSMUSG00000022793,1.5844690269644819 -B4galt5,ENSMUSG00000017929,1.8207445115376273 -B4galt6,ENSMUSG00000056124,2.3260889258220403 -B4galt7,ENSMUSG00000021504,1.2877660686725652 -B4gat1,ENSMUSG00000047379,1.5323609051033718 -Baat,ENSMUSG00000039653,1.3468347059790344 -Bag6,ENSMUSG00000024392,1.7544992552788266 -Bard1,ENSMUSG00000026196,1.4074104285385776 -Bbox1,ENSMUSG00000041660,2.903221497361324 -Bcap31,ENSMUSG00000002015,2.4218455451237193 -Bcat1,ENSMUSG00000030268,1.749555414143653 -Bcat2,ENSMUSG00000030826,1.5636593670138443 -Bche,ENSMUSG00000027792,1.943113943 -Bckdha,ENSMUSG00000060376,1.8491199130641838 -Bckdhb,ENSMUSG00000032263,2.3997219056310386 -Bckdk,ENSMUSG00000030802,1.579344064283372 -Bco1,ENSMUSG00000031845,1.5925752145306162 -Bco2,ENSMUSG00000032066,2.0728239664378862 -Bdh1,ENSMUSG00000046598,1.4661512551021334 -Bdh2,ENSMUSG00000028167,3.344482 -Bet1,ENSMUSG00000032757,1.5983358897207796 -Bhmt,ENSMUSG00000074768,3.344482 -Bhmt2,ENSMUSG00000042118,2.8266967416347675 -Birc6,ENSMUSG00000024073,3.092950102490304 -Blvra,ENSMUSG00000001999,1.6381082996021152 -Blvrb,ENSMUSG00000040466,2.8992597072487705 -Bmp1,ENSMUSG00000022098,2.0409262964685615 -Bpgm,ENSMUSG00000038871,2.1634935356795753 -Bpnt1,ENSMUSG00000026617,1.5943728177231458 -Bpnt2,ENSMUSG00000066324,1.9692827541522564 -Brap,ENSMUSG00000029458,1.565980300924381 -Brpf1,ENSMUSG00000001632,1.4853103011941506 -Bscl2,ENSMUSG00000071657,1.9320873784195616 -Bst1,ENSMUSG00000029082,3.344482 -Btd,ENSMUSG00000021900,1.7588187480906405 -C1galt1,ENSMUSG00000042460,1.70115192 -C1galt1c1,ENSMUSG00000048970,1.6200365064405091 -Cad,ENSMUSG00000013629,1.183390482796522 -Calm1,ENSMUSG00000001175,3.344482 -Calm2,ENSMUSG00000036438,3.344482 -Calm3,ENSMUSG00000019370,3.344482 -Calr,ENSMUSG00000003814,3.344482 -Cant1,ENSMUSG00000025575,1.3557642321285088 -Canx,ENSMUSG00000020368,3.344482 -Capn3,ENSMUSG00000079110,2.8106701504473453 -Car1,ENSMUSG00000027556,3.344482 -Car12,ENSMUSG00000032373,2.415041011312979 -Car13,ENSMUSG00000027555,1.732715771 -Car14,ENSMUSG00000038526,2.925314061 -Car2,ENSMUSG00000027562,3.344482 -Car3,ENSMUSG00000027559,3.344482 -Car4,ENSMUSG00000000805,3.344482 -Car5a,ENSMUSG00000025317,2.402007268495702 -Car5b,ENSMUSG00000031373,2.823808346847763 -Car6,ENSMUSG00000028972,2.405958092569966 -Car7,ENSMUSG00000031883,1.201674832772355 -Car9,ENSMUSG00000028463,1.934779683686543 -Carns1,ENSMUSG00000075289,1.687113404 -Cars1,ENSMUSG00000010755,1.538245013500799 -Cat,ENSMUSG00000027187,2.5284688757216456 -Cbl,ENSMUSG00000034342,2.074721416874239 -Cblb,ENSMUSG00000022637,2.546708856590386 -Cblc,ENSMUSG00000040525,1.6129289527990103 -Cblif,ENSMUSG00000024682,1.239032710156059 -Cbll1,ENSMUSG00000020659,1.4463785912519218 -Cbr1,ENSMUSG00000051483,1.8555476858485251 -Cbr3,ENSMUSG00000022947,2.5996345050570797 -Cbr4,ENSMUSG00000031641,1.2177464982941892 -Cbs,ENSMUSG00000024039,2.627125337 -Ccnb1ip1,ENSMUSG00000071470,1.124328373803084 -Cd36,ENSMUSG00000002944,3.344482 -Cd38,ENSMUSG00000029084,3.344482 -Cda,ENSMUSG00000028755,2.3682893156259692 -Cdc34,ENSMUSG00000020307,1.4531574489969878 -Cdipt,ENSMUSG00000030682,1.8472550997282902 -Cdo1,ENSMUSG00000033022,2.535532039407907 -Cds1,ENSMUSG00000029330,1.6204958387969655 -Cds2,ENSMUSG00000058793,2.595446925556028 -Cel,ENSMUSG00000026818,3.344482 -Cept1,ENSMUSG00000040774,1.978115652077292 -Cerk,ENSMUSG00000035891,2.4581748015516056 -Cers1,ENSMUSG00000087408,1.3397512061614107 -Cers2,ENSMUSG00000015714,2.390870196735465 -Cers3,ENSMUSG00000030510,1.2997581340464428 -Cers4,ENSMUSG00000008206,2.2204098536069656 -Cers5,ENSMUSG00000023021,1.9620423282354593 -Cers6,ENSMUSG00000027035,3.1390952081738326 -Cert1,ENSMUSG00000021669,2.0085785821486737 -Ces1d,ENSMUSG00000056973,3.344482 -Ces2h,ENSMUSG00000091813,1.694348355278191 -Ces3a,ENSMUSG00000069922,3.344482 -Ces3b,ENSMUSG00000062181,3.344482 -Ces5a,ENSMUSG00000058019,1.1184887499646992 -Ch25h,ENSMUSG00000050370,2.3938466213737506 -Chat,ENSMUSG00000021919,2.373359286205527 -Chdh,ENSMUSG00000015970,2.521872590468161 -Chfr,ENSMUSG00000014668,2.0729610085027255 -Chi3l1,ENSMUSG00000064246,3.344482 -Chia1,ENSMUSG00000062778,2.5964499715388696 -Chit1,ENSMUSG00000026450,2.2387707983284564 -Chka,ENSMUSG00000024843,2.7151932111884687 -Chkb,ENSMUSG00000022617,2.0100299489315447 -Chpf,ENSMUSG00000032997,1.3819346744881527 -Chpf2,ENSMUSG00000038181,1.3754459523702445 -Chpt1,ENSMUSG00000060002,3.285310343 -Chst1,ENSMUSG00000027221,2.4453547606766017 -Chst10,ENSMUSG00000026080,1.4779871885194453 -Chst11,ENSMUSG00000034612,2.3940829028510087 -Chst12,ENSMUSG00000036599,1.6072562850668843 -Chst13,ENSMUSG00000056643,1.5532918952329136 -Chst14,ENSMUSG00000074916,1.3729031170596582 -Chst15,ENSMUSG00000030930,1.6321328910011734 -Chst2,ENSMUSG00000033350,1.7871187116808716 -Chst3,ENSMUSG00000057337,2.485100086236142 -Chst4,ENSMUSG00000035930,2.4824092770097876 -Chst5,ENSMUSG00000031952,1.9963058132771643 -Chst7,ENSMUSG00000037347,2.2248620963808006 -Chst8,ENSMUSG00000060402,1.6354101598050874 -Chst9,ENSMUSG00000047161,3.344482 -Chsy1,ENSMUSG00000032640,1.7510175343577765 -Chsy3,ENSMUSG00000058152,3.344482 -Cinp,ENSMUSG00000021276,1.5249218181783257 -Ckb,ENSMUSG00000001270,3.344482 -Ckm,ENSMUSG00000030399,3.344482 -Ckmt1,ENSMUSG00000000308,2.149350135826207 -Ckmt2,ENSMUSG00000021622,3.344482 -Clcf1,ENSMUSG00000040663,1.8635077004884764 -Clock,ENSMUSG00000029238,2.4063020008322527 -Clps,ENSMUSG00000024225,3.344482 -Clta,ENSMUSG00000028478,3.344482 -Cltb,ENSMUSG00000047547,2.8013854089794767 -Cltc,ENSMUSG00000047126,3.289200951449451 -Cltrn,ENSMUSG00000015401,3.344482 -Clybl,ENSMUSG00000025545,2.9645224303496893 -Cma1,ENSMUSG00000022225,3.344482 -Cmas,ENSMUSG00000030282,1.9655746509861327 -Cmpk1,ENSMUSG00000028719,2.2343844408155964 -Cmpk2,ENSMUSG00000020638,1.2846404423197295 -Cmtr1,ENSMUSG00000024019,1.2470188905913286 -Cndp1,ENSMUSG00000056162,2.2136230162878916 -Cndp2,ENSMUSG00000024644,2.3472707610752708 -Cnot4,ENSMUSG00000038784,2.8119003900083803 -Cnp,ENSMUSG00000006782,3.344482 -Coasy,ENSMUSG00000001755,1.453428656674387 -Colgalt1,ENSMUSG00000034807,1.6501740505250346 -Colgalt2,ENSMUSG00000032649,1.7071678829108234 -Comt,ENSMUSG00000000326,2.6801309319263917 -Comtd1,ENSMUSG00000021773,1.5790644234886146 -Cop1,ENSMUSG00000040782,2.165556619 -Copa,ENSMUSG00000026553,2.1901445981417766 -Copb1,ENSMUSG00000030754,2.0125409832180536 -Copb2,ENSMUSG00000032458,1.9050053210806495 -Cope,ENSMUSG00000055681,2.6993357705899483 -Copg1,ENSMUSG00000030058,1.9493072467306227 -Copg2,ENSMUSG00000025607,2.1884296217951076 -Copz1,ENSMUSG00000060992,2.043250077562769 -Copz2,ENSMUSG00000018672,2.301228108306103 -Coq2,ENSMUSG00000029319,1.671966512711062 -Coq3,ENSMUSG00000028247,1.6208797433724216 -Coq5,ENSMUSG00000041733,1.6556790945935436 -Coq6,ENSMUSG00000021235,1.3416841863410516 -Coq7,ENSMUSG00000030652,1.7849947261056203 -Cox10,ENSMUSG00000042148,1.5470298866294685 -Cox4i1,ENSMUSG00000031818,3.344482 -Cox4i2,ENSMUSG00000009876,3.344482 -Cox5a,ENSMUSG00000000088,3.344482 -Cox5b,ENSMUSG00000061518,3.344482 -Cox6a1,ENSMUSG00000041697,3.344482 -Cox6a2,ENSMUSG00000030785,3.344482 -Cox6b1,ENSMUSG00000036751,3.344482 -Cox6b2,ENSMUSG00000051811,1.8547750686166833 -Cox6c,ENSMUSG00000014313,3.344482 -Cox7a1,ENSMUSG00000074218,2.9543399011040385 -Cox7a2,ENSMUSG00000032330,3.344482 -Cox7b,ENSMUSG00000031231,3.344482 -Cox7b2,ENSMUSG00000049387,1.0618355019810812 -Cox7c,ENSMUSG00000017778,3.344482 -Cox8a,ENSMUSG00000035885,3.344482 -Cp,ENSMUSG00000003617,3.344482 -Cpa1,ENSMUSG00000054446,3.344482 -Cpa2,ENSMUSG00000071553,3.344482 -Cpa3,ENSMUSG00000001865,3.344482 -Cpa5,ENSMUSG00000029788,0.842318 -Cpa6,ENSMUSG00000042501,1.8304515802561834 -Cpne7,ENSMUSG00000034796,2.544617113294978 -Cpox,ENSMUSG00000022742,1.7823639645241598 -Cps1,ENSMUSG00000025991,2.6327023976513244 -Cpt1a,ENSMUSG00000024900,2.714067987721285 -Cpt1b,ENSMUSG00000078937,1.4795767117337228 -Cpt1c,ENSMUSG00000007783,1.7233984710049433 -Cpt2,ENSMUSG00000028607,1.8028221562522797 -Crat,ENSMUSG00000026853,1.563770813372735 -Crebbp,ENSMUSG00000022521,3.020146075256585 -Crisp1,ENSMUSG00000025431,3.344482 -Crls1,ENSMUSG00000027357,1.3334582515160902 -Crot,ENSMUSG00000003623,2.0600106615446343 -Cryl1,ENSMUSG00000021947,2.048690449307115 -Cryz,ENSMUSG00000028199,1.6773719176287802 -Cs,ENSMUSG00000005683,2.1938298443868085 -Csad,ENSMUSG00000023044,1.7850849045180424 -Csgalnact1,ENSMUSG00000036356,2.3196489909681417 -Csgalnact2,ENSMUSG00000042042,1.5052111025995318 -Csnk1g2,ENSMUSG00000003345,1.6388471717423119 -Ctbp1,ENSMUSG00000037373,2.3789650881860314 -Ctdspl2,ENSMUSG00000033411,2.0273487650536746 -Cth,ENSMUSG00000028179,2.1740160966066084 -Ctps1,ENSMUSG00000028633,1.4207993365407419 -Ctps2,ENSMUSG00000031360,1.920827073169529 -Ctsa,ENSMUSG00000017760,2.633377482 -Ctsb,ENSMUSG00000021939,3.344482 -Ctsc,ENSMUSG00000030560,3.344482 -Ctsd,ENSMUSG00000007891,3.344482 -Ctse,ENSMUSG00000004552,3.344482 -Ctsf,ENSMUSG00000083282,2.087493079957073 -Ctsg,ENSMUSG00000040314,3.344482 -Ctsh,ENSMUSG00000032359,3.344482 -Ctsk,ENSMUSG00000028111,3.344482 -Ctsl,ENSMUSG00000021477,3.344482 -Ctso,ENSMUSG00000028015,2.1855713769400595 -Ctss,ENSMUSG00000038642,3.344482 -Ctsw,ENSMUSG00000024910,3.344482 -Ctsz,ENSMUSG00000016256,3.344482 -Cubn,ENSMUSG00000026726,3.344482 -Cul1,ENSMUSG00000029686,2.4356920194691885 -Cwc27,ENSMUSG00000021715,1.9885512889753458 -Cyb5d1,ENSMUSG00000044795,0.9034368399049393 -Cyb5r1,ENSMUSG00000026456,1.5995043646173515 -Cyb5r2,ENSMUSG00000048065,1.4437935626841227 -Cyb5r3,ENSMUSG00000018042,2.490897942089283 -Cyb5r4,ENSMUSG00000032872,1.6648785094267773 -Cyb5rl,ENSMUSG00000028621,1.3296256172272474 -Cybrd1,ENSMUSG00000027015,2.036468675227202 -Cyc1,ENSMUSG00000022551,2.8280968461105958 -Cyld,ENSMUSG00000036712,2.1860977491781934 -Cyp11a1,ENSMUSG00000032323,1.0603116434527833 -Cyp11b1,ENSMUSG00000075604,1.394641495227085 -Cyp11b2,ENSMUSG00000022589,1.2536247052178766 -Cyp17a1,ENSMUSG00000003555,2.9335561796631655 -Cyp19a1,ENSMUSG00000032274,1.2766208705834345 -Cyp1a1,ENSMUSG00000032315,3.344482 -Cyp1a2,ENSMUSG00000032310,3.344482 -Cyp1b1,ENSMUSG00000024087,2.8308187603265598 -Cyp21a1,ENSMUSG00000024365,1.312291103610247 -Cyp24a1,ENSMUSG00000038567,1.6803230651690022 -Cyp26a1,ENSMUSG00000024987,2.0555860688479823 -Cyp26b1,ENSMUSG00000063415,3.344482 -Cyp27a1,ENSMUSG00000026170,3.344482 -Cyp27b1,ENSMUSG00000006724,0.8967958580669441 -Cyp2a4,ENSMUSG00000074254,3.344482 -Cyp2a5,ENSMUSG00000005547,3.344482 -Cyp2b10,ENSMUSG00000030483,3.096613456464715 -Cyp2c29,ENSMUSG00000003053,3.344482 -Cyp2c38,ENSMUSG00000032808,1.4121664457807146 -Cyp2c39,ENSMUSG00000025003,0.8559876450541779 -Cyp2c54,ENSMUSG00000067225,2.121743413590022 -Cyp2c55,ENSMUSG00000025002,3.344482 -Cyp2c65,ENSMUSG00000067231,2.1226391574323276 -Cyp2c66,ENSMUSG00000067229,1.3811765530232716 -Cyp2d22,ENSMUSG00000061740,3.281162812584106 -Cyp2e1,ENSMUSG00000025479,3.344482 -Cyp2f2,ENSMUSG00000052974,3.344482 -Cyp2j6,ENSMUSG00000052914,2.1404849256404406 -Cyp2j9,ENSMUSG00000015224,3.2947829538789697 -Cyp2r1,ENSMUSG00000030670,1.3231009968125633 -Cyp2s1,ENSMUSG00000040703,1.3523225043483384 -Cyp2u1,ENSMUSG00000027983,1.310537895965402 -Cyp39a1,ENSMUSG00000023963,1.766478417682886 -Cyp3a13,ENSMUSG00000029727,1.2541162212787753 -Cyp3a16,ENSMUSG00000038656,0.9318780852685818 -Cyp3a25,ENSMUSG00000029630,3.344482 -Cyp3a41a,ENSMUSG00000075551,1.621416397656929 -Cyp3a41b,ENSMUSG00000075552,0.842318 -Cyp3a44,ENSMUSG00000054417,2.552401197365634 -Cyp3a57,ENSMUSG00000070419,1.650494673415481 -Cyp46a1,ENSMUSG00000021259,1.7232569917825074 -Cyp4a10,ENSMUSG00000066072,3.344482 -Cyp4a12a,ENSMUSG00000066071,3.344482 -Cyp4a12b,ENSMUSG00000078597,1.3023846030502337 -Cyp4a31,ENSMUSG00000028712,3.344482 -Cyp4a32,ENSMUSG00000063929,3.1114290596764698 -Cyp4b1,ENSMUSG00000028713,3.344482 -Cyp4f14,ENSMUSG00000024292,2.868193707681485 -Cyp4f15,ENSMUSG00000073424,2.8072756085442436 -Cyp4f17,ENSMUSG00000091586,2.4119418317739627 -Cyp4f18,ENSMUSG00000003484,3.344482 -Cyp4f39,ENSMUSG00000061126,1.790358965 -Cyp4f40,ENSMUSG00000090700,1.6294975381733696 -Cyp4v3,ENSMUSG00000079057,1.955233675553847 -Cyp4x1,ENSMUSG00000047155,1.2098546200766325 -Cyp51,ENSMUSG00000001467,2.0630164488592038 -Cyp7a1,ENSMUSG00000028240,2.020393174547786 -Cyp7b1,ENSMUSG00000039519,2.648503354109764 -Cyp8b1,ENSMUSG00000050445,3.2567708842012157 -Cytb,ENSMUSG00000064370,3.344482 -Dad1,ENSMUSG00000022174,3.344482 -Dagla,ENSMUSG00000035735,1.4826337577783815 -Daglb,ENSMUSG00000039206,1.9345632600127147 -Dao,ENSMUSG00000042096,3.344482 -Dars1,ENSMUSG00000026356,1.8110279555786404 -Dbh,ENSMUSG00000000889,2.775199347132415 -Dbi,ENSMUSG00000026385,3.344482 -Dbp,ENSMUSG00000059824,2.493925891496995 -Dbt,ENSMUSG00000000340,1.4975054394017309 -Dck,ENSMUSG00000029366,1.3846516663258024 -Dct,ENSMUSG00000022129,3.0070309196623897 -Dctd,ENSMUSG00000031562,1.1713237683172968 -Dctpp1,ENSMUSG00000042462,1.843203883920151 -Dcxr,ENSMUSG00000039450,2.8664793183340698 -Ddah1,ENSMUSG00000028194,3.344482 -Ddah2,ENSMUSG00000007039,3.344482 -Ddc,ENSMUSG00000020182,2.507221779371253 -Ddo,ENSMUSG00000063428,2.6645570504626703 -Ddost,ENSMUSG00000028757,2.517109332978934 -Ddx19b,ENSMUSG00000033658,1.3204118265953066 -Decr1,ENSMUSG00000028223,1.902896329579262 -Decr2,ENSMUSG00000036775,1.2836116527488488 -Degs1,ENSMUSG00000038633,2.2669161491428973 -Degs2,ENSMUSG00000021263,2.700680337003842 -Dera,ENSMUSG00000030225,1.7309004070356542 -Derl1,ENSMUSG00000022365,1.8973505546757912 -Derl3,ENSMUSG00000009092,1.5932231153114835 -Dgat1,ENSMUSG00000022555,1.878496038980407 -Dgat2,ENSMUSG00000030747,1.7376123780346922 -Dgat2l6,ENSMUSG00000067597,0.936452633 -Dgka,ENSMUSG00000025357,1.9861030212302968 -Dgkb,ENSMUSG00000036095,3.344482 -Dgkd,ENSMUSG00000070738,2.7062326560799104 -Dgke,ENSMUSG00000000276,1.6363950831421288 -Dgkg,ENSMUSG00000022861,3.344482 -Dgkh,ENSMUSG00000034731,3.268608333 -Dgki,ENSMUSG00000038665,3.344482 -Dgkk,ENSMUSG00000062393,2.1562310268892726 -Dgkq,ENSMUSG00000004815,1.4516398418000345 -Dgkz,ENSMUSG00000040479,2.5533607096599282 -Dguok,ENSMUSG00000014554,1.8397439896218484 -Dhcr24,ENSMUSG00000034926,1.6667878445220936 -Dhcr7,ENSMUSG00000058454,1.434884186639839 -Dhdds,ENSMUSG00000012117,1.8794281420573493 -Dhdh,ENSMUSG00000011382,1.962114446251483 -Dhfr,ENSMUSG00000021707,1.6120229151619108 -Dhodh,ENSMUSG00000031730,1.3733225896114816 -Dhps,ENSMUSG00000060038,1.6291993362283395 -Dhrs2,ENSMUSG00000022209,1.363839504114833 -Dhrs3,ENSMUSG00000066026,3.344482 -Dhrs4,ENSMUSG00000022210,1.909082920329671 -Dhrs9,ENSMUSG00000027068,3.344482 -Dhtkd1,ENSMUSG00000025815,1.5952737004337374 -Dio1,ENSMUSG00000034785,1.2868299179424119 -Dio2,ENSMUSG00000007682,2.9073232265862394 -Dio3,ENSMUSG00000075707,1.4109693475547573 -Dlat,ENSMUSG00000000168,1.884426777428765 -Dld,ENSMUSG00000020664,1.8617495436547848 -Dlst,ENSMUSG00000004789,1.887174201 -Dmgdh,ENSMUSG00000042102,1.5655519107405076 -Dnajc1,ENSMUSG00000026740,2.9912289342808243 -Dnm1,ENSMUSG00000026825,3.344482 -Dnm1l,ENSMUSG00000022789,2.4216744022070453 -Dnm2,ENSMUSG00000033335,2.3533229233678132 -Dnm3,ENSMUSG00000040265,3.344482 -Dnmt1,ENSMUSG00000004099,1.6166550260581216 -Dnmt3a,ENSMUSG00000020661,3.043020656 -Dnmt3b,ENSMUSG00000027478,1.6765685230361755 -Dnmt3l,ENSMUSG00000000730,1.3597602893026681 -Dolk,ENSMUSG00000075419,1.422594981608011 -Dolpp1,ENSMUSG00000026856,1.2665598201264938 -Dot1l,ENSMUSG00000061589,2.013144033407828 -Dpagt1,ENSMUSG00000032123,1.4694526379587094 -Dpep1,ENSMUSG00000019278,3.344482 -Dpep2,ENSMUSG00000053687,2.347521717555567 -Dpep2,ENSMUSG00000115067,2.347521717555567 -Dpep2,ENSMUSG00000053687,3.344482 -Dpep2,ENSMUSG00000115067,3.344482 -Dpep3,ENSMUSG00000031898,2.282277430180172 -Dph5,ENSMUSG00000033554,1.4822042346040758 -Dpm1,ENSMUSG00000078919,2.0802950044432045 -Dpm2,ENSMUSG00000026810,1.6768648908752815 -Dpm3,ENSMUSG00000042737,2.203853263452995 -Dpyd,ENSMUSG00000033308,2.999785376607155 -Dpys,ENSMUSG00000022304,1.108461991578927 -Dpysl2,ENSMUSG00000022048,3.344482 -Dpysl3,ENSMUSG00000024501,3.344482 -Dse,ENSMUSG00000039497,2.0077917654279482 -Dtymk,ENSMUSG00000026281,1.8717968357710264 -Duox1,ENSMUSG00000033268,1.7140941753646346 -Duox2,ENSMUSG00000068452,3.141026183791631 -Dusp11,ENSMUSG00000030002,2.056039261257001 -Dut,ENSMUSG00000027203,2.0732206285367902 -Dzip3,ENSMUSG00000064061,2.200876944405823 -Ebp,ENSMUSG00000031168,1.8010544607834869 -Ech1,ENSMUSG00000053898,2.645645105344032 -Echdc2,ENSMUSG00000028601,1.9013089881974126 -Echs1,ENSMUSG00000025465,2.0864323801336977 -Eci1,ENSMUSG00000024132,2.149327260871877 -Eci2,ENSMUSG00000021417,2.0440852424014615 -Edem1,ENSMUSG00000030104,1.8064001126081888 -Edem2,ENSMUSG00000038312,1.7941374235531697 -Edem3,ENSMUSG00000043019,1.6381094415116741 -Eef1a1,ENSMUSG00000037742,3.344482 -Eef1a2,ENSMUSG00000016349,2.8466780710881574 -Eef2,ENSMUSG00000034994,3.344482 -Efl1,ENSMUSG00000038563,1.6964352311979392 -Egfbp2,ENSMUSG00000053719,0.842318 -Egfl8,ENSMUSG00000015467,2.411963199637949 -Egfr,ENSMUSG00000020122,3.344482 -Ehhadh,ENSMUSG00000022853,2.3415216075994043 -Ehmt1,ENSMUSG00000036893,2.5238541655939595 -Ehmt2,ENSMUSG00000013787,1.661226753580957 -Eif4ebp3,ENSMUSG00000090264,1.1095057244437743 -Elovl1,ENSMUSG00000006390,2.1835020489868384 -Elovl2,ENSMUSG00000021364,1.5067293271525621 -Elovl3,ENSMUSG00000038754,3.344482 -Elovl4,ENSMUSG00000032262,1.8534483792590233 -Elovl5,ENSMUSG00000032349,2.2007388317785685 -Elovl6,ENSMUSG00000041220,2.0034167053630507 -Elovl7,ENSMUSG00000021696,2.2334449244486536 -Elp3,ENSMUSG00000022031,1.4615835287449177 -Engase,ENSMUSG00000033857,1.3692469343358482 -Eno1,ENSMUSG00000063524,3.344482 -Eno1b,ENSMUSG00000059040,1.0233778483725946 -Eno2,ENSMUSG00000004267,3.344482 -Eno3,ENSMUSG00000060600,3.344482 -Enoph1,ENSMUSG00000029326,1.3181021010812353 -Enpp1,ENSMUSG00000037370,2.3547722256539445 -Enpp2,ENSMUSG00000022425,3.344482 -Enpp3,ENSMUSG00000019989,2.3227091943147524 -Enpp6,ENSMUSG00000038173,3.344482 -Enpp7,ENSMUSG00000046697,1.2744495443946167 -Entpd1,ENSMUSG00000048120,3.344482 -Entpd2,ENSMUSG00000015085,3.344482 -Entpd3,ENSMUSG00000041608,1.1215105489862593 -Entpd4,ENSMUSG00000095463,1.2823444897926828 -Entpd5,ENSMUSG00000021236,1.6184589282653163 -Entpd6,ENSMUSG00000033068,1.4287739837236846 -Entpd8,ENSMUSG00000036813,1.898736046177997 -Ep300,ENSMUSG00000055024,2.13237162 -Ephx1,ENSMUSG00000038776,2.777443380560246 -Ephx2,ENSMUSG00000022040,2.5884296468951637 -Eprs1,ENSMUSG00000026615,2.2158512140986604 -Epx,ENSMUSG00000052234,1.9332859492712373 -Ero1a,ENSMUSG00000021831,1.3693261722679784 -Ero1b,ENSMUSG00000057069,1.784057355408324 -Esco1,ENSMUSG00000024293,1.857452084 -Esco2,ENSMUSG00000022034,1.894194363786879 -Esd,ENSMUSG00000021996,2.563421742102147 -Etfa,ENSMUSG00000032314,2.3836366972759433 -Etfb,ENSMUSG00000004610,3.1190114712832537 -Etfdh,ENSMUSG00000027809,1.7012425482058027 -Etnk1,ENSMUSG00000030275,3.081468479552048 -Etnk2,ENSMUSG00000070644,1.3378320722520165 -Etnppl,ENSMUSG00000019232,3.344482 -Exoc2,ENSMUSG00000021357,1.7613382826860897 -Exoc3,ENSMUSG00000034152,1.9235092136953247 -Exoc4,ENSMUSG00000029763,3.344482 -Exoc5,ENSMUSG00000061244,2.046516013793274 -Exoc6b,ENSMUSG00000033769,3.344482 -Exoc7,ENSMUSG00000020792,1.6965306659667687 -Exoc8,ENSMUSG00000074030,1.270581171050572 -Ext1,ENSMUSG00000061731,3.344482 -Ext2,ENSMUSG00000027198,1.7741472567514132 -Extl1,ENSMUSG00000028838,1.0844553431068877 -Extl2,ENSMUSG00000027963,1.7134270790569157 -Extl3,ENSMUSG00000021978,2.0587680159686728 -Ezh1,ENSMUSG00000006920,1.8497622608947817 -Ezh2,ENSMUSG00000029687,2.5352285923136413 -F13a1,ENSMUSG00000039109,3.344482 -F13b,ENSMUSG00000026368,2.236443073953543 -F2,ENSMUSG00000027249,3.344482 -Faah,ENSMUSG00000034171,1.576152671611264 -Fabp1,ENSMUSG00000054422,3.344482 -Fabp12,ENSMUSG00000027530,3.344482 -Fabp2,ENSMUSG00000023057,3.344482 -Fabp3,ENSMUSG00000028773,2.639552013429348 -Fabp4,ENSMUSG00000062515,3.344482 -Fabp5,ENSMUSG00000027533,3.344482 -Fabp6,ENSMUSG00000020405,3.344482 -Fabp7,ENSMUSG00000019874,3.344482 -Fabp9,ENSMUSG00000027528,1.7341356553858327 -Fads1,ENSMUSG00000010663,1.6848284664529887 -Fads2,ENSMUSG00000024665,2.3873414120575562 -Fads3,ENSMUSG00000024664,1.470732687765871 -Fah,ENSMUSG00000030630,1.6885022336531201 -Fahd1,ENSMUSG00000045316,1.3269025054457193 -Fam20b,ENSMUSG00000033557,1.5210188277567276 -Fam227b,ENSMUSG00000027209,1.5456507041447476 -Fancl,ENSMUSG00000004018,1.502903537607811 -Far1,ENSMUSG00000030759,2.1982251793146617 -Far2,ENSMUSG00000030303,1.4684808809708403 -Farsa,ENSMUSG00000003808,1.726398499664983 -Farsb,ENSMUSG00000026245,1.6874656686025786 -Fasn,ENSMUSG00000025153,1.6443359174334713 -Faxdc2,ENSMUSG00000086962,1.2702136895568794 -Fbp1,ENSMUSG00000069805,3.344482 -Fbp2,ENSMUSG00000021456,2.401625827252717 -Fbxo2,ENSMUSG00000041556,1.795001355 -Fcsk,ENSMUSG00000033703,1.2954453766910874 -Fdft1,ENSMUSG00000021273,1.917203604658264 -Fdps,ENSMUSG00000059743,2.6003577463305994 -Fdxr,ENSMUSG00000018861,1.6551462240004604 -Fech,ENSMUSG00000024588,1.9201361748310546 -Fga,ENSMUSG00000028001,3.344482 -Fggy,ENSMUSG00000028573,2.1754456543403533 -Fh1,ENSMUSG00000026526,1.7949990154695559 -Fhit,ENSMUSG00000060579,3.344482 -Fig4,ENSMUSG00000038417,1.5423431820985227 -Fitm1,ENSMUSG00000022215,3.344482 -Fitm2,ENSMUSG00000048486,1.2731061055520692 -Fkbp10,ENSMUSG00000001555,2.1083245246778346 -Fkbp11,ENSMUSG00000003355,1.9459587360883006 -Fkbp14,ENSMUSG00000038074,1.5836262699425725 -Fkbp1a,ENSMUSG00000032966,3.344482 -Fkbp1b,ENSMUSG00000020635,1.4953048360534347 -Fkbp2,ENSMUSG00000056629,2.6081688700730097 -Fkbp3,ENSMUSG00000020949,3.326592766683953 -Fkbp4,ENSMUSG00000030357,2.8529078662631537 -Fkbp5,ENSMUSG00000024222,2.7697157093390876 -Fkbp6,ENSMUSG00000040013,2.2701748961693347 -Fkbp7,ENSMUSG00000002732,2.197173045587863 -Fkbp8,ENSMUSG00000019428,2.492141816303911 -Fkbp9,ENSMUSG00000029781,2.3106161531931604 -Flad1,ENSMUSG00000042642,1.4854895689571384 -Fmo1,ENSMUSG00000040181,3.344482 -Fmo2,ENSMUSG00000040170,3.344482 -Fmo3,ENSMUSG00000026691,3.007776986569663 -Fmo4,ENSMUSG00000026692,2.237153347055152 -Fmo5,ENSMUSG00000028088,2.934762889777698 -Fn3k,ENSMUSG00000025175,1.4452975075068673 -Fn3krp,ENSMUSG00000039253,1.3573246606238132 -Fnta,ENSMUSG00000015994,1.9213275506057517 -Fntb,ENSMUSG00000033373,1.9853757125535227 -Folr1,ENSMUSG00000001827,3.344482 -Folr2,ENSMUSG00000032725,3.317599676969459 -Fosl1,ENSMUSG00000024912,2.3460976279148196 -Fpgs,ENSMUSG00000009566,1.5308086714386473 -Fpgt,ENSMUSG00000053870,1.2352592838230907 -Ftcd,ENSMUSG00000001155,2.248490971952295 -Fth1,ENSMUSG00000024661,3.344482 -Ftmt,ENSMUSG00000024510,2.8015968334075296 -Fuca1,ENSMUSG00000028673,2.350834365690013 -Fuca2,ENSMUSG00000019810,1.6305060001372371 -Fut1,ENSMUSG00000008461,1.3590954163951414 -Fut10,ENSMUSG00000046152,1.8518046890028197 -Fut11,ENSMUSG00000039357,1.3369299462408535 -Fut2,ENSMUSG00000055978,1.3998969361248241 -Fut4,ENSMUSG00000049307,1.2345519647882603 -Fut7,ENSMUSG00000036587,1.6592964954251839 -Fut8,ENSMUSG00000021065,3.344482 -Fut9,ENSMUSG00000055373,3.344482 -Fxn,ENSMUSG00000059363,1.454808716072071 -Fxyd2,ENSMUSG00000059412,3.344482 -G6pc1,ENSMUSG00000078650,3.344482 -G6pc2,ENSMUSG00000005232,3.344482 -G6pc3,ENSMUSG00000034793,1.520416260289877 -G6pdx,ENSMUSG00000031400,1.7290919596418737 -Gaa,ENSMUSG00000025579,2.5737921402664767 -Gad1,ENSMUSG00000070880,3.344482 -Gad2,ENSMUSG00000026787,3.344482 -Gal3st1,ENSMUSG00000049721,2.0208032478308273 -Gal3st2,ENSMUSG00000094651,1.1230215754864166 -Gal3st2b,ENSMUSG00000093805,1.2397301203472246 -Gal3st2c,ENSMUSG00000073608,2.123557514 -Gal3st3,ENSMUSG00000047658,1.132752283693595 -Gal3st4,ENSMUSG00000075593,1.074711287832698 -Galc,ENSMUSG00000021003,1.5769907150118678 -Gale,ENSMUSG00000028671,1.1756714179097238 -Galk1,ENSMUSG00000020766,1.909101650300808 -Galk2,ENSMUSG00000027207,1.6234947570633573 -Galm,ENSMUSG00000035473,2.107310331272107 -Galns,ENSMUSG00000015027,1.4772897839530938 -Galnt1,ENSMUSG00000000420,2.227546256692306 -Galnt10,ENSMUSG00000020520,2.139957397643494 -Galnt11,ENSMUSG00000038072,1.9666440889445007 -Galnt12,ENSMUSG00000039774,1.5532233480828155 -Galnt13,ENSMUSG00000060988,3.344482 -Galnt14,ENSMUSG00000024064,2.5860452222052013 -Galnt15,ENSMUSG00000021903,3.344482 -Galnt16,ENSMUSG00000021130,2.001553004641813 -Galnt17,ENSMUSG00000034040,3.344482 -Galnt18,ENSMUSG00000038296,2.8180341043487442 -Galnt2,ENSMUSG00000089704,1.3193074043144373 -Galnt3,ENSMUSG00000026994,1.2939549188154418 -Galnt4,ENSMUSG00000090035,1.544450758696324 -Galnt5,ENSMUSG00000026828,2.0791041493457016 -Galnt6,ENSMUSG00000037280,2.978219914109694 -Galnt7,ENSMUSG00000031608,2.797305140890335 -Galnt9,ENSMUSG00000033316,2.2240970140878833 -Galntl6,ENSMUSG00000096914,3.344482 -Galt,ENSMUSG00000036073,1.580884792162879 -Gamt,ENSMUSG00000020150,2.266083445864923 -Ganab,ENSMUSG00000071650,1.6490722853519433 -Ganc,ENSMUSG00000062646,1.7754081341503403 -Gapdh,ENSMUSG00000057666,3.344482 -Gapdhs,ENSMUSG00000061099,1.4761678458610485 -Gars,ENSMUSG00000029777,1.858807876131798 -Gart,ENSMUSG00000022962,1.5793673831056492 -Gatm,ENSMUSG00000027199,3.344482 -Gba1,ENSMUSG00000028048,1.5547755959951215 -Gba2,ENSMUSG00000028467,1.410096130525863 -Gbe1,ENSMUSG00000022707,2.3582290760549514 -Gbf1,ENSMUSG00000025224,2.659498587515935 -Gbgt1,ENSMUSG00000026829,1.867066389 -Gc,ENSMUSG00000035540,3.344482 -Gcat,ENSMUSG00000006378,1.6209896105929609 -Gcat,ENSMUSG00000116378,1.6209896105929609 -Gcat,ENSMUSG00000006378,1.9862413765188487 -Gcat,ENSMUSG00000116378,1.9862413765188487 -Gcdh,ENSMUSG00000003809,1.5773191353642837 -Gch1,ENSMUSG00000037580,2.8710223497482943 -Gck,ENSMUSG00000041798,1.3856267104579116 -Gclc,ENSMUSG00000032350,1.837001199 -Gclm,ENSMUSG00000028124,2.1133189872190563 -Gcnt1,ENSMUSG00000038843,3.344482 -Gcnt2,ENSMUSG00000021360,2.3742399889846886 -Gcnt3,ENSMUSG00000032226,3.344482 -Gcnt4,ENSMUSG00000091387,0.9404357104598927 -Gcnt7,ENSMUSG00000074569,2.113348533196661 -Gcsh,ENSMUSG00000034424,1.6712406473954295 -Gda,ENSMUSG00000058624,3.344482 -Gde1,ENSMUSG00000033917,2.591910263133803 -Gdpd2,ENSMUSG00000019359,2.5975341086055392 -Get1,ENSMUSG00000023147,1.569816549 -Get3,ENSMUSG00000052456,1.4700684611837276 -Gfm1,ENSMUSG00000027774,1.3851295498632736 -Gfm2,ENSMUSG00000021666,1.657467937715495 -Gfpt1,ENSMUSG00000029992,1.8233878005064428 -Gfpt2,ENSMUSG00000020363,3.344482 -Gfus,ENSMUSG00000022570,1.4368484506251429 -Gga1,ENSMUSG00000033128,1.4822224104436297 -Gga2,ENSMUSG00000030872,1.5343264747788816 -Gga3,ENSMUSG00000020740,1.4177680252964493 -Ggact,ENSMUSG00000041625,3.344482 -Ggct,ENSMUSG00000002797,1.3470845740659039 -Ggh,ENSMUSG00000073987,1.953757409844547 -Ggps1,ENSMUSG00000021302,2.0115410091333485 -Ggt1,ENSMUSG00000006345,3.344482 -Ggt5,ENSMUSG00000006344,3.3094965477397817 -Ggt6,ENSMUSG00000040471,1.2607997582753463 -Ggt7,ENSMUSG00000027603,1.7169905332781996 -Ggta1,ENSMUSG00000035778,2.638175732626519 -Gk,ENSMUSG00000025059,2.674651119479517 -Gk2,ENSMUSG00000050553,1.083058521333679 -Gk5,ENSMUSG00000041440,1.585394900026752 -Gla,ENSMUSG00000031266,1.2593345178387332 -Glb1,ENSMUSG00000045594,1.5573292650316921 -Glb1l,ENSMUSG00000026200,1.7253087103172766 -Glce,ENSMUSG00000032252,1.7937640767476108 -Gldc,ENSMUSG00000024827,3.1104296445864814 -Gle1,ENSMUSG00000019715,1.8203309149526279 -Glo1,ENSMUSG00000024026,2.2604250011861438 -Glod4,ENSMUSG00000017286,1.7289172955796956 -Glrx,ENSMUSG00000021591,1.6611941848650162 -Glrx2,ENSMUSG00000018196,1.805936091503656 -Gls,ENSMUSG00000026103,3.344482 -Gls2,ENSMUSG00000044005,1.4608805692492823 -Glt6d1,ENSMUSG00000036401,1.0112516371789186 -Glt8d1,ENSMUSG00000021916,1.856726080545813 -Glt8d2,ENSMUSG00000020251,1.0981793306134793 -Gltp,ENSMUSG00000011884,2.8119348745663175 -Glud1,ENSMUSG00000021794,2.6261181184618714 -Glul,ENSMUSG00000026473,3.344482 -Glyat,ENSMUSG00000063683,3.344482 -Glyatl3,ENSMUSG00000091043,0.9283730579091448 -Glyctk,ENSMUSG00000020258,1.5964257204988401 -Gm10231,ENSMUSG00000068120,0.842318 -Gm13882,ENSMUSG00000081721,0.842318 -Gm2a,ENSMUSG00000000594,2.6665738904597682 -Gm3776,ENSMUSG00000111709,1.4409784570407573 -Gm4459,ENSMUSG00000083626,0.842318 -Gm5560,ENSMUSG00000067161,0.842318 -Gm5737,ENSMUSG00000109392,1.1942516286375466 -Gm6091,ENSMUSG00000074026,0.842318 -Gm6685,ENSMUSG00000032889,0.842318 -Gm6822,ENSMUSG00000061863,0.842318 -Gmds,ENSMUSG00000038372,2.513257731378796 -Gmppa,ENSMUSG00000033021,1.536953254967779 -Gmppb,ENSMUSG00000070284,1.267130949522671 -Gmpr,ENSMUSG00000000253,1.577145334351078 -Gmpr2,ENSMUSG00000002326,1.5589524963500245 -Gmps,ENSMUSG00000027823,1.9500913278780267 -Gne,ENSMUSG00000028479,1.420859539279743 -Gnmt,ENSMUSG00000002769,3.344482 -Gnpat,ENSMUSG00000031985,1.5920751451195425 -Gnpda1,ENSMUSG00000052102,1.5059129660486967 -Gnpda2,ENSMUSG00000029209,1.5449369688140155 -Gnpnat1,ENSMUSG00000037722,1.3163625720337182 -Gnptab,ENSMUSG00000035311,1.5921123350509854 -Gns,ENSMUSG00000034707,1.9425770186796314 -Gosr1,ENSMUSG00000010392,1.5245615863702664 -Got1,ENSMUSG00000025190,2.7119957558011194 -Got1l1,ENSMUSG00000039720,1.2969308684287832 -Got2,ENSMUSG00000031672,2.182743259071337 -Gpaa1,ENSMUSG00000022561,1.623293024237449 -Gpam,ENSMUSG00000024978,2.288146333295499 -Gpat2,ENSMUSG00000046338,1.3462657596629282 -Gpat3,ENSMUSG00000029314,1.902596147560085 -Gpat4,ENSMUSG00000031545,1.7283474111655945 -Gpcpd1,ENSMUSG00000027346,2.6941622214379777 -Gpd1,ENSMUSG00000023019,1.796317625339604 -Gpd1l,ENSMUSG00000050627,1.4194349015828929 -Gpd2,ENSMUSG00000026827,2.0197102853603996 -Gphn,ENSMUSG00000047454,3.344482 -Gpi1,ENSMUSG00000036427,3.344482 -Gpihbp1,ENSMUSG00000022579,3.344482 -Gpld1,ENSMUSG00000021340,2.376908882376687 -Gpt,ENSMUSG00000022546,1.7769106367108778 -Gpt2,ENSMUSG00000031700,1.6999270756300549 -Gpx1,ENSMUSG00000063856,3.344482 -Gpx2,ENSMUSG00000042808,3.344482 -Gpx3,ENSMUSG00000018339,3.344482 -Gpx4,ENSMUSG00000075706,3.344482 -Gpx5,ENSMUSG00000004344,1.1930459029562772 -Gpx6,ENSMUSG00000004341,3.344482 -Gpx7,ENSMUSG00000028597,1.7987867697373934 -Gpx8,ENSMUSG00000021760,2.530429942634369 -Grhpr,ENSMUSG00000035637,1.6901414884464325 -Grk1,ENSMUSG00000031450,3.344482 -Grk2,ENSMUSG00000024858,1.7322526380769439 -Grk3,ENSMUSG00000042249,2.2796505478492173 -Gsr,ENSMUSG00000031584,2.468063768035433 -Gss,ENSMUSG00000027610,1.8422806745555431 -Gsta1,ENSMUSG00000074183,1.8376077463805203 -Gsta2,ENSMUSG00000057933,3.344482 -Gsta5,ENSMUSG00000074179,0.842318 -Gstk1,ENSMUSG00000029864,1.9082643376008328 -Gstm2,ENSMUSG00000040562,3.339830751162688 -Gstm4,ENSMUSG00000027890,1.1613139610265644 -Gstm5,ENSMUSG00000004032,2.6698329087481234 -Gstm7,ENSMUSG00000004035,1.9751666462250936 -Gsto1,ENSMUSG00000025068,2.5373916719346874 -Gsto2,ENSMUSG00000025069,1.377804163062762 -Gstp1,ENSMUSG00000060803,3.001755973929735 -Gstp2,ENSMUSG00000038155,1.2241622848756064 -Gstt2,ENSMUSG00000033318,2.8446103571633286 -Gstz1,ENSMUSG00000021033,1.6921867146328995 -Gtf3c4,ENSMUSG00000035666,1.220237578385363 -Gucy1a1,ENSMUSG00000033910,2.7495397009912157 -Gucy1a2,ENSMUSG00000041624,2.603646146008029 -Gucy1b1,ENSMUSG00000028005,2.2147291453830316 -Gucy1b2,ENSMUSG00000021933,1.5663874043499224 -Gucy2c,ENSMUSG00000042638,1.2644632624073124 -Gucy2e,ENSMUSG00000020890,2.885551870126058 -Gucy2f,ENSMUSG00000042282,3.344482 -Guk1,ENSMUSG00000020444,2.760336701959847 -Gulo,ENSMUSG00000034450,0.915607412 -Gusb,ENSMUSG00000025534,1.8817202303630431 -Gyg1,ENSMUSG00000019528,1.944536803663365 -Gys1,ENSMUSG00000003865,1.7296625898491065 -Gys2,ENSMUSG00000030244,0.842318 -H6pd,ENSMUSG00000028980,1.7354008623523904 -Haao,ENSMUSG00000000673,2.9796256580761717 -Hacd1,ENSMUSG00000063275,1.8257213007865882 -Hacd2,ENSMUSG00000035376,2.6188225477496085 -Hacd3,ENSMUSG00000033629,2.195105036509113 -Hacd4,ENSMUSG00000028497,2.6556298317688736 -Hace1,ENSMUSG00000038822,1.9276210261193127 -Hacl1,ENSMUSG00000021884,1.9346271700712694 -Hadh,ENSMUSG00000027984,2.700724248957214 -Hadha,ENSMUSG00000025745,2.0967829846542703 -Hadhb,ENSMUSG00000059447,2.0894493545705366 -Hagh,ENSMUSG00000024158,2.2822578273789507 -Haghl,ENSMUSG00000061046,1.8566435102597114 -Hal,ENSMUSG00000020017,2.356899821027137 -Hao1,ENSMUSG00000027261,1.2897610403475988 -Hao2,ENSMUSG00000027870,3.344482 -Hars1,ENSMUSG00000001380,1.6709089520783742 -Has1,ENSMUSG00000003665,3.344482 -Has2,ENSMUSG00000022367,2.558569827539805 -Has3,ENSMUSG00000031910,1.3933634943824347 -Hat1,ENSMUSG00000027018,1.9212790656270549 -Hccs,ENSMUSG00000031352,1.4030893023570803 -Hcn1,ENSMUSG00000021730,3.344482 -Hcn4,ENSMUSG00000032338,1.3695784958008526 -Hcst,ENSMUSG00000064109,3.344482 -Hdc,ENSMUSG00000027360,3.344482 -Hdlbp,ENSMUSG00000034088,2.266554545708884 -Hectd1,ENSMUSG00000035247,2.3394296522432954 -Hectd2,ENSMUSG00000041180,1.5428082816675366 -Hectd3,ENSMUSG00000046861,1.3408609782702006 -Hecw1,ENSMUSG00000021301,3.344482 -Hecw2,ENSMUSG00000042807,3.344482 -Heph,ENSMUSG00000031209,3.344482 -Herc1,ENSMUSG00000038664,3.327674798139074 -Herc2,ENSMUSG00000030451,2.4335354440490438 -Herc3,ENSMUSG00000029804,2.6069073472771565 -Herc4,ENSMUSG00000020064,2.210887581778038 -Hexa,ENSMUSG00000025232,2.5936028840423693 -Hexb,ENSMUSG00000021665,3.344482 -Hexd,ENSMUSG00000039307,1.4593226678639732 -Hgd,ENSMUSG00000022821,3.344482 -Hgsnat,ENSMUSG00000037260,1.6200230468121484 -Hhat,ENSMUSG00000037375,1.522487410399768 -Hibadh,ENSMUSG00000029776,2.274282701138404 -Hibch,ENSMUSG00000041426,1.7218697856968908 -Hif1a,ENSMUSG00000021109,2.6090097302604685 -Hif1an,ENSMUSG00000036450,1.3650845915631253 -Higd2a,ENSMUSG00000025868,2.6038691053701477 -Hirip3,ENSMUSG00000042606,1.481100055667882 -Hk1,ENSMUSG00000037012,2.3858822813751592 -Hk2,ENSMUSG00000000628,3.344482 -Hk3,ENSMUSG00000025877,3.311573942315279 -Hkdc1,ENSMUSG00000020080,0.9486845900145265 -Hlcs,ENSMUSG00000040820,2.1766416285210717 -Hltf,ENSMUSG00000002428,1.8260073064000086 -Hmbs,ENSMUSG00000032126,2.0862636879275342 -Hmgcl,ENSMUSG00000028672,1.9959637418293712 -Hmgcll1,ENSMUSG00000007908,2.163716520286817 -Hmgcr,ENSMUSG00000021670,2.217077441701847 -Hmgcs1,ENSMUSG00000093930,3.2009062625688074 -Hmgcs2,ENSMUSG00000027875,3.344482 -Hmox1,ENSMUSG00000005413,3.344482 -Hmox2,ENSMUSG00000004070,1.945894791502807 -Hnmt,ENSMUSG00000026986,1.3775525425095867 -Hoga1,ENSMUSG00000025176,3.2341108824997384 -Hpd,ENSMUSG00000029445,3.344482 -Hpgd,ENSMUSG00000031613,3.344482 -Hpgds,ENSMUSG00000029919,3.344482 -Hprt1,ENSMUSG00000025630,2.556064383037753 -Hps3,ENSMUSG00000027615,1.7473932606576263 -Hpse,ENSMUSG00000035273,1.831484122958785 -Hpse2,ENSMUSG00000074852,1.9107391535182867 -Hs2st1,ENSMUSG00000040151,2.3994047971438994 -Hs3st1,ENSMUSG00000051022,2.2415036645270554 -Hs3st2,ENSMUSG00000046321,2.634332198358882 -Hs3st3a1,ENSMUSG00000047759,1.6800074731627213 -Hs3st3b1,ENSMUSG00000070407,2.232288180185415 -Hs3st4,ENSMUSG00000078591,3.344482 -Hs3st5,ENSMUSG00000044499,3.344482 -Hs3st6,ENSMUSG00000039628,1.2712962862791677 -Hs6st1,ENSMUSG00000045216,1.4557764710835082 -Hs6st2,ENSMUSG00000062184,2.2268118102518657 -Hs6st3,ENSMUSG00000053465,3.344482 -Hsd11b1,ENSMUSG00000016194,3.344482 -Hsd11b2,ENSMUSG00000031891,3.344482 -Hsd17b1,ENSMUSG00000019301,1.026483379972225 -Hsd17b10,ENSMUSG00000025260,2.0800996458643377 -Hsd17b11,ENSMUSG00000029311,1.8751714022282135 -Hsd17b12,ENSMUSG00000027195,2.210577465956071 -Hsd17b14,ENSMUSG00000030825,1.0121279122122637 -Hsd17b2,ENSMUSG00000031844,1.6240255547156566 -Hsd17b3,ENSMUSG00000033122,1.2762993685823993 -Hsd17b4,ENSMUSG00000024507,1.9381532318705115 -Hsd17b6,ENSMUSG00000025396,0.856255141 -Hsd17b7,ENSMUSG00000026675,1.3194745207229304 -Hsd17b8,ENSMUSG00000073422,1.6877590803055695 -Hsd3b1,ENSMUSG00000027871,2.401130800708398 -Hsd3b2,ENSMUSG00000063730,2.6434167734647804 -Hsd3b3,ENSMUSG00000062410,2.029518548881377 -Hsd3b4,ENSMUSG00000095143,3.344482 -Hsd3b6,ENSMUSG00000027869,1.667389807270379 -Hsd3b7,ENSMUSG00000042289,2.0263117907785886 -Hsd3b8,ENSMUSG00000095388,1.4703194646326507 -Hsd3b9,ENSMUSG00000090817,0.842318 -Hsp90b1,ENSMUSG00000020048,3.344482 -Hspa5,ENSMUSG00000026864,3.344482 -Htatip2,ENSMUSG00000039745,1.290597700214297 -Huwe1,ENSMUSG00000025261,2.8044780400948848 -Hyal1,ENSMUSG00000010051,1.7742319205947317 -Hyal2,ENSMUSG00000010047,1.8131488583745792 -Hyal3,ENSMUSG00000036091,1.3009590340462962 -Hyal4,ENSMUSG00000029680,1.2625497351193213 -Hyal5,ENSMUSG00000029678,1.0888398574208145 -Hyal6,ENSMUSG00000029679,1.5089059002296332 -Hyi,ENSMUSG00000006395,2.8778774683407153 -Hykk,ENSMUSG00000035878,2.449137734900371 -Hyou1,ENSMUSG00000032115,1.4080960507333198 -Iars1,ENSMUSG00000037851,1.5367196803547059 -Icmt,ENSMUSG00000039662,1.416303649729755 -Idh1,ENSMUSG00000025950,2.459554090346241 -Idh2,ENSMUSG00000030541,3.2768941839803576 -Idh3a,ENSMUSG00000032279,2.1372422885959708 -Idh3b,ENSMUSG00000027406,2.306200082992481 -Idh3g,ENSMUSG00000002010,2.3259675468758405 -Idi1,ENSMUSG00000058258,1.9007880163339588 -Idi2,ENSMUSG00000033520,1.5231215686404114 -Idnk,ENSMUSG00000050002,1.5816513247437214 -Ido1,ENSMUSG00000031551,2.324701656707251 -Ido2,ENSMUSG00000031549,1.140738683370394 -Ids,ENSMUSG00000035847,2.4162812100343425 -Idua,ENSMUSG00000033540,1.6892510643997263 -Il4i1b,ENSMUSG00000074141,1.8081912355544274 -Impa1,ENSMUSG00000027531,1.604755937998033 -Impa2,ENSMUSG00000024525,1.4213090179610501 -Impdh1,ENSMUSG00000003500,1.684108151659034 -Impdh2,ENSMUSG00000062867,2.2355786652122895 -Inmt,ENSMUSG00000003477,3.344482 -Inpp1,ENSMUSG00000026102,1.6498165521688521 -Inpp4a,ENSMUSG00000026113,2.5405075092865355 -Inpp4b,ENSMUSG00000037940,3.344482 -Inpp5a,ENSMUSG00000025477,2.0482249316786123 -Inpp5b,ENSMUSG00000028894,1.7099508549495526 -Inpp5d,ENSMUSG00000026288,3.344482 -Inpp5e,ENSMUSG00000026925,1.3180364523709698 -Inpp5f,ENSMUSG00000042105,2.278606002821213 -Inpp5j,ENSMUSG00000034570,1.5724918281926787 -Inpp5k,ENSMUSG00000006127,1.6990213334307773 -Inppl1,ENSMUSG00000032737,1.6121028120589758 -Ip6k1,ENSMUSG00000032594,1.9797511800122758 -Ip6k2,ENSMUSG00000032599,2.0001303759091233 -Ip6k3,ENSMUSG00000024210,2.9395152371419084 -Ipmk,ENSMUSG00000060733,1.5461101151892713 -Ippk,ENSMUSG00000021385,1.352274377926834 -Ireb2,ENSMUSG00000032293,1.8649327964209443 -Isyna1,ENSMUSG00000019139,2.306089726802939 -Itch,ENSMUSG00000027598,2.767355313490033 -Itpa,ENSMUSG00000074797,1.5777795754102337 -Itpk1,ENSMUSG00000057963,2.049920451178755 -Itpka,ENSMUSG00000027296,1.7105356413070243 -Itpkb,ENSMUSG00000038855,3.344482 -Itpkc,ENSMUSG00000003752,1.4454253797063685 -Ivd,ENSMUSG00000027332,1.9973809949840233 -Kansl3,ENSMUSG00000010453,1.7994893187829053 -Kars1,ENSMUSG00000031948,1.6174804481397658 -Kat2a,ENSMUSG00000020918,1.2342458884122771 -Kat2b,ENSMUSG00000000708,3.2182529828291204 -Kat5,ENSMUSG00000024926,1.3372762261504914 -Kat6a,ENSMUSG00000031540,2.1908134532502404 -Kat6b,ENSMUSG00000021767,2.4897129590679943 -Kat7,ENSMUSG00000038909,1.6368377585795322 -Kat8,ENSMUSG00000030801,1.4301528836190291 -Kcnj11,ENSMUSG00000096146,0.916963425 -Kcnj8,ENSMUSG00000030247,3.344482 -Kdsr,ENSMUSG00000009905,1.5660800390403156 -Khk,ENSMUSG00000029162,2.9957678088665283 -Kl,ENSMUSG00000058488,3.344482 -Klhl23,ENSMUSG00000042155,1.6016586900411234 -Klk1,ENSMUSG00000063903,3.344482 -Kmo,ENSMUSG00000039783,3.062662448301255 -Kmt2a,ENSMUSG00000002028,2.8508686412146846 -Kmt2b,ENSMUSG00000006307,1.580133418761919 -Kmt2c,ENSMUSG00000038056,3.048214659191409 -Kmt2d,ENSMUSG00000048154,1.8925894456357593 -Kmt5a,ENSMUSG00000049327,1.7916309020165098 -Kmt5b,ENSMUSG00000045098,2.2841450888900376 -Kmt5c,ENSMUSG00000059851,1.8310188704579604 -Kpna6,ENSMUSG00000003731,1.4755518112897177 -Krtap11-1,ENSMUSG00000091212,3.344482 -Kyat1,ENSMUSG00000039648,2.073190552247557 -Kyat3,ENSMUSG00000040213,1.7196398917453062 -Kynu,ENSMUSG00000026866,2.459877904357479 -L2hgdh,ENSMUSG00000020988,1.3382152445425657 -Lalba,ENSMUSG00000022991,2.061287607505199 -Lap3,ENSMUSG00000039682,2.1270426642907942 -Lars1,ENSMUSG00000024493,1.8873141201812265 -Lbr,ENSMUSG00000004880,2.2528155914580816 -Lcat,ENSMUSG00000035237,3.1804303226431716 -Lclat1,ENSMUSG00000054469,1.6525593624379282 -Lct,ENSMUSG00000026354,1.819131182135254 -Ldha,ENSMUSG00000063229,3.344482 -Ldhal6b,ENSMUSG00000101959,1.4629649859800185 -Ldhb,ENSMUSG00000030246,3.344482 -Ldhc,ENSMUSG00000030851,1.2455086512488365 -Ldhd,ENSMUSG00000031958,1.7361551280239322 -Ldlr,ENSMUSG00000032193,2.1497262745117816 -Lenep,ENSMUSG00000078173,0.842318 -Lgmn,ENSMUSG00000021190,3.344482 -Lgsn,ENSMUSG00000050217,1.4513289057021002 -Lhpp,ENSMUSG00000030946,1.2268974253464888 -Lias,ENSMUSG00000029199,1.5513292916298218 -Lipa,ENSMUSG00000024781,2.0382632649450256 -Lipc,ENSMUSG00000032207,1.823896285992875 -Lipe,ENSMUSG00000003123,2.198387297468544 -Lipf,ENSMUSG00000024768,3.344482 -Lipg,ENSMUSG00000053846,1.0850547236709587 -Lipt1,ENSMUSG00000037216,0.9665480970259587 -Lipt2,ENSMUSG00000030725,1.017938966373994 -Lman1l,ENSMUSG00000056271,1.1448945477007095 -Lman2,ENSMUSG00000021484,1.877741160364777 -Lox,ENSMUSG00000024529,3.344482 -Loxl2,ENSMUSG00000034205,2.4531192496893457 -Lpcat1,ENSMUSG00000021608,1.7408166079703284 -Lpcat2,ENSMUSG00000033192,3.344482 -Lpcat3,ENSMUSG00000004270,2.042200888 -Lpcat4,ENSMUSG00000027134,1.203619863701512 -Lpgat1,ENSMUSG00000026623,3.0978749332867657 -Lpin1,ENSMUSG00000020593,2.0299585357107706 -Lpin2,ENSMUSG00000024052,2.140716826729022 -Lpin3,ENSMUSG00000027412,2.0039811550575233 -Lpl,ENSMUSG00000015568,3.344482 -Lpo,ENSMUSG00000009356,1.7229432876527526 -Lrat,ENSMUSG00000028003,2.9216056310526755 -Lrp2,ENSMUSG00000027070,3.344482 -Lrsam1,ENSMUSG00000026792,1.3642096649956148 -Lss,ENSMUSG00000033105,1.4272254617166342 -Lta4h,ENSMUSG00000015889,1.8351812309131754 -Ltc4s,ENSMUSG00000020377,3.344482 -Lypla1,ENSMUSG00000025903,1.8130260165993244 -Lypla2,ENSMUSG00000028670,1.5438475202579574 -Lyzl1,ENSMUSG00000024233,1.2139369888545488 -Macrod1,ENSMUSG00000036278,2.350778069280082 -Macrod2,ENSMUSG00000068205,3.344482 -Man1a,ENSMUSG00000003746,3.344482 -Man1a2,ENSMUSG00000008763,2.4940737403217983 -Man1b1,ENSMUSG00000036646,1.5355373337177265 -Man1c1,ENSMUSG00000037306,2.7126852764806495 -Man2a1,ENSMUSG00000024085,2.418570178186228 -Man2a2,ENSMUSG00000038886,2.038024148765371 -Man2b1,ENSMUSG00000005142,2.3109676697029404 -Man2b2,ENSMUSG00000029119,1.5230779260471974 -Man2c1,ENSMUSG00000032295,1.4104555026399155 -Manba,ENSMUSG00000028164,2.147913347712945 -Mansc1,ENSMUSG00000032718,1.0815787006091342 -Maoa,ENSMUSG00000025037,1.7073805922767937 -Maob,ENSMUSG00000040147,1.7459283211833072 -Marchf1,ENSMUSG00000036469,3.344482 -Marchf10,ENSMUSG00000078627,0.842318 -Marchf11,ENSMUSG00000022269,1.8201985698623444 -Marchf2,ENSMUSG00000079557,2.237333618200664 -Marchf3,ENSMUSG00000032656,3.344482 -Marchf4,ENSMUSG00000039372,1.3030683976896895 -Marchf5,ENSMUSG00000023307,1.9341064534643675 -Marchf6,ENSMUSG00000039100,2.5738619051180582 -Marchf7,ENSMUSG00000026977,2.187024633497375 -Marchf8,ENSMUSG00000025702,1.8676766315640125 -Marchf9,ENSMUSG00000040502,1.2894306314341473 -Mars1,ENSMUSG00000040354,1.4785505267514123 -Mars2,ENSMUSG00000046994,1.1494005967910899 -Mat1a,ENSMUSG00000037798,1.9724928131135009 -Mat2a,ENSMUSG00000053907,3.232388857272524 -Mat2b,ENSMUSG00000042032,2.0519545227938463 -Mboat1,ENSMUSG00000038732,2.2673677245002946 -Mboat2,ENSMUSG00000020646,1.9095448527332062 -Mboat4,ENSMUSG00000071113,0.842318 -Mboat7,ENSMUSG00000035596,1.6608665026337208 -Mcat,ENSMUSG00000048755,1.1738575566967067 -Mccc1,ENSMUSG00000027709,1.6862407360453702 -Mccc2,ENSMUSG00000021646,1.7092103368364333 -Mcee,ENSMUSG00000033429,1.7365135415205242 -Mdh1,ENSMUSG00000020321,3.344482 -Mdh1b,ENSMUSG00000025963,1.0600896721889825 -Mdh2,ENSMUSG00000019179,3.344482 -Mdm2,ENSMUSG00000020184,1.7811432616043867 -Mdp1,ENSMUSG00000002329,1.5562404254635827 -Me1,ENSMUSG00000032418,1.8703916008653663 -Me2,ENSMUSG00000024556,1.556944083430213 -Me3,ENSMUSG00000030621,3.344482 -Mecr,ENSMUSG00000028910,1.6193389036958281 -Mettl1,ENSMUSG00000006732,1.4195735635769282 -Mettl3,ENSMUSG00000022160,1.5572072792117153 -Mgam,ENSMUSG00000068587,2.3881643855692887 -Mgat1,ENSMUSG00000020346,1.6281070570712621 -Mgat2,ENSMUSG00000043998,1.6094589182821866 -Mgat3,ENSMUSG00000042428,1.7840523637100307 -Mgat4a,ENSMUSG00000026110,1.801930522533503 -Mgat4b,ENSMUSG00000036620,1.8141630916336895 -Mgat4c,ENSMUSG00000019888,3.344482 -Mgat5,ENSMUSG00000036155,2.755135892476252 -Mgat5b,ENSMUSG00000043857,1.4694974913475614 -Mgll,ENSMUSG00000033174,3.344482 -Mgmt,ENSMUSG00000054612,2.0166565230365476 -Mgrn1,ENSMUSG00000022517,1.9251177916813709 -Mgst1,ENSMUSG00000008540,3.344482 -Mgst2,ENSMUSG00000074604,2.235134850693103 -Mgst3,ENSMUSG00000026688,2.6431203485936883 -Mia3,ENSMUSG00000056050,1.9944480700301954 -Mib1,ENSMUSG00000024294,2.2508137525423426 -Mib2,ENSMUSG00000029060,1.4433080982878908 -Mid1,ENSMUSG00000035299,2.5853370680149044 -Mif,ENSMUSG00000033307,3.344482 -Minpp1,ENSMUSG00000024896,1.5753204578482156 -Miox,ENSMUSG00000022613,3.344482 -Mkrn1,ENSMUSG00000029922,2.2957428887527134 -Mkrn2,ENSMUSG00000000439,1.3265329765198703 -Mkrn3,ENSMUSG00000070527,1.6014418580290233 -Mlycd,ENSMUSG00000074064,1.4503285991824038 -Mmaa,ENSMUSG00000037022,1.4856695169297218 -Mmab,ENSMUSG00000029575,1.2003139286409275 -Mmut,ENSMUSG00000023921,1.5908019333133863 -Mocs1,ENSMUSG00000064120,1.6235768358544083 -Mocs2,ENSMUSG00000015536,1.8395521322110284 -Mogat1,ENSMUSG00000012187,1.9415785180537357 -Mogat2,ENSMUSG00000052396,1.2380501672376867 -Mogs,ENSMUSG00000030036,1.3077006049667157 -Moxd1,ENSMUSG00000020000,2.2063617567342315 -Mpc1,ENSMUSG00000023861,3.0794185128883136 -Mpc2,ENSMUSG00000026568,2.8999226055974554 -Mpi,ENSMUSG00000032306,1.2911308634772285 -Mpo,ENSMUSG00000009350,3.344482 -Mpst,ENSMUSG00000071711,1.711759932635098 -Mri1,ENSMUSG00000004996,1.6053297695370035 -Mrpl58,ENSMUSG00000018858,1.8907570934608986 -Msmo1,ENSMUSG00000031604,2.4521408508517024 -Msra,ENSMUSG00000054733,3.344482 -mt-Atp6,ENSMUSG00000064357,3.344482 -mt-Atp8,ENSMUSG00000064356,3.344482 -mt-Co1,ENSMUSG00000064351,3.344482 -mt-Co2,ENSMUSG00000064354,3.344482 -mt-Co3,ENSMUSG00000064358,3.344482 -Mtap,ENSMUSG00000062937,1.5169770703934482 -Mtfmt,ENSMUSG00000059183,1.2673956805364006 -Mthfd1,ENSMUSG00000021048,1.5874723704927756 -Mthfd1l,ENSMUSG00000040675,2.079277215827649 -Mthfd2,ENSMUSG00000005667,1.6599549934895268 -Mthfd2l,ENSMUSG00000029376,1.5834876571943335 -Mthfr,ENSMUSG00000029009,1.3673786652462163 -Mthfs,ENSMUSG00000066442,1.7504070449873255 -Mthfsl,ENSMUSG00000079427,1.4024095672167856 -Mtm1,ENSMUSG00000031337,2.041814703247753 -Mtmr1,ENSMUSG00000015214,1.8013538771983262 -Mtmr12,ENSMUSG00000039458,1.8835541265256739 -Mtmr14,ENSMUSG00000030269,1.6281987486109408 -Mtmr2,ENSMUSG00000031918,1.6510063359220228 -Mtmr3,ENSMUSG00000034354,2.4779736848781573 -Mtmr6,ENSMUSG00000021987,1.8547560870871516 -Mtmr7,ENSMUSG00000039431,1.638187749522103 -Mtpap,ENSMUSG00000024234,1.5250949196578691 -Mtr,ENSMUSG00000021311,1.5898120805687859 -Mtrex,ENSMUSG00000016018,1.7086837119244362 -Mtrr,ENSMUSG00000034617,1.2249408092983722 -Mul1,ENSMUSG00000041241,1.322262181537446 -Mvd,ENSMUSG00000006517,1.4855653383491518 -Mvk,ENSMUSG00000041939,1.425705228403138 -Mycbp2,ENSMUSG00000033004,3.344482 -Mylip,ENSMUSG00000038175,3.344482 -Mylk,ENSMUSG00000022836,3.0810072613704045 -Mylk2,ENSMUSG00000027470,3.344482 -Mylk3,ENSMUSG00000031698,1.7482437501108778 -Mylk4,ENSMUSG00000044951,3.344482 -Myo5b,ENSMUSG00000025885,1.8810778030451618 -Naa10,ENSMUSG00000031388,1.759877754 -Naa11,ENSMUSG00000046000,1.116411643226504 -Naa15,ENSMUSG00000063273,2.0860849479200807 -Naa20,ENSMUSG00000002728,2.008634055096536 -Naa30,ENSMUSG00000036282,1.3362878002892065 -Naa40,ENSMUSG00000024764,1.6206326255256767 -Naa50,ENSMUSG00000022698,1.9500116940110115 -Naa60,ENSMUSG00000005982,1.6811862548559076 -Naa80,ENSMUSG00000079334,1.299093205143128 -Naaa,ENSMUSG00000029413,2.102964655060483 -Nadk,ENSMUSG00000029063,1.8819033982513842 -Nadk2,ENSMUSG00000022253,1.8932773837376922 -Nadsyn1,ENSMUSG00000031090,1.5498448421433868 -Nae1,ENSMUSG00000031878,1.946462212102799 -Naga,ENSMUSG00000022453,1.6685050946392443 -Nagk,ENSMUSG00000034744,1.7599567421815614 -Naglu,ENSMUSG00000001751,1.6290338307753534 -Nagpa,ENSMUSG00000023143,1.6176094275750155 -Nags,ENSMUSG00000048217,1.1891761525305713 -Nalcn,ENSMUSG00000000197,3.124430453965136 -Nampt,ENSMUSG00000020572,1.7735857973250868 -Nanp,ENSMUSG00000053916,1.1017136155165084 -Nans,ENSMUSG00000028334,1.6328982239251932 -Napa,ENSMUSG00000006024,2.4362011586899195 -Naprt,ENSMUSG00000022574,2.084950626851731 -Nars1,ENSMUSG00000024587,2.4014348806493904 -Nat1,ENSMUSG00000025588,1.9418629696013714 -Nat10,ENSMUSG00000027185,1.3093715858328165 -Nat14,ENSMUSG00000035285,1.611960178122813 -Nat2,ENSMUSG00000051147,1.7104438865345324 -Nat8,ENSMUSG00000030004,3.344482 -Nat8l,ENSMUSG00000048142,2.1344128602333816 -Nat9,ENSMUSG00000015542,1.320506426 -Ncoa1,ENSMUSG00000020647,3.344482 -Ncoa3,ENSMUSG00000027678,2.299245427838266 -Nd1,ENSMUSG00000064341,3.344482 -Nd2,ENSMUSG00000064345,3.344482 -Nd3,ENSMUSG00000064360,3.344482 -Nd4,ENSMUSG00000064363,3.344482 -Nd4l,ENSMUSG00000065947,3.344482 -Nd5,ENSMUSG00000064367,3.344482 -Nd6,ENSMUSG00000064368,3.344482 -Ndc1,ENSMUSG00000028614,1.3326987234811103 -Ndst1,ENSMUSG00000054008,1.5310736073855387 -Ndst2,ENSMUSG00000039308,1.480573739927988 -Ndst3,ENSMUSG00000027977,3.344482 -Ndst4,ENSMUSG00000027971,2.6928268917083744 -Ndufa1,ENSMUSG00000016427,3.097121973360066 -Ndufa10,ENSMUSG00000026260,2.548332549705327 -Ndufa11,ENSMUSG00000002379,3.2498659470067577 -Ndufa12,ENSMUSG00000020022,2.7926876548961697 -Ndufa13,ENSMUSG00000036199,3.344482 -Ndufa2,ENSMUSG00000014294,3.344482 -Ndufa3,ENSMUSG00000035674,3.344482 -Ndufa4,ENSMUSG00000029632,3.344482 -Ndufa5,ENSMUSG00000023089,3.318185418062353 -Ndufa6,ENSMUSG00000022450,3.344482 -Ndufa7,ENSMUSG00000041881,3.344482 -Ndufa8,ENSMUSG00000026895,2.698279637 -Ndufa9,ENSMUSG00000000399,2.121433375130678 -Ndufab1,ENSMUSG00000030869,3.153727850350043 -Ndufb1,ENSMUSG00000113902,3.344482 -Ndufb10,ENSMUSG00000040048,3.1919375556136353 -Ndufb11,ENSMUSG00000031059,3.344482 -Ndufb2,ENSMUSG00000002416,2.9506562131209253 -Ndufb3,ENSMUSG00000026032,2.6790162809592015 -Ndufb4,ENSMUSG00000022820,2.8343396070479425 -Ndufb5,ENSMUSG00000027673,3.2946462317260585 -Ndufb6,ENSMUSG00000071014,2.6611400016993496 -Ndufb7,ENSMUSG00000033938,3.127678841050384 -Ndufb8,ENSMUSG00000025204,3.344482 -Ndufb9,ENSMUSG00000022354,3.344482 -Ndufc1,ENSMUSG00000037152,3.344482 -Ndufc2,ENSMUSG00000030647,3.344482 -Ndufs1,ENSMUSG00000025968,2.1913800182022225 -Ndufs2,ENSMUSG00000013593,2.682925900362596 -Ndufs3,ENSMUSG00000005510,2.3006223723947974 -Ndufs4,ENSMUSG00000021764,2.766285806 -Ndufs5,ENSMUSG00000028648,3.237778190781628 -Ndufs6,ENSMUSG00000021606,2.9848080614944683 -Ndufs7,ENSMUSG00000020153,2.8691294775020633 -Ndufs8,ENSMUSG00000059734,2.387631940951791 -Ndufv1,ENSMUSG00000037916,2.262857982637843 -Ndufv2,ENSMUSG00000024099,2.8269377527394934 -Ndufv3,ENSMUSG00000024038,3.133071244 -Nedd4,ENSMUSG00000032216,3.344482 -Nedd4l,ENSMUSG00000024589,3.344482 -Neu1,ENSMUSG00000007038,1.8359574362420177 -Neu2,ENSMUSG00000079434,1.0691208567002846 -Neu3,ENSMUSG00000035239,1.2641462836540651 -Neu4,ENSMUSG00000034000,3.344482 -Neurl1a,ENSMUSG00000006435,2.013961798559157 -Neurl1b,ENSMUSG00000034413,1.0695855253969382 -Ngly1,ENSMUSG00000021785,1.710851796176069 -Nhlrc1,ENSMUSG00000044231,1.1204169707451122 -Nit2,ENSMUSG00000022751,1.6030296052417499 -Nktr,ENSMUSG00000032525,3.227685831156642 -Nln,ENSMUSG00000021710,1.5524982067900401 -Nme1,ENSMUSG00000037601,3.344482 -Nme2,ENSMUSG00000020857,3.344482 -Nme3,ENSMUSG00000073435,1.485713805655827 -Nme4,ENSMUSG00000024177,1.5257835531745103 -Nme6,ENSMUSG00000032478,1.434191263337312 -Nme7,ENSMUSG00000026575,1.6788507016177856 -Nmnat1,ENSMUSG00000028992,1.4360814261326507 -Nmnat2,ENSMUSG00000042751,3.344482 -Nmnat3,ENSMUSG00000032456,2.6632209833539195 -Nmrk1,ENSMUSG00000037847,1.719067841228829 -Nmrk2,ENSMUSG00000004939,3.344482 -Nmt1,ENSMUSG00000020936,2.1644972644496123 -Nmt2,ENSMUSG00000026643,2.390446360644367 -Nnmt,ENSMUSG00000032271,2.2919585504665534 -Nnt,ENSMUSG00000025453,2.5688723081377134 -Nnt,ENSMUSG00000116207,2.5688723081377134 -Nnt,ENSMUSG00000025453,2.1269382804918826 -Nnt,ENSMUSG00000116207,2.1269382804918826 -Nol9,ENSMUSG00000028948,1.342659934013132 -Nos1,ENSMUSG00000029361,2.523038324704775 -Nos2,ENSMUSG00000020826,2.302910372761703 -Nos3,ENSMUSG00000028978,2.040501035272696 -Npc1,ENSMUSG00000024413,1.9184588839059533 -Npc1l1,ENSMUSG00000020447,1.1398609242317184 -Npepps,ENSMUSG00000001441,2.932384565887921 -Npl,ENSMUSG00000042684,1.7399835648064401 -Nploc4,ENSMUSG00000039703,1.6722294489405842 -Npr1,ENSMUSG00000027931,2.615929338727577 -Npr2,ENSMUSG00000028469,1.561312837062568 -Nqo1,ENSMUSG00000003849,1.8455244418425147 -Nqo2,ENSMUSG00000046949,1.6340479147669504 -Nrf1,ENSMUSG00000058440,2.2997785753244195 -Nsd1,ENSMUSG00000021488,3.344482 -Nsd2,ENSMUSG00000057406,2.519382799585088 -Nsd3,ENSMUSG00000054823,3.1137220181204204 -Nsdhl,ENSMUSG00000031349,1.5454198033565305 -Nsf,ENSMUSG00000034187,3.344482 -Nt5c,ENSMUSG00000020736,1.7944070162823185 -Nt5c1a,ENSMUSG00000054958,1.0854302695695905 -Nt5c1b,ENSMUSG00000020622,1.5293722124746094 -Nt5c2,ENSMUSG00000025041,2.2489145036657914 -Nt5c3,ENSMUSG00000029780,1.8721335482571897 -Nt5c3b,ENSMUSG00000017176,1.4503999404161412 -Nt5dc3,ENSMUSG00000054027,1.7225040309606325 -Nt5e,ENSMUSG00000032420,2.1161513834697363 -Nt5m,ENSMUSG00000032615,1.4524656575315797 -Ntan1,ENSMUSG00000022681,2.1266593935332385 -Ntaq1,ENSMUSG00000022359,1.3854890798026351 -Ntpcr,ENSMUSG00000031851,1.3973530417736033 -Nudt10,ENSMUSG00000073293,1.1701210759506377 -Nudt11,ENSMUSG00000073295,1.272465500343215 -Nudt12,ENSMUSG00000024228,1.1854512950539595 -Nudt14,ENSMUSG00000002804,2.0612828934481198 -Nudt2,ENSMUSG00000028443,1.330184504099638 -Nudt3,ENSMUSG00000024213,2.4661419957545325 -Nudt4,ENSMUSG00000020029,2.8253313575295658 -Nudt5,ENSMUSG00000025817,1.7984183061814303 -Nudt9,ENSMUSG00000029310,1.628530577284993 -Nup107,ENSMUSG00000052798,1.4095070271127168 -Nup133,ENSMUSG00000039509,1.3689654315816928 -Nup153,ENSMUSG00000021374,1.599932693146042 -Nup155,ENSMUSG00000022142,1.496509382676385 -Nup160,ENSMUSG00000051329,1.7550693630122953 -Nup188,ENSMUSG00000052533,1.415475634619132 -Nup205,ENSMUSG00000038759,1.5880866239010445 -Nup210,ENSMUSG00000030091,1.4618297876673705 -Nup210l,ENSMUSG00000027939,1.3031933717113247 -Nup214,ENSMUSG00000001855,1.7213884716694259 -Nup35,ENSMUSG00000026999,1.387200901733506 -Nup37,ENSMUSG00000035351,1.344546040012146 -Nup43,ENSMUSG00000040034,1.4779766333828737 -Nup50,ENSMUSG00000016619,1.4739851466633704 -Nup54,ENSMUSG00000034826,1.4890524208955294 -Nup58,ENSMUSG00000063895,1.8093327108000776 -Nup62,ENSMUSG00000109511,1.53223296 -Nup62cl,ENSMUSG00000072944,1.4633383743531527 -Nup85,ENSMUSG00000020739,1.5720391151950313 -Nup88,ENSMUSG00000040667,1.6139561309343697 -Nup93,ENSMUSG00000032939,1.6112941567840866 -Nup98,ENSMUSG00000063550,2.0429640442711863 -Nupl2,ENSMUSG00000048439,1.3846472533147232 -Oard1,ENSMUSG00000040771,1.591586454347151 -Oat,ENSMUSG00000030934,2.891888990747943 -Oca2,ENSMUSG00000030450,1.2575366529626506 -Ocrl,ENSMUSG00000001173,2.0220975509091077 -Odc1,ENSMUSG00000011179,2.4359772515055678 -Oga,ENSMUSG00000025220,2.414054256839775 -Ogdh,ENSMUSG00000020456,2.4657684932685893 -Ogt,ENSMUSG00000034160,3.344482 -Olah,ENSMUSG00000026645,1.1708335134432764 -Oplah,ENSMUSG00000022562,1.6084326824579385 -Os9,ENSMUSG00000040462,2.0149582271343944 -Otc,ENSMUSG00000031173,2.6771664844283034 -Otub1,ENSMUSG00000024767,2.3308670579438218 -Otud5,ENSMUSG00000031154,1.5648252030379317 -Oxct1,ENSMUSG00000022186,3.344482 -Oxct2a,ENSMUSG00000076436,0.842318 -Oxct2b,ENSMUSG00000076438,0.842318 -Oxsm,ENSMUSG00000021786,1.1500598427691442 -P4ha1,ENSMUSG00000019916,2.153092020591323 -P4ha2,ENSMUSG00000018906,1.6354656371664609 -P4ha3,ENSMUSG00000051048,1.3168209432944755 -P4hb,ENSMUSG00000025130,2.739102882081756 -Padi1,ENSMUSG00000025329,1.9435234404838029 -Padi2,ENSMUSG00000028927,2.3149437350575375 -Padi3,ENSMUSG00000025328,0.9021065390387247 -Padi4,ENSMUSG00000025330,2.7345661048355625 -Padi6,ENSMUSG00000040935,0.842318 -Pafah1b1,ENSMUSG00000020745,3.344482 -Pafah1b2,ENSMUSG00000003131,2.2457004843095967 -Pafah1b3,ENSMUSG00000005447,2.7665199633401634 -Pafah2,ENSMUSG00000037366,1.473708247463042 -Pah,ENSMUSG00000020051,3.344482 -Paics,ENSMUSG00000029247,2.1703318703441905 -Pam,ENSMUSG00000026335,3.344482 -Pank1,ENSMUSG00000033610,1.701161662430427 -Pank2,ENSMUSG00000037514,1.7917475951675914 -Pank3,ENSMUSG00000018846,1.6693872208527465 -Pank4,ENSMUSG00000029056,1.5321162217174387 -Paox,ENSMUSG00000025464,1.1364014978888939 -Papola,ENSMUSG00000021111,2.6876727595076098 -Papolb,ENSMUSG00000074817,1.3963899132564261 -Papolg,ENSMUSG00000020273,1.4613812551898522 -Papss1,ENSMUSG00000028032,1.8163968794891943 -Papss2,ENSMUSG00000024899,2.8139691959054844 -Parp1,ENSMUSG00000026496,1.7027992399946967 -Parp10,ENSMUSG00000063268,2.0129249991015374 -Parp11,ENSMUSG00000037997,1.5041494135428297 -Parp12,ENSMUSG00000038507,1.8846866380537453 -Parp14,ENSMUSG00000034422,3.121450984 -Parp16,ENSMUSG00000032392,1.6462849075619712 -Parp2,ENSMUSG00000036023,1.616934500621216 -Parp3,ENSMUSG00000023249,2.488912469120655 -Parp4,ENSMUSG00000054509,2.442124719348311 -Parp6,ENSMUSG00000025237,1.8041439395424295 -Parp8,ENSMUSG00000021725,2.2700998394427137 -Parp9,ENSMUSG00000022906,2.224227394701777 -Pcbd1,ENSMUSG00000020098,2.6973723154857483 -Pcbd2,ENSMUSG00000021496,1.7144756357526385 -Pcca,ENSMUSG00000041650,3.344482 -Pccb,ENSMUSG00000032527,1.670607527126404 -Pck1,ENSMUSG00000027513,3.344482 -Pck2,ENSMUSG00000040618,1.5116031745886305 -Pcmt1,ENSMUSG00000019795,2.6686195354116866 -Pctp,ENSMUSG00000020553,1.6110718580058097 -Pcx,ENSMUSG00000024892,2.5059436659362135 -Pcyox1,ENSMUSG00000029998,1.5778628368464185 -Pcyt1a,ENSMUSG00000005615,1.7106513081427595 -Pcyt1b,ENSMUSG00000035246,1.421250719074222 -Pcyt2,ENSMUSG00000025137,2.2401508923595794 -Pde10a,ENSMUSG00000023868,3.344482 -Pde11a,ENSMUSG00000075270,3.344482 -Pde1a,ENSMUSG00000059173,3.344482 -Pde1b,ENSMUSG00000022489,1.4433558378799405 -Pde1c,ENSMUSG00000004347,3.344482 -Pde2a,ENSMUSG00000110195,2.2158646882993907 -Pde3a,ENSMUSG00000041741,3.344482 -Pde3b,ENSMUSG00000030671,3.344482 -Pde4a,ENSMUSG00000032177,2.124856791100265 -Pde4b,ENSMUSG00000028525,3.344482 -Pde4c,ENSMUSG00000031842,2.9014270805182316 -Pde4d,ENSMUSG00000021699,3.344482 -Pde5a,ENSMUSG00000053965,2.1769884813626694 -Pde6a,ENSMUSG00000024575,3.344482 -Pde6b,ENSMUSG00000029491,3.344482 -Pde6c,ENSMUSG00000024992,3.344482 -Pde6d,ENSMUSG00000026239,1.8402562615793787 -Pde6g,ENSMUSG00000025386,3.344482 -Pde6h,ENSMUSG00000064330,3.344482 -Pde7a,ENSMUSG00000069094,2.2542210291921756 -Pde7b,ENSMUSG00000019990,3.344482 -Pde8a,ENSMUSG00000025584,3.344482 -Pde8b,ENSMUSG00000021684,2.9102519476827333 -Pde9a,ENSMUSG00000041119,2.0685012320833205 -Pdf,ENSMUSG00000078931,1.2499286514179149 -Pdha1,ENSMUSG00000031299,1.9963380827235713 -Pdha2,ENSMUSG00000047674,0.842318 -Pdhb,ENSMUSG00000021748,2.121623580661967 -Pdhx,ENSMUSG00000010914,1.5213513426914231 -Pdia3,ENSMUSG00000027248,3.344482 -Pdia4,ENSMUSG00000025823,2.17414794 -Pdia5,ENSMUSG00000022844,1.5828581659002463 -Pdia6,ENSMUSG00000020571,3.239689213055428 -Pdk1,ENSMUSG00000006494,1.4925968326042602 -Pdk2,ENSMUSG00000038967,1.7814198996515445 -Pdk3,ENSMUSG00000035232,1.4415763637661723 -Pdk4,ENSMUSG00000019577,3.0057559280261956 -Pdp1,ENSMUSG00000049225,2.303722201495485 -Pdp2,ENSMUSG00000048371,1.580527882470901 -Pdpr,ENSMUSG00000033624,1.9154712141038897 -Pdss1,ENSMUSG00000026784,1.7426492934708737 -Pdss2,ENSMUSG00000038240,2.260947760995865 -Pdxk,ENSMUSG00000032788,1.801074032080114 -Pdxp,ENSMUSG00000116165,2.497676955954301 -Pdzd4,ENSMUSG00000002006,2.2149495316024006 -Pecr,ENSMUSG00000026189,2.463419738 -Pemt,ENSMUSG00000000301,1.2044309622134024 -Pepd,ENSMUSG00000063931,1.9432303555031283 -Pfas,ENSMUSG00000020899,1.5417648849647978 -Pfkfb1,ENSMUSG00000025271,2.455370199 -Pfkfb2,ENSMUSG00000026409,1.5596943807882382 -Pfkfb3,ENSMUSG00000026773,2.158652965218754 -Pfkfb4,ENSMUSG00000025648,1.7406770714457338 -Pfkl,ENSMUSG00000020277,1.8440429447962254 -Pfkm,ENSMUSG00000033065,2.0101115935049143 -Pfkp,ENSMUSG00000021196,2.7719909531957696 -Pgam1,ENSMUSG00000011752,3.344482 -Pgam2,ENSMUSG00000020475,3.344482 -Pgap1,ENSMUSG00000073678,1.927938660510571 -Pgd,ENSMUSG00000028961,2.032189169368781 -Pgghg,ENSMUSG00000062031,1.6837939799663217 -Pgk1,ENSMUSG00000062070,3.109839865932231 -Pgk2,ENSMUSG00000031233,3.344482 -Pgls,ENSMUSG00000031807,2.6279195415357033 -Pglyrp1,ENSMUSG00000030413,3.344482 -Pglyrp2,ENSMUSG00000079563,2.8524477682408635 -Pglyrp3,ENSMUSG00000042244,1.0757871961208634 -Pglyrp4,ENSMUSG00000042250,1.2543085416129767 -Pgm1,ENSMUSG00000025791,1.9875495732614332 -Pgm2,ENSMUSG00000029171,1.468773603820168 -Pgm2l1,ENSMUSG00000030729,3.344482 -Pgm3,ENSMUSG00000056131,1.4460840398470007 -Pgp,ENSMUSG00000043445,1.9994971410602604 -Pgs1,ENSMUSG00000017715,1.4688177901258765 -Phgdh,ENSMUSG00000053398,3.344482 -Phka1,ENSMUSG00000034055,3.344482 -Phka2,ENSMUSG00000031295,1.7782789432753296 -Phkb,ENSMUSG00000036879,2.405216141434663 -Phkg1,ENSMUSG00000025537,3.344482 -Phkg2,ENSMUSG00000030815,1.4966126121519454 -Phospho1,ENSMUSG00000050860,2.4683456163841937 -Phospho2,ENSMUSG00000027088,1.3408597020249438 -Phpt1,ENSMUSG00000036504,2.1597953767708593 -Phyh,ENSMUSG00000026664,2.159309863133455 -Phykpl,ENSMUSG00000020359,1.9373658097419975 -Pi4k2a,ENSMUSG00000025178,1.649654865949617 -Pi4k2b,ENSMUSG00000029186,1.7869665001350892 -Pi4ka,ENSMUSG00000041720,3.1470434019808686 -Pi4kb,ENSMUSG00000038861,2.223285334035375 -Piga,ENSMUSG00000031381,1.4715544069288529 -Pigb,ENSMUSG00000079469,1.5535196766619457 -Pigc,ENSMUSG00000026698,1.4781648597816959 -Pigf,ENSMUSG00000024145,1.3768571672485217 -Pigg,ENSMUSG00000029263,1.2635420072381849 -Pigh,ENSMUSG00000021120,1.3974910709543489 -Pigk,ENSMUSG00000039047,1.9302948798637534 -Pigl,ENSMUSG00000014245,1.388931227237714 -Pigm,ENSMUSG00000050229,1.3180851938930551 -Pign,ENSMUSG00000056536,1.775578423739806 -Pigo,ENSMUSG00000028454,1.3516574165433286 -Pigp,ENSMUSG00000022940,1.8045891753547298 -Pigq,ENSMUSG00000025728,1.4811474667721107 -Pigs,ENSMUSG00000041958,1.608687390699967 -Pigt,ENSMUSG00000017721,1.6408318266855935 -Pigu,ENSMUSG00000038383,1.714001640941826 -Pigv,ENSMUSG00000043257,1.6595305258843907 -Pigw,ENSMUSG00000045140,1.1044556946151325 -Pigx,ENSMUSG00000023791,1.6946269879558866 -Pigyl,ENSMUSG00000010607,1.7151180986580783 -Pigz,ENSMUSG00000045625,1.5290458259966362 -Pik3c2a,ENSMUSG00000030660,2.3072476341324446 -Pik3c2b,ENSMUSG00000026447,1.9128145731672639 -Pik3c2g,ENSMUSG00000030228,3.344482 -Pik3c3,ENSMUSG00000033628,1.492606017269906 -Pik3ca,ENSMUSG00000027665,2.208752089572162 -Pik3cb,ENSMUSG00000032462,1.8557501224661583 -Pik3cd,ENSMUSG00000039936,1.9179144798428926 -Pik3cg,ENSMUSG00000020573,2.7022429483182226 -Pik3r1,ENSMUSG00000041417,3.058904303078418 -Pik3r2,ENSMUSG00000031834,1.3342970267650103 -Pik3r3,ENSMUSG00000028698,3.344482 -Pik3r5,ENSMUSG00000020901,3.344482 -Pikfyve,ENSMUSG00000025949,1.7802080023246292 -Pin1,ENSMUSG00000032171,2.158052902390036 -Pin4,ENSMUSG00000079480,1.6610994953705265 -Pip4k2a,ENSMUSG00000026737,2.622448432 -Pip4k2b,ENSMUSG00000018547,1.6106806052906764 -Pip4k2c,ENSMUSG00000025417,1.637877785224323 -Pip4p1,ENSMUSG00000035953,1.8103107485632002 -Pip4p2,ENSMUSG00000028221,1.8088309244597813 -Pip5k1a,ENSMUSG00000028126,2.089661591 -Pip5k1b,ENSMUSG00000024867,3.344482 -Pip5k1c,ENSMUSG00000034902,2.3563120633156207 -Pip5kl1,ENSMUSG00000046854,0.9356353598820056 -Pipox,ENSMUSG00000017453,3.344482 -Pisd,ENSMUSG00000023452,1.6496343083726948 -Pja1,ENSMUSG00000034403,2.1228846619223853 -Pja2,ENSMUSG00000024083,3.344482 -Pklr,ENSMUSG00000041237,1.333533503014003 -Pkm,ENSMUSG00000032294,3.344482 -Pla2g10,ENSMUSG00000022683,1.7156901741671682 -Pla2g12a,ENSMUSG00000027999,1.4699872065037696 -Pla2g15,ENSMUSG00000031903,1.5928699315748525 -Pla2g1b,ENSMUSG00000029522,3.344482 -Pla2g2a,ENSMUSG00000058908,2.224543367903735 -Pla2g2d,ENSMUSG00000041202,2.063258599758463 -Pla2g2e,ENSMUSG00000028751,1.8080204370118012 -Pla2g2f,ENSMUSG00000028749,1.1652487889798135 -Pla2g3,ENSMUSG00000034579,2.6221789656038315 -Pla2g4a,ENSMUSG00000056220,2.6134755680125914 -Pla2g4b,ENSMUSG00000098488,1.1894647102637157 -Pla2g4c,ENSMUSG00000033847,1.9594410565721438 -Pla2g4d,ENSMUSG00000070719,0.842318 -Pla2g4e,ENSMUSG00000050211,1.6683583427160926 -Pla2g4f,ENSMUSG00000046971,1.0425213269381337 -Pla2g5,ENSMUSG00000041193,1.437686740476118 -Pla2g6,ENSMUSG00000042632,1.4967357834506259 -Pla2g7,ENSMUSG00000023913,3.344482 -Plaat3,ENSMUSG00000060675,3.2459513867510537 -Plb1,ENSMUSG00000029134,1.2658591369744638 -Plcb1,ENSMUSG00000051177,3.344482 -Plcb2,ENSMUSG00000040061,1.5971723082040892 -Plcb3,ENSMUSG00000024960,1.6947243911774854 -Plcb4,ENSMUSG00000039943,3.344482 -Plcd1,ENSMUSG00000010660,1.494176434955691 -Plcd3,ENSMUSG00000020937,1.520216189618429 -Plcd4,ENSMUSG00000026173,2.8907982404744073 -Plce1,ENSMUSG00000024998,3.344482 -Plcg1,ENSMUSG00000016933,1.7173502512082812 -Plcg2,ENSMUSG00000034330,3.1405929440129063 -Plch1,ENSMUSG00000036834,2.2116593254170067 -Plch2,ENSMUSG00000029055,1.892262896027152 -Plcl1,ENSMUSG00000038349,3.344482 -Plcxd2,ENSMUSG00000087141,2.425140298391834 -Plcz1,ENSMUSG00000030230,1.4485065101429675 -Pld1,ENSMUSG00000027695,3.2291457569534363 -Pld2,ENSMUSG00000020828,1.9835441208379574 -Pld6,ENSMUSG00000043648,1.1935082449774885 -Plg,ENSMUSG00000059481,3.344482 -Plin1,ENSMUSG00000030546,3.344482 -Plin2,ENSMUSG00000028494,3.344482 -Plin3,ENSMUSG00000024197,2.299727986053988 -Plin4,ENSMUSG00000002831,3.344482 -Plod1,ENSMUSG00000019055,2.3437330309764506 -Plod2,ENSMUSG00000032374,2.214970433 -Plod3,ENSMUSG00000004846,1.6201015559190433 -Plpbp,ENSMUSG00000031485,1.7585838174138613 -Plpp1,ENSMUSG00000021759,2.853220729564107 -Plpp2,ENSMUSG00000052151,1.757271104252014 -Plpp3,ENSMUSG00000028517,3.344482 -Plpp4,ENSMUSG00000070366,2.5349429247109905 -Plpp5,ENSMUSG00000031570,1.4059252739848986 -Plpp6,ENSMUSG00000040105,1.295040709684952 -Plppr2,ENSMUSG00000040563,2.1009004748653903 -Plppr3,ENSMUSG00000035835,2.07373225 -Plppr4,ENSMUSG00000044667,3.344482 -Pmm1,ENSMUSG00000022474,2.088987474752286 -Pmm2,ENSMUSG00000022711,1.6457073587304607 -Pmpca,ENSMUSG00000026926,1.4417527527764984 -Pmvk,ENSMUSG00000027952,1.749517098450806 -Pnck,ENSMUSG00000002012,2.024191773765193 -Pnkp,ENSMUSG00000002963,1.6706204367997157 -Pnlip,ENSMUSG00000046008,3.344482 -Pnliprp1,ENSMUSG00000042179,3.344482 -Pnliprp2,ENSMUSG00000025091,3.344482 -Pnmt,ENSMUSG00000038216,1.140293584824391 -Pnp,ENSMUSG00000115338,2.746997136608927 -Pnp2,ENSMUSG00000068417,1.7350313012731238 -Pnpla2,ENSMUSG00000025509,2.211583900858876 -Pnpla3,ENSMUSG00000041653,3.344482 -Pnpla6,ENSMUSG00000004565,1.479478666579399 -Pnpla7,ENSMUSG00000036833,2.6300510604944147 -Pnpla8,ENSMUSG00000036257,2.1541201687799796 -Pnpo,ENSMUSG00000018659,1.4177998751099765 -Pola1,ENSMUSG00000006678,2.1336267538640583 -Pola2,ENSMUSG00000024833,3.344482 -Polb,ENSMUSG00000031536,2.4253369712506725 -Pold1,ENSMUSG00000038644,1.5392445505275256 -Pold2,ENSMUSG00000020471,1.5304877666534091 -Pold3,ENSMUSG00000030726,1.4615313947064845 -Pold4,ENSMUSG00000024854,1.9269510736767956 -Pole,ENSMUSG00000007080,1.5376425308342923 -Pole2,ENSMUSG00000020974,1.417464811 -Pole3,ENSMUSG00000028394,1.4628765136296116 -Pole4,ENSMUSG00000030042,1.7692026015765527 -Polg,ENSMUSG00000039176,1.5104936320254372 -Polg2,ENSMUSG00000020718,1.6805651767376995 -Polh,ENSMUSG00000023953,1.760806585 -Poli,ENSMUSG00000038425,1.185016478730111 -Polk,ENSMUSG00000021668,1.7252760484921394 -Poll,ENSMUSG00000025218,1.3025988389989795 -Polm,ENSMUSG00000020474,1.6510827210248553 -Poln,ENSMUSG00000045102,1.6164485621938054 -Polq,ENSMUSG00000034206,1.311487385152805 -Polr1a,ENSMUSG00000049553,1.368381105908051 -Polr1b,ENSMUSG00000027395,2.1397719047479846 -Polr1c,ENSMUSG00000067148,1.601377951159284 -Polr1d,ENSMUSG00000029642,2.6035008519528757 -Polr1e,ENSMUSG00000028318,1.144688677299907 -Polr1h,ENSMUSG00000036315,1.483444198398002 -Polr2a,ENSMUSG00000005198,1.9892638944629224 -Polr2b,ENSMUSG00000029250,1.5998562897755293 -Polr2c,ENSMUSG00000031783,1.9336086292085795 -Polr2d,ENSMUSG00000024258,1.5169560286036197 -Polr2e,ENSMUSG00000004667,1.983041223317458 -Polr2f,ENSMUSG00000033020,2.2772784297214694 -Polr2g,ENSMUSG00000071662,2.0198204436316325 -Polr2h,ENSMUSG00000021018,1.5027730676180329 -Polr2i,ENSMUSG00000019738,1.913097707716193 -Polr2j,ENSMUSG00000039771,2.006933128174594 -Polr2k,ENSMUSG00000045996,1.9752727838488042 -Polr2l,ENSMUSG00000038489,2.0495187767430343 -Polr3a,ENSMUSG00000025280,1.5073820518946555 -Polr3b,ENSMUSG00000034453,1.5511913116953358 -Polr3c,ENSMUSG00000028099,1.4734047091875568 -Polr3d,ENSMUSG00000000776,1.392628970281372 -Polr3e,ENSMUSG00000030880,1.8610026152666679 -Polr3f,ENSMUSG00000027427,1.4208816286860517 -Polr3g,ENSMUSG00000035834,1.2407068834810846 -Polr3gl,ENSMUSG00000028104,1.6119129516233444 -Polr3h,ENSMUSG00000022476,1.413176651341289 -Polr3k,ENSMUSG00000038628,1.6252558860120867 -Polrmt,ENSMUSG00000020329,1.5640326839362282 -Pom121,ENSMUSG00000053293,1.471457208 -Pomgnt1,ENSMUSG00000028700,1.7517263259112326 -Pomt1,ENSMUSG00000039254,1.4473335353314813 -Pomt2,ENSMUSG00000034126,1.3756396054716085 -Pon1,ENSMUSG00000002588,2.3132376583579948 -Pon2,ENSMUSG00000032667,2.7079254660489127 -Pon3,ENSMUSG00000029759,2.519349463659444 -Por,ENSMUSG00000005514,2.2457003890012706 -Porcn,ENSMUSG00000031169,1.7632023229068885 -Ppa1,ENSMUSG00000020089,2.124917721798595 -Ppa2,ENSMUSG00000028013,1.758314891573556 -Ppat,ENSMUSG00000029246,1.3212695183812706 -Ppcdc,ENSMUSG00000063849,1.659911776923348 -Ppcs,ENSMUSG00000028636,1.3982089016116463 -Ppia,ENSMUSG00000071866,3.344482 -Ppib,ENSMUSG00000032383,3.344482 -Ppic,ENSMUSG00000024538,3.344482 -Ppid,ENSMUSG00000027804,1.8452564194995376 -Ppie,ENSMUSG00000028651,1.5384849507642473 -Ppif,ENSMUSG00000021868,1.3058382266000275 -Ppig,ENSMUSG00000042133,2.6159746829212613 -Ppih,ENSMUSG00000060288,1.468122193262965 -Ppil1,ENSMUSG00000024007,1.5037302824834875 -Ppil2,ENSMUSG00000022771,1.8991714794122418 -Ppil3,ENSMUSG00000026035,1.4280141561870563 -Ppil4,ENSMUSG00000015757,1.7927870399226258 -Ppip5k1,ENSMUSG00000033526,2.159394632697256 -Ppip5k2,ENSMUSG00000040648,1.704733723559159 -Ppm1l,ENSMUSG00000027784,3.344482 -Ppox,ENSMUSG00000062729,1.6392928145732784 -Ppp1r3b,ENSMUSG00000046794,2.082722024 -Ppp1r3c,ENSMUSG00000067279,2.3078593445927296 -Ppt1,ENSMUSG00000028657,2.2171853241972697 -Ppt2,ENSMUSG00000015474,1.578676327404981 -Ppwd1,ENSMUSG00000021713,1.6401192998933445 -Prdx1,ENSMUSG00000028691,3.344482 -Prdx2,ENSMUSG00000005161,3.344482 -Prdx3,ENSMUSG00000024997,1.8542604705956347 -Prdx5,ENSMUSG00000024953,3.344482 -Prdx6,ENSMUSG00000026701,3.344482 -Preb,ENSMUSG00000045302,1.8168573266881012 -Prep,ENSMUSG00000019849,1.4127701230039575 -Prkd1,ENSMUSG00000002688,3.344482 -Prkn,ENSMUSG00000023826,3.344482 -Prodh,ENSMUSG00000003526,2.0869880517078103 -Prodh2,ENSMUSG00000036892,3.344482 -Prps1,ENSMUSG00000031432,1.5333472632066616 -Prps1l1,ENSMUSG00000092305,2.677330346391685 -Prps2,ENSMUSG00000025742,1.3330640852233469 -Prune1,ENSMUSG00000015711,1.6523430393226666 -Psap,ENSMUSG00000004207,3.344482 -Psat1,ENSMUSG00000024640,2.0371073206377117 -Psma1,ENSMUSG00000030751,2.564891472086077 -Psma2,ENSMUSG00000015671,2.9241769045626027 -Psma3,ENSMUSG00000060073,3.2618911927514955 -Psma4,ENSMUSG00000032301,2.6218337163010577 -Psma5,ENSMUSG00000068749,2.3482422042765987 -Psma7,ENSMUSG00000027566,3.344482 -Psma8,ENSMUSG00000036743,1.3840280451874603 -Psmb1,ENSMUSG00000014769,3.344482 -Psmb10,ENSMUSG00000031897,1.8740699133453178 -Psmb11,ENSMUSG00000072423,1.5957276568816172 -Psmb2,ENSMUSG00000028837,2.898569667215671 -Psmb3,ENSMUSG00000069744,3.0784108655008318 -Psmb4,ENSMUSG00000005779,2.8786160425840888 -Psmb5,ENSMUSG00000022193,2.8283888686980267 -Psmb6,ENSMUSG00000018286,3.344482 -Psmb7,ENSMUSG00000026750,2.317256737111325 -Psmb8,ENSMUSG00000024338,3.344482 -Psmb9,ENSMUSG00000096727,3.1988117659592663 -Psmd1,ENSMUSG00000026229,2.242268577407217 -Psmd10,ENSMUSG00000031429,1.3964955990279362 -Psmd11,ENSMUSG00000017428,2.3040216356926004 -Psmd12,ENSMUSG00000020720,2.077533333280678 -Psmd13,ENSMUSG00000025487,2.001939850472274 -Psmd14,ENSMUSG00000026914,2.253897890066433 -Psmd2,ENSMUSG00000006998,2.105000424191405 -Psmd4,ENSMUSG00000005625,2.5778592581130857 -Psmd5,ENSMUSG00000026869,1.597004931877055 -Psmd6,ENSMUSG00000021737,2.1307987128168073 -Psmd7,ENSMUSG00000039067,2.619406036910478 -Psmd8,ENSMUSG00000030591,2.4385205713749785 -Psmd9,ENSMUSG00000029440,1.7248105349419551 -Psmg1,ENSMUSG00000022913,1.4089311541516287 -Psmg2,ENSMUSG00000024537,1.617351529027397 -Psmg3,ENSMUSG00000029551,1.458175569769763 -Psmg4,ENSMUSG00000071451,1.6559658811478268 -Psph,ENSMUSG00000029446,1.5757474828233966 -Ptdss1,ENSMUSG00000021518,1.603308499588254 -Ptdss2,ENSMUSG00000025495,1.5663003845932646 -Pten,ENSMUSG00000013663,3.0051821140705037 -Ptgds,ENSMUSG00000015090,3.344482 -Ptges,ENSMUSG00000050737,1.8903158339562731 -Ptges2,ENSMUSG00000026820,1.3201814956846276 -Ptges3,ENSMUSG00000071072,2.8407709257561637 -Ptgis,ENSMUSG00000017969,2.615341631522615 -Ptgr1,ENSMUSG00000028378,1.9122553986128132 -Ptgs1,ENSMUSG00000047250,3.3016446575212197 -Ptgs2,ENSMUSG00000032487,2.348888500098222 -Ptpmt1,ENSMUSG00000063235,1.7330458603833552 -Ptprq,ENSMUSG00000035916,2.342740108822739 -Ptrh1,ENSMUSG00000053746,1.0191375171094967 -Ptrh2,ENSMUSG00000072582,1.4052942272137465 -Pts,ENSMUSG00000032067,1.7141585538524773 -Pus1,ENSMUSG00000029507,1.2972331207296401 -Pxdn,ENSMUSG00000020674,1.695513030954251 -Pxylp1,ENSMUSG00000043587,2.1056209225980664 -Pycr1,ENSMUSG00000025140,1.1137597783435522 -Pycr2,ENSMUSG00000026520,1.6778966083915885 -Pycr3,ENSMUSG00000022571,1.4791840725791066 -Pygb,ENSMUSG00000033059,2.1036510463161053 -Pygl,ENSMUSG00000021069,2.832484539372109 -Pygm,ENSMUSG00000032648,3.344482 -Pyurf,ENSMUSG00000043162,1.427776377399896 -Qars1,ENSMUSG00000032604,1.6044228847398663 -Qdpr,ENSMUSG00000015806,2.960265299260475 -Qpct,ENSMUSG00000024084,3.311487571806402 -Qprt,ENSMUSG00000030674,2.1277548360066683 -Qtrt1,ENSMUSG00000002825,1.5248205835785944 -Qtrt2,ENSMUSG00000022704,1.5080903475211733 -Rab1a,ENSMUSG00000020149,2.962939981874213 -Rab6b,ENSMUSG00000032549,3.344482 -Rab8b,ENSMUSG00000036943,2.324431489078389 -Rad1,ENSMUSG00000022248,1.2303114182798272 -Rad18,ENSMUSG00000030254,1.4630049676021202 -Rad9a,ENSMUSG00000024824,1.3858560956299837 -Rae1,ENSMUSG00000027509,1.6706574620954289 -Rag1,ENSMUSG00000061311,3.344482 -Ralbp1,ENSMUSG00000024096,2.5794218374570375 -Ranbp2,ENSMUSG00000003226,2.090456708308825 -Rars1,ENSMUSG00000018848,1.5877188264585027 -Rbak,ENSMUSG00000061898,1.444026667853376 -Rbbp6,ENSMUSG00000030779,2.4088697658046545 -Rbks,ENSMUSG00000029136,1.6279174942376242 -Rbp1,ENSMUSG00000046402,3.344482 -Rbp2,ENSMUSG00000032454,3.344482 -Rbp3,ENSMUSG00000041534,3.344482 -Rbp4,ENSMUSG00000024990,3.344482 -Rchy1,ENSMUSG00000029397,1.9494907724847201 -Rdh1,ENSMUSG00000089789,1.1366420884881419 -Rdh10,ENSMUSG00000025921,1.668970099642784 -Rdh11,ENSMUSG00000066441,1.3756199156251823 -Rdh12,ENSMUSG00000021123,2.889771445585166 -Rdh13,ENSMUSG00000008435,1.405009357971215 -Rdh14,ENSMUSG00000020621,1.6012498694562416 -Rdh16,ENSMUSG00000069456,3.344482 -Rdh16f2,ENSMUSG00000074639,3.344482 -Rdh19,ENSMUSG00000054052,1.2388946180206417 -Rdh5,ENSMUSG00000025350,2.88622885 -Rdh7,ENSMUSG00000040134,3.344482 -Rdh8,ENSMUSG00000053773,3.344482 -Rdh9,ENSMUSG00000056148,1.044251972 -Renbp,ENSMUSG00000031387,2.3062341397995914 -Rev3l,ENSMUSG00000019841,3.2034044239466644 -Rfc5,ENSMUSG00000029363,1.2297862863897617 -Rfk,ENSMUSG00000024712,1.5909938372867527 -Rfwd3,ENSMUSG00000033596,1.7267975735509709 -Rgn,ENSMUSG00000023070,2.972536561829463 -Rhag,ENSMUSG00000023926,3.344482 -Rhbg,ENSMUSG00000104445,2.8863891160712614 -Rhcg,ENSMUSG00000030549,3.344482 -Ring1,ENSMUSG00000024325,1.6044133052373983 -Rlbp1,ENSMUSG00000039194,3.344482 -Rnf103,ENSMUSG00000052656,1.6735699098668293 -Rnf115,ENSMUSG00000028098,1.9523396992475186 -Rnf123,ENSMUSG00000041528,1.6827642620379821 -Rnf125,ENSMUSG00000033107,2.6923804463961303 -Rnf126,ENSMUSG00000035890,1.5332151997918522 -Rnf128,ENSMUSG00000031438,1.9033633712953415 -Rnf13,ENSMUSG00000036503,2.5348382030394463 -Rnf130,ENSMUSG00000020376,2.532464967039581 -Rnf133,ENSMUSG00000051956,1.131614031174789 -Rnf138,ENSMUSG00000024317,1.7729673404807516 -Rnf139,ENSMUSG00000037075,1.732227147288801 -Rnf14,ENSMUSG00000060450,2.733148732326088 -Rnf144a,ENSMUSG00000020642,1.9744965012239766 -Rnf144b,ENSMUSG00000038068,1.7676422123361741 -Rnf146,ENSMUSG00000038876,1.6993238310848509 -Rnf149,ENSMUSG00000048234,1.5868166439524438 -Rnf152,ENSMUSG00000047496,3.1295463033433153 -Rnf167,ENSMUSG00000040746,1.8815496285545568 -Rnf180,ENSMUSG00000021720,1.7053748905311257 -Rnf182,ENSMUSG00000044164,2.9005984376267278 -Rnf185,ENSMUSG00000020448,1.6281516948832202 -Rnf187,ENSMUSG00000020496,3.344482 -Rnf19a,ENSMUSG00000022280,1.8006009681184714 -Rnf19b,ENSMUSG00000028793,1.5641471493633212 -Rnf2,ENSMUSG00000026484,1.6575864095574175 -Rnf20,ENSMUSG00000028309,1.693187751310974 -Rnf216,ENSMUSG00000045078,2.2160041481939543 -Rnf217,ENSMUSG00000063760,1.6677720013953272 -Rnf25,ENSMUSG00000026171,1.5272643672223132 -Rnf31,ENSMUSG00000047098,1.4263021214166707 -Rnf40,ENSMUSG00000030816,1.324464949288397 -Rnf41,ENSMUSG00000025373,1.654264025 -Rnf5,ENSMUSG00000015478,1.7674829593192658 -Rnf8,ENSMUSG00000090083,1.601554627 -Rngtt,ENSMUSG00000028274,2.088836052778103 -Rnmt,ENSMUSG00000009535,1.6585128669917413 -Rnpep,ENSMUSG00000041926,1.889383445717009 -Rpe,ENSMUSG00000026005,1.3791137720764253 -Rpe65,ENSMUSG00000028174,3.344482 -Rpia,ENSMUSG00000053604,1.4205970158128367 -Rpl36a,ENSMUSG00000079435,3.344482 -Rpn1,ENSMUSG00000030062,2.1926290140216635 -Rpn2,ENSMUSG00000027642,2.5915960442352066 -Rpp14,ENSMUSG00000023156,1.3266838616475898 -Rpusd4,ENSMUSG00000032044,1.2595950636301965 -Rrbp1,ENSMUSG00000027422,3.344482 -Rrm1,ENSMUSG00000030978,1.9298348194588082 -Rrm2,ENSMUSG00000020649,3.344482 -Rrm2b,ENSMUSG00000022292,3.344482 -Rtca,ENSMUSG00000000339,1.464716781946257 -Rwdd2a,ENSMUSG00000032417,1.5248681102551314 -Sacm1l,ENSMUSG00000025240,1.9922772980883774 -Sae1,ENSMUSG00000052833,1.9538082499735645 -Sapcd1,ENSMUSG00000036185,2.7699649165965576 -Sar1b,ENSMUSG00000020386,2.0361685007255677 -Sardh,ENSMUSG00000009614,2.253592304091518 -Sars1,ENSMUSG00000068739,2.2528274903126047 -Sat1,ENSMUSG00000025283,3.344482 -Sat2,ENSMUSG00000069835,1.6448657064611103 -Satl1,ENSMUSG00000025527,3.344482 -Sc5d,ENSMUSG00000032018,1.7596609781662966 -Scarb1,ENSMUSG00000037936,1.9803231705541953 -Scarf2,ENSMUSG00000012017,1.7496520534560014 -Sccpdh,ENSMUSG00000038936,1.8762065941854482 -Scd1,ENSMUSG00000037071,3.344482 -Scd2,ENSMUSG00000025203,3.344482 -Scd3,ENSMUSG00000025202,1.3298839928614756 -Scly,ENSMUSG00000026307,1.4378576463246446 -Scn10a,ENSMUSG00000034533,3.344482 -Scn11a,ENSMUSG00000034115,3.344482 -Scn1a,ENSMUSG00000064329,3.344482 -Scn2a,ENSMUSG00000075318,3.344482 -Scn3a,ENSMUSG00000057182,2.202244212198973 -Scn4a,ENSMUSG00000001027,3.344482 -Scn5a,ENSMUSG00000032511,1.707426304553458 -Scn7a,ENSMUSG00000034810,3.344482 -Scn8a,ENSMUSG00000023033,3.344482 -Scn9a,ENSMUSG00000075316,2.550135122117076 -Scnn1a,ENSMUSG00000030340,2.155291567699985 -Scnn1b,ENSMUSG00000030873,1.4711879377482906 -Scnn1g,ENSMUSG00000000216,1.7007023680688829 -Scp2,ENSMUSG00000028603,3.140565239237276 -Sdc1,ENSMUSG00000020592,2.5287319163294155 -Sdha,ENSMUSG00000021577,2.659261555595542 -Sdhb,ENSMUSG00000009863,2.8964789354429508 -Sdhc,ENSMUSG00000058076,2.065301421191725 -Sdhd,ENSMUSG00000000171,2.050330141255342 -Sdr16c5,ENSMUSG00000028236,1.5657576782717098 -Sdr42e1,ENSMUSG00000034308,1.077878497525402 -Sdr9c7,ENSMUSG00000040127,0.8747593909775868 -Sds,ENSMUSG00000029597,1.9373937566684973 -Sdsl,ENSMUSG00000029596,1.4764527480095926 -Sec11a,ENSMUSG00000025724,2.248329357022402 -Sec11c,ENSMUSG00000024516,2.593033791959037 -Sec13,ENSMUSG00000030298,1.955923190326242 -Sec16a,ENSMUSG00000026924,1.5226512854899026 -Sec22b,ENSMUSG00000027879,1.7174472047508444 -Sec23a,ENSMUSG00000020986,1.8318709097739363 -Sec24a,ENSMUSG00000036391,1.9595878581994008 -Sec31a,ENSMUSG00000035325,1.8183454908746424 -Sec61a1,ENSMUSG00000030082,1.8873721631579443 -Sec61b,ENSMUSG00000053317,3.344482 -Sec61g,ENSMUSG00000078974,3.344482 -Sec62,ENSMUSG00000027706,3.344482 -Sec63,ENSMUSG00000019802,2.0971111838483383 -Seh1l,ENSMUSG00000079614,1.469841232734972 -Sel1l,ENSMUSG00000020964,2.337435903149589 -Selenoi,ENSMUSG00000075703,1.8204306612310663 -Selenos,ENSMUSG00000075701,2.4100076237540384 -Sephs1,ENSMUSG00000026662,1.471630470713766 -Sephs2,ENSMUSG00000049091,1.7858900545266374 -Serp1,ENSMUSG00000027808,2.6027012709991655 -Serpina1a,ENSMUSG00000066366,3.344482 -Serpina1b,ENSMUSG00000071178,3.344482 -Serpina1d,ENSMUSG00000071177,3.344482 -Serpina1e,ENSMUSG00000072849,3.344482 -Serpina3c,ENSMUSG00000066361,2.047119543644316 -Serpina3f,ENSMUSG00000066363,3.344482 -Serpina3g,ENSMUSG00000041481,3.344482 -Serpina3i,ENSMUSG00000079014,1.0733865407264784 -Serpina3k,ENSMUSG00000058207,3.344482 -Serpina3m,ENSMUSG00000079012,2.7247885608396154 -Serpina3n,ENSMUSG00000021091,2.588799480208777 -Setd1a,ENSMUSG00000042308,1.3623009875505696 -Setd1b,ENSMUSG00000038384,1.5494181643073903 -Setd2,ENSMUSG00000044791,2.206356877614843 -Setd5,ENSMUSG00000034269,2.7575463208438906 -Setd7,ENSMUSG00000037111,2.2220623537153115 -Setdb1,ENSMUSG00000015697,1.803637775210024 -Setdb2,ENSMUSG00000071350,1.7249340147969023 -Setmar,ENSMUSG00000034639,0.9888629405458402 -Sfxn1,ENSMUSG00000021474,2.054099503051713 -Sfxn3,ENSMUSG00000025212,1.617970863853294 -Sgms1,ENSMUSG00000040451,3.1289399748253044 -Sgms2,ENSMUSG00000050931,2.925031221135008 -Sgpl1,ENSMUSG00000020097,1.8435550785943153 -Sgpp1,ENSMUSG00000021054,1.638536255132828 -Sgpp2,ENSMUSG00000032908,3.050771409574168 -Sgsh,ENSMUSG00000005043,1.4304659029484847 -Sh3bp1,ENSMUSG00000022436,2.0979590025032295 -Sh3glb1,ENSMUSG00000037062,2.6984800483501097 -Sh3rf1,ENSMUSG00000031642,2.2423692321960194 -Sh3rf2,ENSMUSG00000057719,1.959048407756437 -Sh3rf3,ENSMUSG00000037990,2.440378220794908 -Shmt1,ENSMUSG00000020534,1.5854952909543696 -Shmt2,ENSMUSG00000025403,1.5518115948752385 -Shpk,ENSMUSG00000005951,1.5009172398194353 -Shprh,ENSMUSG00000090112,1.8950506148836372 -Siae,ENSMUSG00000001942,1.3690586415321473 -Siah1a,ENSMUSG00000036840,1.638797413160965 -Siah1b,ENSMUSG00000040749,1.1428934852768864 -Siah2,ENSMUSG00000036432,1.3618206246395559 -Sil1,ENSMUSG00000024357,2.1189867992411053 -Sirt1,ENSMUSG00000020063,1.6137037131560166 -Sirt2,ENSMUSG00000015149,2.374405359357556 -Sirt3,ENSMUSG00000025486,1.6601351412533263 -Sirt5,ENSMUSG00000054021,1.4935743308287495 -Sirt6,ENSMUSG00000034748,1.3018932341824907 -Sirt7,ENSMUSG00000025138,1.7729748724222758 -Sis,ENSMUSG00000027790,2.626087684583286 -Skp1,ENSMUSG00000036309,3.344482 -Slc10a1,ENSMUSG00000021135,2.120426424 -Slc10a2,ENSMUSG00000023073,3.344482 -Slc10a6,ENSMUSG00000029321,3.344482 -Slc11a1,ENSMUSG00000026177,3.344482 -Slc11a2,ENSMUSG00000023030,1.4140360950321758 -Slc12a1,ENSMUSG00000027202,3.344482 -Slc12a2,ENSMUSG00000024597,3.157216336207449 -Slc12a3,ENSMUSG00000031766,3.344482 -Slc12a4,ENSMUSG00000017765,1.991433058189052 -Slc12a5,ENSMUSG00000017740,3.344482 -Slc12a6,ENSMUSG00000027130,2.4119587024753155 -Slc12a7,ENSMUSG00000017756,1.8928045992666496 -Slc13a1,ENSMUSG00000029700,3.344482 -Slc13a2,ENSMUSG00000001095,2.367336849309474 -Slc13a3,ENSMUSG00000018459,3.344482 -Slc13a4,ENSMUSG00000029843,2.777982380442642 -Slc13a5,ENSMUSG00000020805,1.4387642460091965 -Slc14a1,ENSMUSG00000059336,3.1166057447328406 -Slc14a2,ENSMUSG00000024552,3.344482 -Slc15a1,ENSMUSG00000025557,1.9269117657687456 -Slc15a2,ENSMUSG00000022899,3.275454731340272 -Slc15a3,ENSMUSG00000024737,2.3771332670794236 -Slc15a4,ENSMUSG00000029416,1.4795908390781545 -Slc16a1,ENSMUSG00000032902,1.9339382849805882 -Slc16a10,ENSMUSG00000019838,2.6788874310376847 -Slc16a12,ENSMUSG00000009378,2.6798342215016975 -Slc16a13,ENSMUSG00000044367,1.4874713037409248 -Slc16a2,ENSMUSG00000033965,3.191758515450674 -Slc16a3,ENSMUSG00000025161,2.410164679925098 -Slc16a4,ENSMUSG00000027896,2.3704622091987146 -Slc16a5,ENSMUSG00000045775,3.344482 -Slc16a6,ENSMUSG00000041920,1.870963168168336 -Slc16a7,ENSMUSG00000020102,2.1384921426190933 -Slc16a8,ENSMUSG00000032988,3.344482 -Slc16a9,ENSMUSG00000037762,3.0034937332980363 -Slc17a1,ENSMUSG00000021335,3.344482 -Slc17a2,ENSMUSG00000036110,2.038540492 -Slc17a3,ENSMUSG00000036083,3.344482 -Slc17a4,ENSMUSG00000021336,1.9922968336788818 -Slc17a5,ENSMUSG00000049624,1.731251524359146 -Slc17a6,ENSMUSG00000030500,3.03813602 -Slc17a7,ENSMUSG00000070570,3.344482 -Slc17a8,ENSMUSG00000019935,2.478108167396172 -Slc18a1,ENSMUSG00000036330,2.7056863803359943 -Slc18a2,ENSMUSG00000025094,1.8930196700073603 -Slc18a3,ENSMUSG00000100241,2.3141133948255015 -Slc19a1,ENSMUSG00000001436,1.4365330310861826 -Slc19a2,ENSMUSG00000040918,1.1530898406562569 -Slc19a3,ENSMUSG00000038496,1.8325006381629103 -Slc1a1,ENSMUSG00000024935,1.7942921796480735 -Slc1a2,ENSMUSG00000005089,3.344482 -Slc1a3,ENSMUSG00000005360,3.344482 -Slc1a4,ENSMUSG00000020142,1.5570684066140743 -Slc1a5,ENSMUSG00000001918,3.344482 -Slc1a6,ENSMUSG00000005357,1.6658132468949665 -Slc1a7,ENSMUSG00000008932,3.344482 -Slc20a1,ENSMUSG00000027397,1.6347010012510104 -Slc20a2,ENSMUSG00000037656,2.1156999920769413 -Slc22a1,ENSMUSG00000023829,3.344482 -Slc22a12,ENSMUSG00000061742,3.344482 -Slc22a13,ENSMUSG00000074028,2.2522398882497394 -Slc22a15,ENSMUSG00000033147,1.7018531300375581 -Slc22a16,ENSMUSG00000019834,0.9252358294915461 -Slc22a18,ENSMUSG00000000154,3.344482 -Slc22a19,ENSMUSG00000024757,2.3570250332982416 -Slc22a2,ENSMUSG00000040966,3.344482 -Slc22a3,ENSMUSG00000023828,1.6587836519671755 -Slc22a4,ENSMUSG00000020334,2.7817325264310546 -Slc22a5,ENSMUSG00000018900,1.7265513326435618 -Slc22a6,ENSMUSG00000024650,3.344482 -Slc22a7,ENSMUSG00000067144,3.344482 -Slc22a8,ENSMUSG00000063796,3.344482 -Slc23a1,ENSMUSG00000024354,2.1700491971364606 -Slc23a2,ENSMUSG00000027340,2.435457104004616 -Slc24a1,ENSMUSG00000034452,3.344482 -Slc24a2,ENSMUSG00000037996,3.344482 -Slc24a3,ENSMUSG00000063873,3.344482 -Slc24a4,ENSMUSG00000041771,1.9652871632872617 -Slc24a5,ENSMUSG00000035183,2.6996256768756948 -Slc25a1,ENSMUSG00000003528,1.5092485954276342 -Slc25a10,ENSMUSG00000025792,1.6910626836429359 -Slc25a11,ENSMUSG00000014606,2.044358881534924 -Slc25a12,ENSMUSG00000027010,2.388777926736931 -Slc25a13,ENSMUSG00000015112,2.7880268753390673 -Slc25a14,ENSMUSG00000031105,1.4850833248623363 -Slc25a15,ENSMUSG00000031482,1.4801714152314767 -Slc25a16,ENSMUSG00000071253,1.4522161832950304 -Slc25a17,ENSMUSG00000022404,1.7291931198952906 -Slc25a18,ENSMUSG00000004902,3.344482 -Slc25a19,ENSMUSG00000020744,1.427986110700773 -Slc25a2,ENSMUSG00000050304,1.1194198012322494 -Slc25a20,ENSMUSG00000032602,1.6229175459751517 -Slc25a21,ENSMUSG00000035472,3.344482 -Slc25a22,ENSMUSG00000019082,1.9184902020071326 -Slc25a26,ENSMUSG00000045100,1.4888931430508616 -Slc25a27,ENSMUSG00000023912,2.1332014548735816 -Slc25a28,ENSMUSG00000040414,1.489092616427687 -Slc25a29,ENSMUSG00000021265,1.3638182455529386 -Slc25a3,ENSMUSG00000061904,3.344482 -Slc25a32,ENSMUSG00000022299,1.3652599538066923 -Slc25a33,ENSMUSG00000028982,1.6631996288843642 -Slc25a36,ENSMUSG00000032449,2.1327767264969966 -Slc25a37,ENSMUSG00000034248,2.0284904356306357 -Slc25a38,ENSMUSG00000032519,1.440990018923554 -Slc25a39,ENSMUSG00000018677,1.9528171691825058 -Slc25a4,ENSMUSG00000031633,3.344482 -Slc25a40,ENSMUSG00000054099,1.5147633369043698 -Slc25a42,ENSMUSG00000002346,1.5240547375337081 -Slc25a5,ENSMUSG00000016319,3.344482 -Slc26a1,ENSMUSG00000046959,2.3233448545539646 -Slc26a11,ENSMUSG00000039908,2.0225168647774825 -Slc26a2,ENSMUSG00000034320,1.7470112410784837 -Slc26a3,ENSMUSG00000001225,2.6002068924912107 -Slc26a4,ENSMUSG00000020651,1.2260291708889666 -Slc26a6,ENSMUSG00000023259,1.5173797912740288 -Slc26a7,ENSMUSG00000040569,2.5615166729958223 -Slc26a8,ENSMUSG00000036196,1.1502583736334506 -Slc26a9,ENSMUSG00000042268,0.842318 -Slc27a1,ENSMUSG00000031808,2.4369625146547778 -Slc27a2,ENSMUSG00000027359,3.344482 -Slc27a3,ENSMUSG00000027932,1.4211049969131946 -Slc27a4,ENSMUSG00000059316,1.4126776239521208 -Slc27a5,ENSMUSG00000030382,1.1376625534736808 -Slc27a6,ENSMUSG00000024600,1.6673097093643927 -Slc28a1,ENSMUSG00000025726,1.0578347922334932 -Slc28a2,ENSMUSG00000027219,3.344482 -Slc28a2b,ENSMUSG00000079071,1.034151105806311 -Slc28a3,ENSMUSG00000021553,1.578241106084577 -Slc29a1,ENSMUSG00000023942,2.2554374843282576 -Slc29a2,ENSMUSG00000024891,1.158588112084603 -Slc29a3,ENSMUSG00000020100,2.324748584228093 -Slc29a4,ENSMUSG00000050822,2.0064401114228887 -Slc2a1,ENSMUSG00000028645,3.2151225050809127 -Slc2a10,ENSMUSG00000027661,1.8238256421341434 -Slc2a12,ENSMUSG00000037490,1.591781780556135 -Slc2a13,ENSMUSG00000036298,3.344482 -Slc2a2,ENSMUSG00000027690,2.2643600969223443 -Slc2a3,ENSMUSG00000003153,2.2481423795317417 -Slc2a4,ENSMUSG00000018566,3.344482 -Slc2a5,ENSMUSG00000028976,3.344482 -Slc2a6,ENSMUSG00000036067,1.234678101012701 -Slc2a7,ENSMUSG00000062064,1.2818325609875354 -Slc2a8,ENSMUSG00000026791,1.526027334038339 -Slc2a9,ENSMUSG00000005107,1.9084024181306267 -Slc30a1,ENSMUSG00000037434,1.3629432458278672 -Slc30a6,ENSMUSG00000024069,1.541605276532882 -Slc30a7,ENSMUSG00000054414,1.6898683082615953 -Slc31a1,ENSMUSG00000066150,1.7670439501435249 -Slc32a1,ENSMUSG00000037771,3.344482 -Slc33a1,ENSMUSG00000027822,1.5722644799543521 -Slc34a1,ENSMUSG00000021490,3.344482 -Slc34a2,ENSMUSG00000029188,3.344482 -Slc34a3,ENSMUSG00000006469,2.3714925083220004 -Slc35a1,ENSMUSG00000028293,1.5674011930015819 -Slc35a2,ENSMUSG00000031156,1.4653779081529184 -Slc35a3,ENSMUSG00000027957,1.740013721755282 -Slc35b2,ENSMUSG00000037089,1.5165761031201086 -Slc35b4,ENSMUSG00000018999,1.2142751297038168 -Slc35c1,ENSMUSG00000049922,1.0792044083581256 -Slc35d1,ENSMUSG00000028521,1.5815775804358214 -Slc35d2,ENSMUSG00000033114,2.196046456962923 -Slc36a1,ENSMUSG00000020261,1.3981196950183927 -Slc36a2,ENSMUSG00000020264,3.344482 -Slc36a3,ENSMUSG00000049491,1.3866884257808005 -Slc36a4,ENSMUSG00000043885,1.3536141319773038 -Slc37a1,ENSMUSG00000024036,1.329091119015705 -Slc37a4,ENSMUSG00000032114,1.6328195027420989 -Slc38a1,ENSMUSG00000023169,2.6673166091848977 -Slc38a2,ENSMUSG00000022462,3.092462429123149 -Slc38a3,ENSMUSG00000010064,3.344482 -Slc38a4,ENSMUSG00000022464,1.4565200229872326 -Slc38a5,ENSMUSG00000031170,3.344482 -Slc39a1,ENSMUSG00000052310,2.025705241151771 -Slc39a10,ENSMUSG00000025986,2.5524783657662105 -Slc39a14,ENSMUSG00000022094,1.4786011332837945 -Slc39a2,ENSMUSG00000072572,1.7031485154886497 -Slc39a3,ENSMUSG00000046822,1.340705721269036 -Slc39a4,ENSMUSG00000063354,2.614535789853179 -Slc39a5,ENSMUSG00000039878,1.3968992365964974 -Slc39a6,ENSMUSG00000024270,1.6566339580533644 -Slc39a7,ENSMUSG00000024327,1.6269695403571114 -Slc39a8,ENSMUSG00000053897,2.6974178686961405 -Slc3a1,ENSMUSG00000024131,1.8436113306260975 -Slc3a2,ENSMUSG00000010095,2.8349565353138044 -Slc40a1,ENSMUSG00000025993,2.6430151023112733 -Slc41a1,ENSMUSG00000013275,1.5473574243245194 -Slc41a2,ENSMUSG00000034591,1.6983140414266387 -Slc43a1,ENSMUSG00000027075,2.115802888761896 -Slc43a2,ENSMUSG00000038178,2.465863886963206 -Slc44a1,ENSMUSG00000028412,2.790921927629239 -Slc44a2,ENSMUSG00000057193,1.8782113288480757 -Slc44a3,ENSMUSG00000039865,1.59300224 -Slc44a4,ENSMUSG00000007034,2.1088180912459134 -Slc44a5,ENSMUSG00000028360,2.541092756795031 -Slc46a1,ENSMUSG00000020829,1.5113922774786153 -Slc47a1,ENSMUSG00000010122,3.344482 -Slc47a2,ENSMUSG00000069855,1.371881389139092 -Slc4a1,ENSMUSG00000006574,3.344482 -Slc4a10,ENSMUSG00000026904,3.344482 -Slc4a2,ENSMUSG00000028962,1.7243451671821086 -Slc4a3,ENSMUSG00000006576,1.6442389168392684 -Slc4a4,ENSMUSG00000060961,3.344482 -Slc4a5,ENSMUSG00000068323,2.0820913025740224 -Slc4a7,ENSMUSG00000021733,2.1145547395636966 -Slc4a8,ENSMUSG00000023032,1.4584767862165797 -Slc4a9,ENSMUSG00000024485,3.344482 -Slc51a,ENSMUSG00000035699,3.344482 -Slc51b,ENSMUSG00000053862,2.6222883708510887 -Slc52a2,ENSMUSG00000022560,1.3554613810946161 -Slc52a3,ENSMUSG00000027463,2.0463983830241097 -Slc5a1,ENSMUSG00000011034,2.4394777953174716 -Slc5a10,ENSMUSG00000042371,3.344482 -Slc5a11,ENSMUSG00000030769,2.652047883659608 -Slc5a12,ENSMUSG00000041644,3.344482 -Slc5a2,ENSMUSG00000030781,3.344482 -Slc5a3,ENSMUSG00000089774,2.398429980629267 -Slc5a5,ENSMUSG00000000792,1.3154059169284398 -Slc5a6,ENSMUSG00000006641,1.2492818710274463 -Slc5a7,ENSMUSG00000023945,3.0895157152169372 -Slc5a8,ENSMUSG00000020062,3.344482 -Slc5a9,ENSMUSG00000028544,2.3087501421050574 -Slc6a1,ENSMUSG00000030310,3.344482 -Slc6a11,ENSMUSG00000030307,3.344482 -Slc6a12,ENSMUSG00000030109,2.5441343602015563 -Slc6a13,ENSMUSG00000030108,3.344482 -Slc6a14,ENSMUSG00000031089,2.228565135534529 -Slc6a15,ENSMUSG00000019894,1.829030371724644 -Slc6a18,ENSMUSG00000021612,3.344482 -Slc6a19,ENSMUSG00000021565,3.344482 -Slc6a2,ENSMUSG00000055368,2.9064252071331436 -Slc6a20a,ENSMUSG00000036814,3.344482 -Slc6a3,ENSMUSG00000021609,2.482451447387742 -Slc6a4,ENSMUSG00000020838,1.7175790633828094 -Slc6a5,ENSMUSG00000039728,2.6259526871914596 -Slc6a6,ENSMUSG00000030096,3.305087958455403 -Slc6a7,ENSMUSG00000052026,1.3827245267382147 -Slc6a8,ENSMUSG00000019558,1.5086252628979024 -Slc6a9,ENSMUSG00000028542,2.129280972533607 -Slc7a1,ENSMUSG00000041313,1.6899632492281011 -Slc7a10,ENSMUSG00000030495,3.344482 -Slc7a11,ENSMUSG00000027737,3.344482 -Slc7a2,ENSMUSG00000031596,3.038575497 -Slc7a3,ENSMUSG00000031297,1.392038782 -Slc7a5,ENSMUSG00000040010,1.702406421418041 -Slc7a6,ENSMUSG00000031904,1.5942718294983536 -Slc7a7,ENSMUSG00000000958,3.1037480305351774 -Slc7a8,ENSMUSG00000022180,1.993506119754601 -Slc7a9,ENSMUSG00000030492,3.344482 -Slc8a1,ENSMUSG00000054640,3.344482 -Slc8a2,ENSMUSG00000030376,2.3194878969016433 -Slc8a3,ENSMUSG00000079055,2.7250717612417814 -Slc8b1,ENSMUSG00000032754,2.845184432160281 -Slc9a1,ENSMUSG00000028854,1.7208587292798425 -Slc9a2,ENSMUSG00000026062,2.3012648883492948 -Slc9a3,ENSMUSG00000036123,3.344482 -Slc9a4,ENSMUSG00000026065,1.6342609622207245 -Slc9a5,ENSMUSG00000014786,1.5037427862139159 -Slc9a7,ENSMUSG00000037341,2.0491172671525995 -Slc9a8,ENSMUSG00000039463,1.8846895366891958 -Slc9a9,ENSMUSG00000031129,3.344482 -Slco1a1,ENSMUSG00000041698,3.344482 -Slco1a4,ENSMUSG00000030237,3.344482 -Slco1a5,ENSMUSG00000063975,1.793221840747343 -Slco1b2,ENSMUSG00000030236,3.344482 -Slco1c1,ENSMUSG00000030235,3.344482 -Slco2a1,ENSMUSG00000032548,2.4475298029581913 -Slco2b1,ENSMUSG00000030737,3.344482 -Slco3a1,ENSMUSG00000025790,2.82006974 -Slco4a1,ENSMUSG00000038963,2.5642434188080796 -Smox,ENSMUSG00000027333,2.105686623717096 -Smpd1,ENSMUSG00000037049,1.6633747544433106 -Smpd2,ENSMUSG00000019822,1.9400636923134362 -Smpd3,ENSMUSG00000031906,2.381547303 -Smpd4,ENSMUSG00000005899,1.3804913911408123 -Sms,ENSMUSG00000071708,2.2523274442464274 -Smurf1,ENSMUSG00000038780,1.8788595134279273 -Smurf2,ENSMUSG00000018363,2.521752154054215 -Smyd3,ENSMUSG00000055067,3.344482 -Soat1,ENSMUSG00000026600,1.9700156223723049 -Soat2,ENSMUSG00000023045,1.3527522404134948 -Sod1,ENSMUSG00000022982,2.7850384186192447 -Sod2,ENSMUSG00000006818,2.492492279480128 -Sod3,ENSMUSG00000072941,3.344482 -Sord,ENSMUSG00000027227,2.790973967738938 -Spcs1,ENSMUSG00000021917,2.8197827495114525 -Spcs2,ENSMUSG00000035227,2.9911592753749323 -Spcs3,ENSMUSG00000054408,1.553933371 -Sphk1,ENSMUSG00000061878,1.912801647708567 -Sphk2,ENSMUSG00000057342,1.2637568532593346 -Spr,ENSMUSG00000033735,1.7595808040558503 -Sptlc1,ENSMUSG00000021468,1.5300233474311882 -Sptlc2,ENSMUSG00000021036,2.055961916214845 -Sptlc3,ENSMUSG00000039092,1.727124514507138 -Sqle,ENSMUSG00000022351,1.8781804942951807 -Srd5a1,ENSMUSG00000021594,1.3006940200827535 -Srd5a2,ENSMUSG00000038541,1.7291501653126795 -Srd5a3,ENSMUSG00000029233,1.3469561368524838 -Srm,ENSMUSG00000006442,1.7669669495346403 -Srp14,ENSMUSG00000009549,2.9909265299452867 -Srp19,ENSMUSG00000014504,2.040193378883658 -Srp54a,ENSMUSG00000073079,1.261752859082216 -Srp68,ENSMUSG00000020780,1.5179262029425133 -Srp72,ENSMUSG00000036323,1.8896478383946724 -Srpk3,ENSMUSG00000002007,2.4682799881481374 -Srpra,ENSMUSG00000032042,1.9744804793011173 -Srprb,ENSMUSG00000032553,1.5023121483311683 -Srr,ENSMUSG00000001323,1.9753921752326211 -Ssr1,ENSMUSG00000021427,2.329406763638462 -Ssr2,ENSMUSG00000041355,2.679822260773885 -Ssr3,ENSMUSG00000027828,2.2283296782702653 -Ssr4,ENSMUSG00000002014,3.195979569481532 -St3gal1,ENSMUSG00000013846,1.7194754723166334 -St3gal2,ENSMUSG00000031749,1.8565974105140233 -St3gal3,ENSMUSG00000028538,2.485846368793768 -St3gal4,ENSMUSG00000032038,3.344482 -St3gal5,ENSMUSG00000056091,3.0059800314259157 -St3gal6,ENSMUSG00000022747,2.882692029120179 -St6gal1,ENSMUSG00000022885,2.592499521233833 -St6gal2,ENSMUSG00000024172,1.760637875540141 -St6galnac1,ENSMUSG00000009588,1.6180555171645312 -St6galnac2,ENSMUSG00000057286,2.5004030690954404 -St6galnac2,ENSMUSG00000110170,2.5004030690954404 -St6galnac2,ENSMUSG00000057286,3.344482 -St6galnac2,ENSMUSG00000110170,3.344482 -St6galnac3,ENSMUSG00000052544,3.344482 -St6galnac4,ENSMUSG00000079442,1.6367418851373694 -St6galnac5,ENSMUSG00000039037,3.344482 -St6galnac6,ENSMUSG00000026811,1.6428331770453624 -St8sia1,ENSMUSG00000030283,1.922240146 -St8sia4,ENSMUSG00000040710,2.640554353101123 -St8sia5,ENSMUSG00000025425,2.564496533799898 -Stambp,ENSMUSG00000006906,1.4559593710726944 -Stambpl1,ENSMUSG00000024776,1.6170110275966916 -Star,ENSMUSG00000031574,1.8031251369624752 -Stard10,ENSMUSG00000030688,1.7930403468701857 -Stard13,ENSMUSG00000016128,3.0323063149891127 -Stard3,ENSMUSG00000018167,1.5461705012800473 -Stard4,ENSMUSG00000024378,1.4827523870403596 -Stard5,ENSMUSG00000046027,2.826539614689892 -Stard6,ENSMUSG00000079608,1.4986267367865678 -Stard7,ENSMUSG00000027367,1.8954156480327662 -Stard8,ENSMUSG00000031216,2.419371911884658 -Stard9,ENSMUSG00000033705,2.591866152232267 -Stra6,ENSMUSG00000032327,1.6425776102896066 -Stt3a,ENSMUSG00000032116,1.7813293711034521 -Stt3b,ENSMUSG00000032437,2.091510698303889 -Stub1,ENSMUSG00000039615,2.644587455355405 -Stx11,ENSMUSG00000039232,2.253309552788984 -Stx12,ENSMUSG00000028879,2.015334471825478 -Stx16,ENSMUSG00000027522,2.2609622798095756 -Stx18,ENSMUSG00000029125,1.7240518506062894 -Stx19,ENSMUSG00000047854,1.760926625432611 -Stx1b,ENSMUSG00000030806,2.842155515096474 -Stx4a,ENSMUSG00000030805,1.8256440755251402 -Stx5a,ENSMUSG00000010110,1.9416554677892037 -Stx6,ENSMUSG00000026470,1.8787826035676027 -Stx7,ENSMUSG00000019998,2.252545279106199 -Stx8,ENSMUSG00000020903,2.1931310629083596 -Sucla2,ENSMUSG00000022110,2.102687761494304 -Suclg1,ENSMUSG00000052738,2.4341728213991076 -Suclg2,ENSMUSG00000061838,2.366379223891579 -Sult1a1,ENSMUSG00000030711,3.344482 -Sult1b1,ENSMUSG00000029269,3.344482 -Sult1c1,ENSMUSG00000023943,1.6016999806692667 -Sult1c2,ENSMUSG00000023122,3.344482 -Sult1e1,ENSMUSG00000029272,3.344482 -Sult2a1,ENSMUSG00000078798,3.344482 -Sult2a2,ENSMUSG00000070811,1.5901223742227717 -Sult2a3,ENSMUSG00000074375,1.272977988128563 -Sult2a4,ENSMUSG00000074377,1.0938081611702195 -Sult2a5,ENSMUSG00000078799,1.3467449235860236 -Sult2a6,ENSMUSG00000070810,1.7661983870015059 -Sult2a7,ENSMUSG00000094156,1.5489304172325034 -Sult2b1,ENSMUSG00000003271,1.1269580832663408 -Sult3a1,ENSMUSG00000069668,0.9794198751079226 -Sult4a1,ENSMUSG00000018865,3.132600990138539 -Suox,ENSMUSG00000049858,1.3850395111463718 -Suv39h1,ENSMUSG00000039231,1.2675380427690401 -Suv39h2,ENSMUSG00000026646,1.1863390444858481 -Synj1,ENSMUSG00000022973,3.344482 -Synj2,ENSMUSG00000023805,1.721421088603628 -Syvn1,ENSMUSG00000024807,1.4107584209631354 -Taf9,ENSMUSG00000052293,2.0890418978127223 -Taldo1,ENSMUSG00000025503,3.344482 -Tars1,ENSMUSG00000022241,1.4747679925651738 -Tat,ENSMUSG00000001670,3.344482 -Tbcb,ENSMUSG00000006095,2.3654312523592362 -Tbxas1,ENSMUSG00000029925,3.344482 -Tcirg1,ENSMUSG00000001750,2.632258853040062 -Tdh,ENSMUSG00000021953,1.173687147329143 -Tdo2,ENSMUSG00000028011,2.6461233634093433 -Tecr,ENSMUSG00000031708,3.344482 -Tecrl,ENSMUSG00000049537,2.339348917853427 -Tent2,ENSMUSG00000042167,1.8940725890282895 -Tent4a,ENSMUSG00000034575,1.416301756330969 -Tfrc,ENSMUSG00000022797,1.8416720719875188 -Tgds,ENSMUSG00000022130,1.3564604388911503 -Tgm1,ENSMUSG00000022218,2.1333626381599227 -Tgm2,ENSMUSG00000037820,3.344482 -Tgm3,ENSMUSG00000027401,2.631106862813789 -Tgm4,ENSMUSG00000025787,3.344482 -Tgm5,ENSMUSG00000053675,2.504319138961429 -Tgm6,ENSMUSG00000027403,0.9752061169887515 -Tgm7,ENSMUSG00000079103,1.0880368887345682 -Th,ENSMUSG00000000214,2.6331293683881554 -Tha1,ENSMUSG00000017713,1.4697597787337193 -Them4,ENSMUSG00000028145,1.545937251113854 -Them5,ENSMUSG00000028148,3.344482 -Thnsl1,ENSMUSG00000048550,1.178089980610993 -Thop1,ENSMUSG00000004929,1.2853103305118376 -Thtpa,ENSMUSG00000045691,3.344482 -Ticrr,ENSMUSG00000046591,1.526300247829371 -Tigar,ENSMUSG00000038028,1.2341762752847918 -Tiparp,ENSMUSG00000034640,2.3719439583355864 -Tk1,ENSMUSG00000025574,1.9826387010748272 -Tk2,ENSMUSG00000035824,1.4513715191909038 -Tkfc,ENSMUSG00000034371,1.4743754493385162 -Tkt,ENSMUSG00000021957,3.1110779848142527 -Tktl1,ENSMUSG00000031397,2.268398214018696 -Tktl2,ENSMUSG00000025519,0.8610340172024312 -Tm7sf2,ENSMUSG00000024799,1.3258104548831398 -Tmem54,ENSMUSG00000028786,1.7365317287358066 -Tmem91,ENSMUSG00000061702,2.0358169045057135 -Tmppe,ENSMUSG00000079260,0.9883034137889116 -Tmx3,ENSMUSG00000024614,1.8838366868439533 -Tnks,ENSMUSG00000031529,2.105807767904624 -Tnks2,ENSMUSG00000024811,2.354513451458991 -Tnni3k,ENSMUSG00000040086,1.4453033600621181 -Tnrc6b,ENSMUSG00000047888,3.344482 -Tns2,ENSMUSG00000037003,2.420325726240388 -Tomt,ENSMUSG00000078630,0.8611211882970392 -Topors,ENSMUSG00000036822,1.637127321390651 -Tpcn1,ENSMUSG00000032741,1.9625504125877462 -Tpcn2,ENSMUSG00000048677,2.3976743209810634 -Tph1,ENSMUSG00000040046,2.072420031350167 -Tph2,ENSMUSG00000006764,1.3520879501193934 -Tpi1,ENSMUSG00000023456,3.344482 -Tpk1,ENSMUSG00000029735,2.357026540003879 -Tpmt,ENSMUSG00000021376,1.7243252181075845 -Tpo,ENSMUSG00000020673,1.2543545436615133 -Tpp1,ENSMUSG00000030894,1.8619476188707793 -Tpr,ENSMUSG00000006005,2.852288754413225 -Tpsab1,ENSMUSG00000024173,3.344482 -Tpsb2,ENSMUSG00000033825,3.344482 -Tpst1,ENSMUSG00000034118,1.8076419988547279 -Tpst2,ENSMUSG00000029344,1.8596756143558708 -Tpte,ENSMUSG00000031481,2.004798649257908 -Traf7,ENSMUSG00000052752,1.570212166281246 -Trappc1,ENSMUSG00000049299,1.779589346632423 -Trappc3,ENSMUSG00000028847,1.8075415166077133 -Trappc4,ENSMUSG00000032112,2.137426827531715 -Trappc5,ENSMUSG00000040236,1.5886424656570208 -Trappc6a,ENSMUSG00000002043,1.708800924446525 -Trappc6b,ENSMUSG00000020993,2.6341317444969623 -Trdmt1,ENSMUSG00000026723,1.4261451148404791 -Treh,ENSMUSG00000032098,3.049052688 -Trex1,ENSMUSG00000049734,2.722076433139447 -Trex2,ENSMUSG00000031372,1.2126117359269306 -Trhde,ENSMUSG00000050663,3.344482 -Trim11,ENSMUSG00000020455,1.564876051650865 -Trim12c,ENSMUSG00000057143,2.3594478677354473 -Trim32,ENSMUSG00000051675,1.8798083713581768 -Trim33,ENSMUSG00000033014,2.194539675321543 -Trim5,ENSMUSG00000060441,2.6950407260910962 -Trim63,ENSMUSG00000028834,3.344482 -Trip12,ENSMUSG00000026219,2.7353658371340956 -Trit1,ENSMUSG00000028653,1.5897936883819053 -Trmt1,ENSMUSG00000001909,1.6076131244857113 -Trmt11,ENSMUSG00000019792,1.5552168604643013 -Trmt12,ENSMUSG00000037085,1.1919520093671352 -Trmu,ENSMUSG00000022386,1.534015011 -Trnt1,ENSMUSG00000013736,1.460179582 -Trp53,ENSMUSG00000059552,2.0718840448112585 -Tst,ENSMUSG00000044986,2.903139846831275 -Ttc3,ENSMUSG00000040785,3.344482 -Ttl,ENSMUSG00000027394,1.5662047769341887 -Tufm,ENSMUSG00000073838,1.5245811920002537 -Tusc3,ENSMUSG00000118664,2.7538361306640935 -Tut1,ENSMUSG00000071645,1.3140203331339304 -Tut4,ENSMUSG00000034610,3.056411203929761 -Tut7,ENSMUSG00000035248,2.0971756032063045 -Txn1,ENSMUSG00000028367,3.344482 -Txn2,ENSMUSG00000005354,2.3530773023738623 -Txnrd1,ENSMUSG00000020250,1.856771775 -Txnrd2,ENSMUSG00000075704,1.361555901 -Txnrd3,ENSMUSG00000000811,1.3130448384186535 -Tymp,ENSMUSG00000022615,0.842318 -Tyms,ENSMUSG00000025747,2.1088912182101693 -Tyr,ENSMUSG00000004651,0.842318 -Tyrp1,ENSMUSG00000005994,3.344482 -Uap1,ENSMUSG00000026670,1.944104667617727 -Uap1l1,ENSMUSG00000026956,1.4822932186179942 -Uba1,ENSMUSG00000001924,2.058482730557038 -Uba2,ENSMUSG00000052997,2.0020752136808007 -Uba3,ENSMUSG00000030061,1.68695594 -Uba5,ENSMUSG00000032557,1.7025635024585533 -Uba6,ENSMUSG00000035898,1.6955218562964325 -Uba7,ENSMUSG00000032596,2.0469791444898857 -Ubac2,ENSMUSG00000041765,2.103451899534679 -Ube2a,ENSMUSG00000016308,1.7824212231872334 -Ube2b,ENSMUSG00000020390,3.344482 -Ube2c,ENSMUSG00000001403,3.344482 -Ube2d1,ENSMUSG00000019927,2.0156673742477156 -Ube2d2a,ENSMUSG00000091896,2.8978425821939764 -Ube2d2b,ENSMUSG00000063447,0.842318 -Ube2d3,ENSMUSG00000078578,3.344482 -Ube2e1,ENSMUSG00000021774,2.143058474523708 -Ube2e2,ENSMUSG00000058317,3.344482 -Ube2e3,ENSMUSG00000027011,2.6225454700086006 -Ube2f,ENSMUSG00000034343,1.6638698996582546 -Ube2g1,ENSMUSG00000020794,2.5253609823599117 -Ube2g2,ENSMUSG00000009293,1.431147995059695 -Ube2h,ENSMUSG00000039159,2.768221226060247 -Ube2i,ENSMUSG00000015120,2.5668091741930623 -Ube2j1,ENSMUSG00000028277,1.6785951283290852 -Ube2j2,ENSMUSG00000023286,1.8431515245708996 -Ube2k,ENSMUSG00000029203,3.0378162697586504 -Ube2l3,ENSMUSG00000038965,2.3275078992592038 -Ube2l6,ENSMUSG00000027078,3.289860962032651 -Ube2m,ENSMUSG00000005575,2.194879639265027 -Ube2n,ENSMUSG00000074781,2.401857634738868 -Ube2o,ENSMUSG00000020802,1.7189635514917057 -Ube2q1,ENSMUSG00000042572,1.5352627476519367 -Ube2q2,ENSMUSG00000032307,1.849692344646507 -Ube2ql1,ENSMUSG00000052981,2.0979259100689864 -Ube2r2,ENSMUSG00000036241,2.510355047901374 -Ube2s,ENSMUSG00000060860,3.344482 -Ube2t,ENSMUSG00000026429,1.2395834732531281 -Ube2u,ENSMUSG00000069733,2.572686889789109 -Ube2w,ENSMUSG00000025939,2.472176643582236 -Ube2z,ENSMUSG00000014349,1.4823194469660637 -Ube3a,ENSMUSG00000025326,3.344482 -Ube3b,ENSMUSG00000029577,1.4697620728432712 -Ube3c,ENSMUSG00000039000,2.474242972 -Ube4a,ENSMUSG00000059890,1.837045739121002 -Ube4b,ENSMUSG00000028960,2.222346835975047 -Ubiad1,ENSMUSG00000047719,1.333423178479824 -Ubr1,ENSMUSG00000027272,2.148731936047814 -Ubr2,ENSMUSG00000023977,2.085808348104883 -Ubr3,ENSMUSG00000044308,2.772130213668812 -Ubr4,ENSMUSG00000066036,1.7241838062818258 -Ubr5,ENSMUSG00000037487,2.695735794454991 -Ubr7,ENSMUSG00000041712,1.3671362097975073 -Uck1,ENSMUSG00000002550,1.408979937012914 -Uck2,ENSMUSG00000026558,1.5106399782804614 -Uckl1,ENSMUSG00000089917,1.7478429133055104 -Ucp1,ENSMUSG00000031710,1.9506311896700295 -Ucp2,ENSMUSG00000033685,3.344482 -Ucp3,ENSMUSG00000032942,3.273011320822738 -Ufd1,ENSMUSG00000005262,1.8039379995874645 -Ugcg,ENSMUSG00000028381,1.7896974418691747 -Ugdh,ENSMUSG00000029201,2.368169978785614 -Uggt1,ENSMUSG00000037470,1.644860514733669 -Uggt2,ENSMUSG00000042104,1.821236647485368 -Ugp2,ENSMUSG00000001891,2.0298597288498375 -Ugt1a1,ENSMUSG00000089960,1.8641018382843622 -Ugt1a2,ENSMUSG00000090171,3.344482 -Ugt1a5,ENSMUSG00000089943,1.9394657030228064 -Ugt1a6a,ENSMUSG00000054545,2.057596817658602 -Ugt1a6b,ENSMUSG00000090145,1.1993042000338348 -Ugt1a9,ENSMUSG00000090175,0.9224109465456745 -Ugt2a1,ENSMUSG00000106677,0.842318 -Ugt2a3,ENSMUSG00000035780,2.0524536452166178 -Ugt2b1,ENSMUSG00000035836,2.654244980448545 -Ugt2b38,ENSMUSG00000061906,3.344482 -Ugt3a1,ENSMUSG00000049152,3.344482 -Ugt3a2,ENSMUSG00000072664,3.344482 -Ugt8a,ENSMUSG00000032854,3.344482 -Uhrf1,ENSMUSG00000001228,1.8703228997054449 -Uhrf2,ENSMUSG00000024817,2.2369153056061166 -Umps,ENSMUSG00000022814,1.308820072536132 -Uox,ENSMUSG00000028186,2.5651857623779772 -Upb1,ENSMUSG00000033427,1.9312148268964977 -Upp1,ENSMUSG00000020407,2.691017011514971 -Upp2,ENSMUSG00000026839,2.9308130614602366 -Uprt,ENSMUSG00000073016,1.3974017717904337 -Uqcr10,ENSMUSG00000059534,3.344482 -Uqcr11,ENSMUSG00000020163,3.344482 -Uqcrb,ENSMUSG00000021520,3.344482 -Uqcrc1,ENSMUSG00000025651,3.0757437702591663 -Uqcrc2,ENSMUSG00000030884,2.4505128954107085 -Uqcrfs1,ENSMUSG00000038462,2.7964939157815043 -Uqcrh,ENSMUSG00000063882,3.344482 -Uqcrh-ps1,ENSMUSG00000037438,0.842318 -Uqcrq,ENSMUSG00000044894,3.344482 -Urad,ENSMUSG00000075543,1.2328058405680031 -Urah,ENSMUSG00000025481,1.400317024302193 -Uroc1,ENSMUSG00000034456,3.344482 -Urod,ENSMUSG00000028684,1.8524111532577896 -Uros,ENSMUSG00000030979,1.3895299262019531 -Usp1,ENSMUSG00000028560,1.7314596387877128 -Usp10,ENSMUSG00000031826,1.6320017979275898 -Usp11,ENSMUSG00000031066,1.6346575155378493 -Usp12,ENSMUSG00000029640,1.687666671395498 -Usp13,ENSMUSG00000056900,1.5268686979389758 -Usp14,ENSMUSG00000047879,2.1790423570382798 -Usp15,ENSMUSG00000020124,2.2714197320706098 -Usp16,ENSMUSG00000025616,1.7080300694305552 -Usp17la,ENSMUSG00000054568,3.320560194278453 -Usp17lb,ENSMUSG00000062369,3.344482 -Usp17lc,ENSMUSG00000058976,1.449058083685175 -Usp17ld,ENSMUSG00000057321,0.842318 -Usp17le,ENSMUSG00000043073,1.0884376215722735 -Usp18,ENSMUSG00000030107,2.632233254785819 -Usp19,ENSMUSG00000006676,1.7247848614262002 -Usp2,ENSMUSG00000032010,2.2017269661437626 -Usp20,ENSMUSG00000026854,1.613454930179268 -Usp21,ENSMUSG00000053483,1.3697717176792323 -Usp22,ENSMUSG00000042506,2.2855839810771372 -Usp24,ENSMUSG00000028514,2.095171498131394 -Usp25,ENSMUSG00000022867,2.0228698029006345 -Usp26,ENSMUSG00000055780,1.5579638909705296 -Usp27x,ENSMUSG00000046269,1.0448167059568674 -Usp28,ENSMUSG00000032267,1.8063473672174999 -Usp29,ENSMUSG00000051527,3.344482 -Usp3,ENSMUSG00000032376,3.177376656671604 -Usp30,ENSMUSG00000029592,1.4550104205045216 -Usp31,ENSMUSG00000063317,1.712070416794758 -Usp32,ENSMUSG00000000804,2.706563529533924 -Usp33,ENSMUSG00000025437,2.2258280197737927 -Usp34,ENSMUSG00000056342,3.344482 -Usp35,ENSMUSG00000035713,1.3022390132852502 -Usp36,ENSMUSG00000033909,1.5866128416467677 -Usp37,ENSMUSG00000033364,2.152775606781759 -Usp38,ENSMUSG00000038250,1.4279317935130493 -Usp4,ENSMUSG00000032612,1.7525466750504477 -Usp40,ENSMUSG00000005501,1.8976235887402328 -Usp42,ENSMUSG00000051306,1.299591208645224 -Usp43,ENSMUSG00000020905,0.9560038406644246 -Usp44,ENSMUSG00000020020,1.4032462221418558 -Usp45,ENSMUSG00000040455,1.8083640755064507 -Usp46,ENSMUSG00000054814,2.3043033503473698 -Usp47,ENSMUSG00000059263,2.183096552045758 -Usp48,ENSMUSG00000043411,1.9069017790900995 -Usp49,ENSMUSG00000090115,1.2274701585079746 -Usp5,ENSMUSG00000038429,1.6216744631447622 -Usp51,ENSMUSG00000067215,1.5463913553997437 -Usp7,ENSMUSG00000022710,1.873737358 -Usp8,ENSMUSG00000027363,1.779927079115993 -Usp9x,ENSMUSG00000031010,2.7722073049761837 -Usp9y,ENSMUSG00000069044,1.5149756477815914 -Ust,ENSMUSG00000047712,3.344482 -Uxs1,ENSMUSG00000057363,1.616573093821257 -Vapb,ENSMUSG00000054455,1.892300872355278 -Vars1,ENSMUSG00000007029,1.728253157575018 -Vcp,ENSMUSG00000028452,3.0714636079438846 -Vkorc1,ENSMUSG00000096145,2.330288604426336 -Vmn2r37,ENSMUSG00000066828,1.4967090298016397 -Vnn1,ENSMUSG00000037440,1.6173170967422636 -Vnn3,ENSMUSG00000020010,2.1328803097718088 -Vps29,ENSMUSG00000029462,2.2626276879303524 -Wars1,ENSMUSG00000021266,1.5253752115555634 -Wwox,ENSMUSG00000004637,3.344482 -Wwp1,ENSMUSG00000041058,2.675174219196344 -Wwp2,ENSMUSG00000031930,1.9535164801037863 -Xdh,ENSMUSG00000024066,3.344482 -Xpo6,ENSMUSG00000000131,1.8330038504062771 -Xpo7,ENSMUSG00000022100,2.5059737860307116 -Xpr1,ENSMUSG00000026469,2.6341566630546556 -Xylb,ENSMUSG00000035769,1.9444940236564303 -Xylt1,ENSMUSG00000030657,3.008169204100133 -Xylt2,ENSMUSG00000020868,1.3957796859884235 -Yars1,ENSMUSG00000028811,1.7544100334649915 -Ykt6,ENSMUSG00000002741,1.4667722021226768 -Zc3hav1,ENSMUSG00000029826,2.6401764729314365 -Zdhhc1,ENSMUSG00000039199,1.5189864565602782 -Zdhhc11,ENSMUSG00000069189,0.9229659899910945 -Zdhhc12,ENSMUSG00000015335,1.4478557752142407 -Zdhhc13,ENSMUSG00000030471,1.412783565098695 -Zdhhc14,ENSMUSG00000034265,3.344482 -Zdhhc15,ENSMUSG00000033906,1.1505112047650523 -Zdhhc16,ENSMUSG00000025157,1.3608309846419313 -Zdhhc17,ENSMUSG00000035798,2.357920526383778 -Zdhhc18,ENSMUSG00000037553,1.7660165769901373 -Zdhhc19,ENSMUSG00000052363,1.8878853981328467 -Zdhhc2,ENSMUSG00000039470,2.4474792932238967 -Zdhhc20,ENSMUSG00000021969,2.4658054517882837 -Zdhhc21,ENSMUSG00000028403,1.9591429932762077 -Zdhhc22,ENSMUSG00000048483,1.5787697446542142 -Zdhhc23,ENSMUSG00000036304,1.053716154125168 -Zdhhc24,ENSMUSG00000006463,1.2492899086698377 -Zdhhc3,ENSMUSG00000025786,1.542988517725778 -Zdhhc4,ENSMUSG00000001844,1.4068179990445986 -Zdhhc5,ENSMUSG00000034075,1.3813069475003434 -Zdhhc6,ENSMUSG00000024982,1.605184182650977 -Zdhhc7,ENSMUSG00000031823,1.3298210292056818 -Zdhhc8,ENSMUSG00000060166,1.5827323078460056 -Zdhhc9,ENSMUSG00000036985,1.521155448853325 -Zmpste24,ENSMUSG00000043207,1.6271107043552893 -Znrf1,ENSMUSG00000033545,2.3490952895548363 -Znrf2,ENSMUSG00000058446,1.8444466809660818 -Zswim2,ENSMUSG00000034552,1.0433937457771398 \ No newline at end of file +symbol,ensembl_id,sccellfie_threshold +A4galt,ENSMUSG00000047878,2.493392887492253 +A4gnt,ENSMUSG00000037953,0.911013001 +Aaas,ENSMUSG00000036678,1.4732659157184338 +Aacs,ENSMUSG00000029482,1.6024100680695 +Aadac,ENSMUSG00000027761,3.344482 +Aadat,ENSMUSG00000057228,2.7170193739054325 +Aanat,ENSMUSG00000020804,0.9635438620868174 +Aars1,ENSMUSG00000031960,1.671185458666224 +Aasdh,ENSMUSG00000055923,1.524130379 +Aasdhppt,ENSMUSG00000025894,1.4335514259856958 +Aass,ENSMUSG00000029695,3.344482 +Abat,ENSMUSG00000057880,2.3246732534021923 +Abca1,ENSMUSG00000015243,3.344482 +Abca3,ENSMUSG00000024130,1.8007487561630795 +Abca4,ENSMUSG00000028125,3.344482 +Abca8b,ENSMUSG00000020620,2.108122441120302 +Abcb11,ENSMUSG00000027048,1.2151442631102662 +Abcb1a,ENSMUSG00000040584,3.344482 +Abcb4,ENSMUSG00000042476,1.8220185592748932 +Abcb6,ENSMUSG00000026198,1.1349997866408914 +Abcc1,ENSMUSG00000023088,1.895718888899544 +Abcc2,ENSMUSG00000025194,3.344482 +Abcc3,ENSMUSG00000020865,2.157937763054824 +Abcc4,ENSMUSG00000032849,2.1886798779447 +Abcc5,ENSMUSG00000022822,2.488818973701028 +Abcc8,ENSMUSG00000040136,1.92710806116626 +Abcc9,ENSMUSG00000030249,3.344482 +Abcd1,ENSMUSG00000031378,1.5600565940206272 +Abcd2,ENSMUSG00000055782,2.131667628370121 +Abcd3,ENSMUSG00000028127,1.990164489456006 +Abcg1,ENSMUSG00000024030,1.993303267 +Abcg2,ENSMUSG00000029802,2.9950175558036243 +Abcg5,ENSMUSG00000040505,1.2467202689811088 +Abcg8,ENSMUSG00000024254,2.5575202735034366 +Abhd12,ENSMUSG00000032046,2.8068071413213214 +Abhd5,ENSMUSG00000032540,1.558955698191255 +Abhd6,ENSMUSG00000025277,1.8312641064061983 +Abo,ENSMUSG00000015787,2.219849799742359 +Abtb2,ENSMUSG00000032724,3.051038289439873 +Acaa1a,ENSMUSG00000036138,1.9356197855257544 +Acaa1b,ENSMUSG00000010651,3.344482 +Acaa2,ENSMUSG00000036880,2.936154326 +Acaca,ENSMUSG00000020532,2.6540202940700937 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+Polr1e,ENSMUSG00000028318,1.144688677299907 +Polr1h,ENSMUSG00000036315,1.483444198398002 +Polr2a,ENSMUSG00000005198,1.9892638944629224 +Polr2b,ENSMUSG00000029250,1.5998562897755293 +Polr2c,ENSMUSG00000031783,1.9336086292085797 +Polr2d,ENSMUSG00000024258,1.5169560286036197 +Polr2e,ENSMUSG00000004667,1.983041223317458 +Polr2f,ENSMUSG00000033020,2.277278429721469 +Polr2g,ENSMUSG00000071662,2.0198204436316325 +Polr2h,ENSMUSG00000021018,1.5027730676180329 +Polr2i,ENSMUSG00000019738,1.913097707716193 +Polr2j,ENSMUSG00000039771,2.006933128174594 +Polr2k,ENSMUSG00000045996,1.975272783848804 +Polr2l,ENSMUSG00000038489,2.0495187767430343 +Polr3a,ENSMUSG00000025280,1.5073820518946557 +Polr3b,ENSMUSG00000034453,1.5511913116953358 +Polr3c,ENSMUSG00000028099,1.4734047091875568 +Polr3d,ENSMUSG00000000776,1.392628970281372 +Polr3e,ENSMUSG00000030880,1.861002615266668 +Polr3f,ENSMUSG00000027427,1.4208816286860515 +Polr3g,ENSMUSG00000035834,1.2407068834810846 +Polr3gl,ENSMUSG00000028104,1.6119129516233444 +Polr3h,ENSMUSG00000022476,1.413176651341289 +Polr3k,ENSMUSG00000038628,1.6252558860120867 +Polrmt,ENSMUSG00000020329,1.5640326839362282 +Pom121,ENSMUSG00000053293,1.471457208 +Pomgnt1,ENSMUSG00000028700,1.7517263259112326 +Pomt1,ENSMUSG00000039254,1.4473335353314811 +Pomt2,ENSMUSG00000034126,1.3756396054716085 +Pon1,ENSMUSG00000002588,2.3132376583579948 +Pon2,ENSMUSG00000032667,2.7079254660489127 +Pon3,ENSMUSG00000029759,2.519349463659444 +Por,ENSMUSG00000005514,2.2457003890012706 +Porcn,ENSMUSG00000031169,1.7632023229068885 +Ppa1,ENSMUSG00000020089,2.124917721798595 +Ppa2,ENSMUSG00000028013,1.758314891573556 +Ppat,ENSMUSG00000029246,1.3212695183812706 +Ppcdc,ENSMUSG00000063849,1.659911776923348 +Ppcs,ENSMUSG00000028636,1.3982089016116463 +Ppia,ENSMUSG00000071866,3.344482 +Ppib,ENSMUSG00000032383,3.344482 +Ppic,ENSMUSG00000024538,3.344482 +Ppid,ENSMUSG00000027804,1.8452564194995376 +Ppie,ENSMUSG00000028651,1.5384849507642473 +Ppif,ENSMUSG00000021868,1.3058382266000277 +Ppig,ENSMUSG00000042133,2.6159746829212613 +Ppih,ENSMUSG00000060288,1.468122193262965 +Ppil1,ENSMUSG00000024007,1.5037302824834875 +Ppil2,ENSMUSG00000022771,1.8991714794122416 +Ppil3,ENSMUSG00000026035,1.4280141561870563 +Ppil4,ENSMUSG00000015757,1.7927870399226258 +Ppip5k1,ENSMUSG00000033526,2.159394632697256 +Ppip5k2,ENSMUSG00000040648,1.704733723559159 +Ppm1l,ENSMUSG00000027784,3.344482 +Ppox,ENSMUSG00000062729,1.6392928145732784 +Ppp1r3b,ENSMUSG00000046794,2.082722024 +Ppp1r3c,ENSMUSG00000067279,2.3078593445927296 +Ppt1,ENSMUSG00000028657,2.2171853241972697 +Ppt2,ENSMUSG00000015474,1.578676327404981 +Ppwd1,ENSMUSG00000021713,1.6401192998933445 +Prdx1,ENSMUSG00000028691,3.344482 +Prdx2,ENSMUSG00000005161,3.344482 +Prdx3,ENSMUSG00000024997,1.8542604705956347 +Prdx5,ENSMUSG00000024953,3.344482 +Prdx6,ENSMUSG00000026701,3.344482 +Preb,ENSMUSG00000045302,1.8168573266881007 +Prep,ENSMUSG00000019849,1.4127701230039575 +Prkd1,ENSMUSG00000002688,3.344482 +Prkn,ENSMUSG00000023826,3.344482 +Prodh,ENSMUSG00000003526,2.0869880517078103 +Prodh2,ENSMUSG00000036892,3.344482 +Prps1,ENSMUSG00000031432,1.5333472632066616 +Prps1l1,ENSMUSG00000092305,2.677330346391685 +Prps2,ENSMUSG00000025742,1.3330640852233469 +Prune1,ENSMUSG00000015711,1.6523430393226666 +Psap,ENSMUSG00000004207,3.344482 +Psat1,ENSMUSG00000024640,2.037107320637712 +Psma1,ENSMUSG00000030751,2.564891472086077 +Psma2,ENSMUSG00000015671,2.9241769045626027 +Psma3,ENSMUSG00000060073,3.2618911927514955 +Psma4,ENSMUSG00000032301,2.6218337163010577 +Psma5,ENSMUSG00000068749,2.3482422042765987 +Psma7,ENSMUSG00000027566,3.344482 +Psma8,ENSMUSG00000036743,1.3840280451874605 +Psmb1,ENSMUSG00000014769,3.344482 +Psmb10,ENSMUSG00000031897,1.8740699133453176 +Psmb11,ENSMUSG00000072423,1.5957276568816172 +Psmb2,ENSMUSG00000028837,2.898569667215671 +Psmb3,ENSMUSG00000069744,3.078410865500832 +Psmb4,ENSMUSG00000005779,2.8786160425840888 +Psmb5,ENSMUSG00000022193,2.8283888686980267 +Psmb6,ENSMUSG00000018286,3.344482 +Psmb7,ENSMUSG00000026750,2.317256737111325 +Psmb8,ENSMUSG00000024338,3.344482 +Psmb9,ENSMUSG00000096727,3.1988117659592663 +Psmd1,ENSMUSG00000026229,2.242268577407217 +Psmd10,ENSMUSG00000031429,1.3964955990279362 +Psmd11,ENSMUSG00000017428,2.3040216356926004 +Psmd12,ENSMUSG00000020720,2.077533333280678 +Psmd13,ENSMUSG00000025487,2.001939850472274 +Psmd14,ENSMUSG00000026914,2.253897890066433 +Psmd2,ENSMUSG00000006998,2.105000424191405 +Psmd4,ENSMUSG00000005625,2.5778592581130857 +Psmd5,ENSMUSG00000026869,1.597004931877055 +Psmd6,ENSMUSG00000021737,2.1307987128168078 +Psmd7,ENSMUSG00000039067,2.619406036910478 +Psmd8,ENSMUSG00000030591,2.4385205713749785 +Psmd9,ENSMUSG00000029440,1.7248105349419551 +Psmg1,ENSMUSG00000022913,1.4089311541516287 +Psmg2,ENSMUSG00000024537,1.617351529027397 +Psmg3,ENSMUSG00000029551,1.458175569769763 +Psmg4,ENSMUSG00000071451,1.6559658811478268 +Psph,ENSMUSG00000029446,1.5757474828233966 +Ptdss1,ENSMUSG00000021518,1.603308499588254 +Ptdss2,ENSMUSG00000025495,1.5663003845932646 +Pten,ENSMUSG00000013663,3.005182114070504 +Ptgds,ENSMUSG00000015090,3.344482 +Ptges,ENSMUSG00000050737,1.890315833956273 +Ptges2,ENSMUSG00000026820,1.3201814956846276 +Ptges3,ENSMUSG00000071072,2.840770925756164 +Ptgis,ENSMUSG00000017969,2.615341631522615 +Ptgr1,ENSMUSG00000028378,1.9122553986128128 +Ptgs1,ENSMUSG00000047250,3.30164465752122 +Ptgs2,ENSMUSG00000032487,2.348888500098222 +Ptpmt1,ENSMUSG00000063235,1.7330458603833552 +Ptprq,ENSMUSG00000035916,2.342740108822739 +Ptrh1,ENSMUSG00000053746,1.0191375171094967 +Ptrh2,ENSMUSG00000072582,1.4052942272137463 +Pts,ENSMUSG00000032067,1.7141585538524773 +Pus1,ENSMUSG00000029507,1.29723312072964 +Pxdn,ENSMUSG00000020674,1.695513030954251 +Pxylp1,ENSMUSG00000043587,2.1056209225980664 +Pycr1,ENSMUSG00000025140,1.1137597783435522 +Pycr2,ENSMUSG00000026520,1.6778966083915885 +Pycr3,ENSMUSG00000022571,1.4791840725791066 +Pygb,ENSMUSG00000033059,2.1036510463161053 +Pygl,ENSMUSG00000021069,2.832484539372109 +Pygm,ENSMUSG00000032648,3.344482 +Pyurf,ENSMUSG00000043162,1.427776377399896 +Qars1,ENSMUSG00000032604,1.6044228847398665 +Qdpr,ENSMUSG00000015806,2.960265299260475 +Qpct,ENSMUSG00000024084,3.311487571806402 +Qprt,ENSMUSG00000030674,2.1277548360066683 +Qtrt1,ENSMUSG00000002825,1.5248205835785944 +Qtrt2,ENSMUSG00000022704,1.508090347521173 +Rab1a,ENSMUSG00000020149,2.962939981874213 +Rab6b,ENSMUSG00000032549,3.344482 +Rab8b,ENSMUSG00000036943,2.324431489078389 +Rad1,ENSMUSG00000022248,1.2303114182798272 +Rad18,ENSMUSG00000030254,1.4630049676021202 +Rad9a,ENSMUSG00000024824,1.3858560956299837 +Rae1,ENSMUSG00000027509,1.6706574620954289 +Rag1,ENSMUSG00000061311,3.344482 +Ralbp1,ENSMUSG00000024096,2.579421837457037 +Ranbp2,ENSMUSG00000003226,2.090456708308825 +Rars1,ENSMUSG00000018848,1.5877188264585027 +Rbak,ENSMUSG00000061898,1.444026667853376 +Rbbp6,ENSMUSG00000030779,2.4088697658046545 +Rbks,ENSMUSG00000029136,1.6279174942376242 +Rbp1,ENSMUSG00000046402,3.344482 +Rbp2,ENSMUSG00000032454,3.344482 +Rbp3,ENSMUSG00000041534,3.344482 +Rbp4,ENSMUSG00000024990,3.344482 +Rchy1,ENSMUSG00000029397,1.94949077248472 +Rdh1,ENSMUSG00000089789,1.136642088488142 +Rdh10,ENSMUSG00000025921,1.668970099642784 +Rdh11,ENSMUSG00000066441,1.3756199156251825 +Rdh12,ENSMUSG00000021123,2.889771445585166 +Rdh13,ENSMUSG00000008435,1.405009357971215 +Rdh14,ENSMUSG00000020621,1.6012498694562416 +Rdh16,ENSMUSG00000069456,3.344482 +Rdh16f2,ENSMUSG00000074639,3.344482 +Rdh19,ENSMUSG00000054052,1.2388946180206415 +Rdh5,ENSMUSG00000025350,2.88622885 +Rdh7,ENSMUSG00000040134,3.344482 +Rdh8,ENSMUSG00000053773,3.344482 +Rdh9,ENSMUSG00000056148,1.044251972 +Renbp,ENSMUSG00000031387,2.306234139799592 +Rev3l,ENSMUSG00000019841,3.2034044239466644 +Rfc5,ENSMUSG00000029363,1.2297862863897615 +Rfk,ENSMUSG00000024712,1.5909938372867527 +Rfwd3,ENSMUSG00000033596,1.7267975735509709 +Rgn,ENSMUSG00000023070,2.972536561829463 +Rhag,ENSMUSG00000023926,3.344482 +Rhbg,ENSMUSG00000104445,2.8863891160712614 +Rhcg,ENSMUSG00000030549,3.344482 +Ring1,ENSMUSG00000024325,1.6044133052373983 +Rlbp1,ENSMUSG00000039194,3.344482 +Rnf103,ENSMUSG00000052656,1.6735699098668293 +Rnf115,ENSMUSG00000028098,1.9523396992475184 +Rnf123,ENSMUSG00000041528,1.682764262037982 +Rnf125,ENSMUSG00000033107,2.6923804463961303 +Rnf126,ENSMUSG00000035890,1.5332151997918522 +Rnf128,ENSMUSG00000031438,1.9033633712953413 +Rnf13,ENSMUSG00000036503,2.5348382030394463 +Rnf130,ENSMUSG00000020376,2.532464967039581 +Rnf133,ENSMUSG00000051956,1.131614031174789 +Rnf138,ENSMUSG00000024317,1.7729673404807516 +Rnf139,ENSMUSG00000037075,1.732227147288801 +Rnf14,ENSMUSG00000060450,2.733148732326088 +Rnf144a,ENSMUSG00000020642,1.9744965012239768 +Rnf144b,ENSMUSG00000038068,1.767642212336174 +Rnf146,ENSMUSG00000038876,1.6993238310848509 +Rnf149,ENSMUSG00000048234,1.5868166439524438 +Rnf152,ENSMUSG00000047496,3.1295463033433157 +Rnf167,ENSMUSG00000040746,1.8815496285545568 +Rnf180,ENSMUSG00000021720,1.7053748905311257 +Rnf182,ENSMUSG00000044164,2.900598437626728 +Rnf185,ENSMUSG00000020448,1.6281516948832202 +Rnf187,ENSMUSG00000020496,3.344482 +Rnf19a,ENSMUSG00000022280,1.8006009681184714 +Rnf19b,ENSMUSG00000028793,1.5641471493633212 +Rnf2,ENSMUSG00000026484,1.6575864095574175 +Rnf20,ENSMUSG00000028309,1.693187751310974 +Rnf216,ENSMUSG00000045078,2.2160041481939543 +Rnf217,ENSMUSG00000063760,1.6677720013953272 +Rnf25,ENSMUSG00000026171,1.5272643672223132 +Rnf31,ENSMUSG00000047098,1.426302121416671 +Rnf40,ENSMUSG00000030816,1.324464949288397 +Rnf41,ENSMUSG00000025373,1.654264025 +Rnf5,ENSMUSG00000015478,1.7674829593192658 +Rnf8,ENSMUSG00000090083,1.601554627 +Rngtt,ENSMUSG00000028274,2.088836052778103 +Rnmt,ENSMUSG00000009535,1.6585128669917413 +Rnpep,ENSMUSG00000041926,1.889383445717009 +Rpe,ENSMUSG00000026005,1.3791137720764253 +Rpe65,ENSMUSG00000028174,3.344482 +Rpia,ENSMUSG00000053604,1.4205970158128367 +Rpl36a,ENSMUSG00000079435,3.344482 +Rpn1,ENSMUSG00000030062,2.1926290140216635 +Rpn2,ENSMUSG00000027642,2.5915960442352066 +Rpp14,ENSMUSG00000023156,1.3266838616475898 +Rpusd4,ENSMUSG00000032044,1.2595950636301965 +Rrbp1,ENSMUSG00000027422,3.344482 +Rrm1,ENSMUSG00000030978,1.929834819458808 +Rrm2,ENSMUSG00000020649,3.344482 +Rrm2b,ENSMUSG00000022292,3.344482 +Rtca,ENSMUSG00000000339,1.464716781946257 +Rwdd2a,ENSMUSG00000032417,1.5248681102551314 +Sacm1l,ENSMUSG00000025240,1.9922772980883772 +Sae1,ENSMUSG00000052833,1.9538082499735645 +Sapcd1,ENSMUSG00000036185,2.7699649165965576 +Sar1b,ENSMUSG00000020386,2.036168500725568 +Sardh,ENSMUSG00000009614,2.253592304091518 +Sars1,ENSMUSG00000068739,2.2528274903126047 +Sat1,ENSMUSG00000025283,3.344482 +Sat2,ENSMUSG00000069835,1.6448657064611103 +Satl1,ENSMUSG00000025527,3.344482 +Sc5d,ENSMUSG00000032018,1.7596609781662966 +Scarb1,ENSMUSG00000037936,1.9803231705541957 +Scarf2,ENSMUSG00000012017,1.7496520534560014 +Sccpdh,ENSMUSG00000038936,1.876206594185448 +Scd1,ENSMUSG00000037071,3.344482 +Scd2,ENSMUSG00000025203,3.344482 +Scd3,ENSMUSG00000025202,1.3298839928614756 +Scly,ENSMUSG00000026307,1.4378576463246446 +Scn10a,ENSMUSG00000034533,3.344482 +Scn11a,ENSMUSG00000034115,3.344482 +Scn1a,ENSMUSG00000064329,3.344482 +Scn2a,ENSMUSG00000075318,3.344482 +Scn3a,ENSMUSG00000057182,2.202244212198973 +Scn4a,ENSMUSG00000001027,3.344482 +Scn5a,ENSMUSG00000032511,1.707426304553458 +Scn7a,ENSMUSG00000034810,3.344482 +Scn8a,ENSMUSG00000023033,3.344482 +Scn9a,ENSMUSG00000075316,2.550135122117076 +Scnn1a,ENSMUSG00000030340,2.155291567699985 +Scnn1b,ENSMUSG00000030873,1.4711879377482906 +Scnn1g,ENSMUSG00000000216,1.7007023680688829 +Scp2,ENSMUSG00000028603,3.140565239237276 +Sdc1,ENSMUSG00000020592,2.5287319163294155 +Sdha,ENSMUSG00000021577,2.659261555595542 +Sdhb,ENSMUSG00000009863,2.8964789354429508 +Sdhc,ENSMUSG00000058076,2.065301421191725 +Sdhd,ENSMUSG00000000171,2.050330141255342 +Sdr16c5,ENSMUSG00000028236,1.5657576782717098 +Sdr42e1,ENSMUSG00000034308,1.077878497525402 +Sdr9c7,ENSMUSG00000040127,0.8747593909775868 +Sds,ENSMUSG00000029597,1.9373937566684971 +Sdsl,ENSMUSG00000029596,1.4764527480095926 +Sec11a,ENSMUSG00000025724,2.248329357022402 +Sec11c,ENSMUSG00000024516,2.593033791959037 +Sec13,ENSMUSG00000030298,1.955923190326242 +Sec16a,ENSMUSG00000026924,1.5226512854899026 +Sec22b,ENSMUSG00000027879,1.7174472047508444 +Sec23a,ENSMUSG00000020986,1.8318709097739363 +Sec24a,ENSMUSG00000036391,1.9595878581994008 +Sec31a,ENSMUSG00000035325,1.8183454908746424 +Sec61a1,ENSMUSG00000030082,1.8873721631579443 +Sec61b,ENSMUSG00000053317,3.344482 +Sec61g,ENSMUSG00000078974,3.344482 +Sec62,ENSMUSG00000027706,3.344482 +Sec63,ENSMUSG00000019802,2.0971111838483383 +Seh1l,ENSMUSG00000079614,1.469841232734972 +Sel1l,ENSMUSG00000020964,2.337435903149589 +Selenoi,ENSMUSG00000075703,1.8204306612310663 +Selenos,ENSMUSG00000075701,2.4100076237540384 +Sephs1,ENSMUSG00000026662,1.471630470713766 +Sephs2,ENSMUSG00000049091,1.7858900545266374 +Serp1,ENSMUSG00000027808,2.602701270999165 +Serpina1a,ENSMUSG00000066366,3.344482 +Serpina1b,ENSMUSG00000071178,3.344482 +Serpina1d,ENSMUSG00000071177,3.344482 +Serpina1e,ENSMUSG00000072849,3.344482 +Serpina3c,ENSMUSG00000066361,2.047119543644316 +Serpina3f,ENSMUSG00000066363,3.344482 +Serpina3g,ENSMUSG00000041481,3.344482 +Serpina3i,ENSMUSG00000079014,1.0733865407264784 +Serpina3k,ENSMUSG00000058207,3.344482 +Serpina3m,ENSMUSG00000079012,2.7247885608396154 +Serpina3n,ENSMUSG00000021091,2.588799480208777 +Setd1a,ENSMUSG00000042308,1.3623009875505696 +Setd1b,ENSMUSG00000038384,1.5494181643073903 +Setd2,ENSMUSG00000044791,2.206356877614843 +Setd5,ENSMUSG00000034269,2.7575463208438906 +Setd7,ENSMUSG00000037111,2.2220623537153115 +Setdb1,ENSMUSG00000015697,1.803637775210024 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82f9f45a27983aeecd850638ac81b599dc7a1e5f Mon Sep 17 00:00:00 2001 From: Erick Armingol Date: Mon, 21 Oct 2024 11:45:25 +0100 Subject: [PATCH 11/18] Added function to handle duplicated indexes --- sccellfie/preprocessing/__init__.py | 2 +- .../preprocessing/database_manipulation.py | 48 ++++++++++- .../tests/test_database_manipulation.py | 82 ++++++++++++++++++- 3 files changed, 128 insertions(+), 4 deletions(-) diff --git a/sccellfie/preprocessing/__init__.py b/sccellfie/preprocessing/__init__.py index 8c23513..6c9f8a2 100644 --- a/sccellfie/preprocessing/__init__.py +++ b/sccellfie/preprocessing/__init__.py @@ -1,3 +1,3 @@ -from .database_manipulation import get_element_associations, add_new_task, combine_and_sort_dataframes +from .database_manipulation import get_element_associations, add_new_task, combine_and_sort_dataframes, handle_duplicate_indexes from .gpr_rules import clean_gene_names, find_genes_gpr, replace_gene_ids_in_gpr, convert_gpr_nomenclature from .prepare_inputs import preprocess_inputs, stratified_subsample_adata, normalize_adata, transform_adata_gene_names \ No newline at end of file diff --git a/sccellfie/preprocessing/database_manipulation.py b/sccellfie/preprocessing/database_manipulation.py index 912c155..a80def7 100644 --- a/sccellfie/preprocessing/database_manipulation.py +++ b/sccellfie/preprocessing/database_manipulation.py @@ -192,4 +192,50 @@ def combine_and_sort_dataframes(df1, df2, preference='max'): # Sort the rows and columns alphabetically combined_df = combined_df.sort_index().sort_index(axis=1).fillna(0) - return combined_df \ No newline at end of file + return combined_df + + +def handle_duplicate_indexes(df, value_column=None, operation='first'): + """ + Handles duplicated indexes in a DataFrame by keeping the min, max, mean, first, or last value + associated with them in a specified column. + + Parameters + ---------- + df : pandas.DataFrame + DataFrame with duplicated indexes. + + value_column : str, optional (default=None) + Name of the column containing values to make a decision + when handling duplicated indexes. This value is optional + only when operation is 'first' or 'last'. + + operation : str, optional (default='first') + Operation to perform when handling duplicated indexes. + Options: 'min', 'max', 'mean', 'first', 'last'. + + Returns + ------- + df_result : pandas.DataFrame + DataFrame with duplicated indexes handled according to the specified operation + """ + if df.empty: + return df.copy() + + if operation not in ['min', 'max', 'mean', 'first', 'last']: + raise ValueError("Operation must be 'min', 'max', 'mean', or 'first'") + + if operation in ['first', 'last']: + return df[~df.index.duplicated(keep=operation)] + + # Group by index and apply the specified operation + assert value_column is not None, "A value column must be provided for operations other than 'first' or 'last'" + if operation == 'mean': + df_grouped = df.groupby(level=0).agg({value_column: 'mean'}) + else: # min or max + df_grouped = df.groupby(level=0).agg({value_column: operation}) + + # Merge the result back with the original DataFrame to keep other columns + df_result = df.loc[~df.index.duplicated(keep='first')].copy() + df_result[value_column] = df_grouped[value_column] + return df_result \ No newline at end of file diff --git a/sccellfie/preprocessing/tests/test_database_manipulation.py b/sccellfie/preprocessing/tests/test_database_manipulation.py index b94cb45..3b86dc8 100644 --- a/sccellfie/preprocessing/tests/test_database_manipulation.py +++ b/sccellfie/preprocessing/tests/test_database_manipulation.py @@ -1,7 +1,7 @@ import pytest import pandas as pd -from sccellfie.preprocessing.database_manipulation import get_element_associations, add_new_task, combine_and_sort_dataframes +from sccellfie.preprocessing.database_manipulation import get_element_associations, add_new_task, combine_and_sort_dataframes, handle_duplicate_indexes def test_get_element_associations(): @@ -99,4 +99,82 @@ def test_combine_and_sort_dataframes(): # Test with invalid preference with pytest.raises(ValueError): - combine_and_sort_dataframes(df1, df2, preference='invalid') \ No newline at end of file + combine_and_sort_dataframes(df1, df2, preference='invalid') + + +@pytest.fixture +def sample_df(): + data = { + 'A': [1, 2, 3, 4, 5, 6], + 'B': [10, 20, 30, 40, 50, 60], + 'C': ['a', 'b', 'c', 'd', 'e', 'f'] + } + index = ['x', 'y', 'x', 'z', 'y', 'w'] + return pd.DataFrame(data, index=index) + +def test_min_operation(sample_df): + result = handle_duplicate_indexes(sample_df, 'A', 'min') + assert result.index.tolist() == ['x', 'y', 'z', 'w'] + assert result['A'].tolist() == [1, 2, 4, 6] + assert result['B'].tolist() == [10, 20, 40, 60] + assert result['C'].tolist() == ['a', 'b', 'd', 'f'] + +def test_max_operation(sample_df): + result = handle_duplicate_indexes(sample_df, 'A', 'max') + assert result.index.tolist() == ['x', 'y', 'z', 'w'] + assert result['A'].tolist() == [3, 5, 4, 6] + assert result['B'].tolist() == [10, 20, 40, 60] + assert result['C'].tolist() == ['a', 'b', 'd', 'f'] + +def test_mean_operation(sample_df): + result = handle_duplicate_indexes(sample_df, 'A', 'mean') + assert result.index.tolist() == ['x', 'y', 'z', 'w'] + assert result['A'].tolist() == [2, 3.5, 4, 6] + assert result['B'].tolist() == [10, 20, 40, 60] + assert result['C'].tolist() == ['a', 'b', 'd', 'f'] + +def test_first_operation(sample_df): + result = handle_duplicate_indexes(sample_df, 'A', 'first') + assert result.index.tolist() == ['x', 'y', 'z', 'w'] + assert result['A'].tolist() == [1, 2, 4, 6] + assert result['B'].tolist() == [10, 20, 40, 60] + assert result['C'].tolist() == ['a', 'b', 'd', 'f'] + +def test_last_operation(sample_df): + result = handle_duplicate_indexes(sample_df, 'A', 'last') + assert result.index.tolist() == ['x', 'z', 'y', 'w'] + assert result['A'].tolist() == [3, 4, 5, 6] + assert result['B'].tolist() == [30, 40, 50, 60] + assert result['C'].tolist() == ['c', 'd', 'e', 'f'] + +def test_invalid_operation(sample_df): + with pytest.raises(ValueError): + handle_duplicate_indexes(sample_df, 'A', 'invalid_operation') + +def test_non_existent_column(sample_df): + with pytest.raises(KeyError): + handle_duplicate_indexes(sample_df, 'D', 'min') + +def test_single_column_df(): + df = pd.DataFrame({'A': [1, 2, 3, 4]}, index=['x', 'y', 'x', 'z']) + result = handle_duplicate_indexes(df, 'A', 'max') + assert result.index.tolist() == ['x', 'y', 'z'] + assert result['A'].tolist() == [3, 2, 4] + +def test_all_duplicates_df(): + df = pd.DataFrame({'A': [1, 2, 3], 'B': [4, 5, 6]}, index=['x', 'x', 'x']) + result = handle_duplicate_indexes(df, 'A', 'mean') + assert len(result) == 1 + assert result.index[0] == 'x' + assert result['A'].values[0] == 2 + assert result['B'].values[0] == 4 + +def test_no_duplicates_df(): + df = pd.DataFrame({'A': [1, 2, 3]}, index=['x', 'y', 'z']) + result = handle_duplicate_indexes(df, 'A', 'min') + pd.testing.assert_frame_equal(result, df) + +def test_empty_df(): + df = pd.DataFrame() + result = handle_duplicate_indexes(df, 'A', 'min') + assert result.empty \ No newline at end of file From 1f1ceb20ccfb09ff44ccee95d34ace089a58e1ae Mon Sep 17 00:00:00 2001 From: Erick Armingol Date: Mon, 21 Oct 2024 12:05:34 +0100 Subject: [PATCH 12/18] Changed default size of violin plots --- sccellfie/plotting/distributions.py | 14 +++++++------- 1 file changed, 7 insertions(+), 7 deletions(-) diff --git a/sccellfie/plotting/distributions.py b/sccellfie/plotting/distributions.py index e1d8cdb..30f7840 100644 --- a/sccellfie/plotting/distributions.py +++ b/sccellfie/plotting/distributions.py @@ -2,7 +2,7 @@ import matplotlib.pyplot as plt -def create_multi_violin_plots(adata, genes, groupby, n_cols=4, figsize=(4, 3), ylabel='Metabolic Activity', fontsize=10, save=None, dpi=300, **kwargs): +def create_multi_violin_plots(adata, genes, groupby, n_cols=4, figsize=(5, 5), ylabel='Metabolic Activity', fontsize=10, save=None, dpi=300, **kwargs): """ Plot a grid of violin plots for multiple genes in Scanpy, controlling the number of columns. @@ -19,25 +19,25 @@ def create_multi_violin_plots(adata, genes, groupby, n_cols=4, figsize=(4, 3), y Key in `adata.obs` containing the groups to plot. For each unique value in this column, a violin plot will be generated. - n_cols : int, optional (default=4) + n_cols : int, optional (default: 4) Number of columns in the grid. - figsize : tuple of float, optional (default=(4, 3)) + figsize : tuple of float, optional (default: (5, 5)) Size of each subplot in inches. - ylabel : str, optional (default='Metabolic Activity') + ylabel : str, optional (default: 'Metabolic Activity') Label for the y-axis. - fontsize : int, optional (default=10) + fontsize : int, optional (default: 10) Font size for the title and axis labels. The tick labels will be set to `fontsize`, while the title will be set to `fontsize + 4`. Ylabel will be set to `fontsize + 2`. - save : str, optional (default=None) + save : str, optional (default: None) Filepath to save the figure. If not provided, the figure will be displayed. - dpi : int, optional (default=300) + dpi : int, optional (default: 300) Resolution of the saved figure. **kwargs : dict From 763e794094fa4dd7cb501e81ad49bc10ab68b19c Mon Sep 17 00:00:00 2001 From: Erick Armingol Date: Mon, 21 Oct 2024 12:08:35 +0100 Subject: [PATCH 13/18] Harmonized docstrings --- sccellfie/datasets/database.py | 16 +++---- sccellfie/datasets/gene_info.py | 2 +- sccellfie/expression/smoothing.py | 4 +- sccellfie/expression/thresholds.py | 30 ++++++------- sccellfie/gene_score.py | 12 ++--- sccellfie/io/load_data.py | 4 +- sccellfie/io/save_data.py | 4 +- sccellfie/metabolic_task.py | 5 ++- sccellfie/plotting/distributions.py | 2 +- .../preprocessing/database_manipulation.py | 15 ++++--- sccellfie/preprocessing/gpr_rules.py | 8 ++-- sccellfie/preprocessing/prepare_inputs.py | 24 +++++----- sccellfie/reaction_activity.py | 5 +-- sccellfie/sccellfie_pipeline.py | 44 +++++++++---------- sccellfie/spatial/assortativity.py | 8 ++-- sccellfie/spatial/hotspots.py | 18 ++++---- sccellfie/spatial/knn_network.py | 9 ++-- sccellfie/stats/markers_from_task.py | 4 +- 18 files changed, 107 insertions(+), 107 deletions(-) diff --git a/sccellfie/datasets/database.py b/sccellfie/datasets/database.py index 5a06789..4fbadb1 100644 --- a/sccellfie/datasets/database.py +++ b/sccellfie/datasets/database.py @@ -10,28 +10,28 @@ def load_sccellfie_database(organism='human', task_folder=None, rxn_info_filenam Parameters ---------- - organism : str, optional (default='human') + organism : str, optional (default: 'human') The organism to retrieve data for. Choose 'human' or 'mouse'. Used when loading from URLs. - task_folder : str, optional (default=None) + task_folder : str, optional (default: None) The local folder path containing CellFie data files. If provided, this takes priority. - rxn_info_filename : str, optional (default=None) + rxn_info_filename : str, optional (default: None) Full path for reaction information JSON file. - task_info_filename : str, optional (default=None) + task_info_filename : str, optional (default: None) Full path for task information CSV file. - task_by_rxn_filename : str, optional (default=None) + task_by_rxn_filename : str, optional (default: None) Full path for task by reaction CSV file. - task_by_gene_filename : str, optional (default=None) + task_by_gene_filename : str, optional (default: None) Full path for task by gene CSV file. - rxn_by_gene_filename : str, optional (default=None) + rxn_by_gene_filename : str, optional (default: None) Full path for reaction by gene CSV file. - thresholds_filename : str, optional (default=None) + thresholds_filename : str, optional (default: None) Full path for thresholds CSV file. Returns diff --git a/sccellfie/datasets/gene_info.py b/sccellfie/datasets/gene_info.py index 1740acd..5d1c465 100644 --- a/sccellfie/datasets/gene_info.py +++ b/sccellfie/datasets/gene_info.py @@ -7,7 +7,7 @@ def retrieve_ensembl2symbol_data(filename=None, organism='human'): Parameters ---------- - filename : str, optional + filename : str, optional (default: None) The file path to a custom CSV file containing Ensembl IDs and gene symbols. organism : str, optional (default: 'human') diff --git a/sccellfie/expression/smoothing.py b/sccellfie/expression/smoothing.py index 814e098..b338c49 100644 --- a/sccellfie/expression/smoothing.py +++ b/sccellfie/expression/smoothing.py @@ -6,7 +6,7 @@ def get_smoothing_matrix(adata, mode, neighbors_key='neighbors'): """ - Calculate the smoothing matrix S based on the nearest neighbor graph in adata.obsp. + Calculates the smoothing matrix S based on the nearest neighbor graph in adata.obsp. Parameters ---------- @@ -58,7 +58,7 @@ def get_smoothing_matrix(adata, mode, neighbors_key='neighbors'): def smooth_expression_knn(adata, key_added='smoothed_X', neighbors_key='neighbors', mode='connectivity', alpha=0.33, n_chunks=None, chunk_size=None, use_raw=False, disable_pbar=False): """ - Smooth expression values based on KNNs of single cells using Scanpy. + Smooths expression values based on KNNs of single cells using Scanpy. Parameters ---------- diff --git a/sccellfie/expression/thresholds.py b/sccellfie/expression/thresholds.py index 9d94987..f238c3c 100644 --- a/sccellfie/expression/thresholds.py +++ b/sccellfie/expression/thresholds.py @@ -3,7 +3,7 @@ def get_local_percentile_threshold(adata, percentile=0.75, lower_bound=1e-5, upper_bound=None, exclude_zeros=False, use_raw=False): - ''' + """ Obtains the local percentile threshold for each gene in a AnnData object. Parameters @@ -32,7 +32,7 @@ def get_local_percentile_threshold(adata, percentile=0.75, lower_bound=1e-5, upp ------- thresholds: pandas.DataFrame A pandas.DataFrame object with the local percentile threshold for each gene. - ''' + """ if use_raw: X = adata.raw.X.toarray() else: @@ -65,7 +65,7 @@ def get_local_percentile_threshold(adata, percentile=0.75, lower_bound=1e-5, upp def get_global_percentile_threshold(adata, percentile=0.75, lower_bound=1e-5, upper_bound=None, exclude_zeros=False, use_raw=False): - ''' + """ Obtains the global percentile threshold for each gene in a AnnData object. Parameters @@ -94,7 +94,7 @@ def get_global_percentile_threshold(adata, percentile=0.75, lower_bound=1e-5, up ------- thresholds: pandas.DataFrame A pandas.DataFrame object with the global percentile threshold for each gene. - ''' + """ if use_raw: X = adata.raw.X.toarray() else: @@ -128,7 +128,7 @@ def get_global_percentile_threshold(adata, percentile=0.75, lower_bound=1e-5, up def get_local_mean_threshold(adata, lower_bound=1e-5, upper_bound=None, exclude_zeros=False, use_raw=False): - ''' + """ Obtains the local mean threshold for each gene in a AnnData object. Parameters @@ -154,7 +154,7 @@ def get_local_mean_threshold(adata, lower_bound=1e-5, upper_bound=None, exclude_ ------- thresholds: pandas.DataFrame A pandas.DataFrame object with the local mean threshold for each gene. - ''' + """ if use_raw: X = adata.raw.X.toarray() else: @@ -184,7 +184,7 @@ def get_local_mean_threshold(adata, lower_bound=1e-5, upper_bound=None, exclude_ def get_global_mean_threshold(adata, lower_bound=1e-5, upper_bound=None, exclude_zeros=False, use_raw=False): - ''' + """ Obtains the global mean threshold for each gene in a AnnData object. Parameters @@ -208,7 +208,7 @@ def get_global_mean_threshold(adata, lower_bound=1e-5, upper_bound=None, exclude ------- thresholds: pandas.DataFrame A pandas.DataFrame object with the global mean threshold for each gene. - ''' + """ if use_raw: X = adata.raw.X.toarray() else: @@ -238,7 +238,7 @@ def get_global_mean_threshold(adata, lower_bound=1e-5, upper_bound=None, exclude def get_local_trimean_threshold(adata, lower_bound=1e-5, upper_bound=None, exclude_zeros=False, use_raw=False): - ''' + """ Obtains the local Tukey's trimean threshold for each gene in a AnnData object. Parameters @@ -264,7 +264,7 @@ def get_local_trimean_threshold(adata, lower_bound=1e-5, upper_bound=None, exclu ------- thresholds: pandas.DataFrame A pandas.DataFrame object with the local Tukey's trimean threshold for each gene. - ''' + """ if use_raw: X = adata.raw.X.toarray() else: @@ -299,7 +299,7 @@ def get_local_trimean_threshold(adata, lower_bound=1e-5, upper_bound=None, exclu def get_global_trimean_threshold(adata, lower_bound=1e-5, upper_bound=None, exclude_zeros=False, use_raw=False): - ''' + """ Obtains the global Tukey's trimean threshold for each gene in a AnnData object. Parameters @@ -325,7 +325,7 @@ def get_global_trimean_threshold(adata, lower_bound=1e-5, upper_bound=None, excl ------- thresholds: pandas.DataFrame A pandas.DataFrame object with the global Tukey's trimean threshold for each gene. - ''' + """ if use_raw: X = adata.raw.X.toarray() else: @@ -360,8 +360,8 @@ def get_global_trimean_threshold(adata, lower_bound=1e-5, upper_bound=None, excl def set_manual_threshold(adata, threshold): - ''' - Set a threshold manually for each gene in a AnnData object. + """ + Sets a threshold manually for each gene in a AnnData object. Parameters ---------- @@ -377,7 +377,7 @@ def set_manual_threshold(adata, threshold): ------- thresholds: pandas.DataFrame A pandas.DataFrame object with the manual threshold for each gene. - ''' + """ if isinstance(threshold, list): assert len(adata.var_names) == len(threshold), "The len of threshold must be the same as gene number in adata" thresholds = pd.DataFrame(data={'threshold-manual': threshold}, index=adata.var_names, dtype=float) diff --git a/sccellfie/gene_score.py b/sccellfie/gene_score.py index 1f4a938..8edd2a2 100644 --- a/sccellfie/gene_score.py +++ b/sccellfie/gene_score.py @@ -7,7 +7,7 @@ def gene_score(gene_expression, gene_threshold): - ''' + """ Computes the gene score for a given gene expression and threshold. Parameters @@ -26,12 +26,12 @@ def gene_score(gene_expression, gene_threshold): Notes ----- This score is computed as previously indicated in the CellFie paper (https://doi.org/10.1016/j.cels.2019.05.012). - ''' + """ return 5*np.log(1 + gene_expression/(gene_threshold + PCOUNT)) # Added small value to threshold to avoid division by zero def compute_gene_scores(adata, thresholds, use_raw=False, layer='gene_scores'): - ''' + """ Computes the gene scores from CellFie for each gene in an AnnData object given specific threshold values. @@ -57,7 +57,7 @@ def compute_gene_scores(adata, thresholds, use_raw=False, layer='gene_scores'): Notes ----- This score is computed as previously indicated in the CellFie paper (https://doi.org/10.1016/j.crmeth.2021.100040). - ''' + """ genes = [g for g in thresholds.index if g in adata.var_names] if use_raw: X = adata[:, genes].raw.X @@ -74,7 +74,7 @@ def compute_gene_scores(adata, thresholds, use_raw=False, layer='gene_scores'): def compute_gpr_gene_score(gpr, gene_scores): - ''' + """ Recursive parsing of gprs into lists of complexes and their scores. Parameters @@ -99,7 +99,7 @@ def compute_gpr_gene_score(gpr, gene_scores): Notes ----- This score is computed as previously indicated in the CellFie paper (https://doi.org/10.1016/j.crmeth.2021.100040). - ''' + """ if isinstance(gpr, cobra.core.gene.GPR): return compute_gpr_gene_score(gpr.body, gene_scores) elif isinstance(gpr, ast.Name): diff --git a/sccellfie/io/load_data.py b/sccellfie/io/load_data.py index 5bc5171..90cc134 100644 --- a/sccellfie/io/load_data.py +++ b/sccellfie/io/load_data.py @@ -7,7 +7,7 @@ def load_adata(folder, filename, reactions_filename=None, metabolic_tasks_filename=None, spatial_network_key='spatial_network', verbose=True): - ''' + """ Loads an AnnData object and its scCellFie attributes from a folder. Parameters @@ -39,7 +39,7 @@ def load_adata(folder, filename, reactions_filename=None, metabolic_tasks_filena Annotated data matrix. If scCellFie attributes are found, they are also loaded into adata.reactions and adata.metabolic_tasks. - ''' + """ if reactions_filename is not None: rxn_filename = f'{folder}/{reactions_filename}.h5ad' else: diff --git a/sccellfie/io/save_data.py b/sccellfie/io/save_data.py index c4f4dcf..8662ff7 100644 --- a/sccellfie/io/save_data.py +++ b/sccellfie/io/save_data.py @@ -4,7 +4,7 @@ def save_adata(adata, folder, filename, spatial_network_key='spatial_network', verbose=True): - ''' + """ Saves an AnnData object and its scCellFie attributes to a folder. Parameters @@ -31,7 +31,7 @@ def save_adata(adata, folder, filename, spatial_network_key='spatial_network', v The scCellFie attributes are saved to: - reactions: folder/filename_reactions.h5ad. - metabolic_tasks: folder/filename_metabolic_tasks.h5ad. - ''' + """ # Check folder path Path(folder).mkdir(parents=True, exist_ok=True) if spatial_network_key in adata.uns.keys(): diff --git a/sccellfie/metabolic_task.py b/sccellfie/metabolic_task.py index d960d52..b16d096 100644 --- a/sccellfie/metabolic_task.py +++ b/sccellfie/metabolic_task.py @@ -1,8 +1,9 @@ import numpy as np import scanpy as sc + def compute_mt_score(adata, task_by_rxn, verbose=True): - ''' + """ Computes the metabolic task score for each cell in an AnnData object given specific reaction activity levels. @@ -33,7 +34,7 @@ def compute_mt_score(adata, task_by_rxn, verbose=True): sccellfie.reaction_activity.compute_reaction_activity() and are stored in adata.reactions.X. This score is computed as previously indicated in the CellFie paper (https://doi.org/10.1016/j.crmeth.2021.100040). - ''' + """ assert hasattr(adata, 'reactions'), "You must run sccellfie.reaction_activity.compute_reaction_activity() first." # RAL matrix diff --git a/sccellfie/plotting/distributions.py b/sccellfie/plotting/distributions.py index 30f7840..2d0b473 100644 --- a/sccellfie/plotting/distributions.py +++ b/sccellfie/plotting/distributions.py @@ -4,7 +4,7 @@ def create_multi_violin_plots(adata, genes, groupby, n_cols=4, figsize=(5, 5), ylabel='Metabolic Activity', fontsize=10, save=None, dpi=300, **kwargs): """ - Plot a grid of violin plots for multiple genes in Scanpy, + Plots a grid of violin plots for multiple genes in Scanpy, controlling the number of columns. Parameters: diff --git a/sccellfie/preprocessing/database_manipulation.py b/sccellfie/preprocessing/database_manipulation.py index a80def7..739749a 100644 --- a/sccellfie/preprocessing/database_manipulation.py +++ b/sccellfie/preprocessing/database_manipulation.py @@ -4,8 +4,9 @@ def get_element_associations(df, element, axis_element=0): - '''Get the tasks, reactions, or genes associated with - a given element in the DataFrame. + """ + Gets the tasks, reactions, or genes associated with + a given element in the DataFrame. Parameters ---------- @@ -24,7 +25,7 @@ def get_element_associations(df, element, axis_element=0): associations : list of str List of tasks, reactions, or genes associated with the given element. - ''' + """ if axis_element == 0: e = df.loc[element, :] elif axis_element == 1: @@ -40,7 +41,7 @@ def get_element_associations(df, element, axis_element=0): def add_new_task(task_by_rxn, task_by_gene, rxn_by_gene, task_info, rxn_info, task_name, task_system, task_subsystem, rxn_names, gpr_hgncs, gpr_symbols): """ - Add a new task and their associated reactions and genes to the database. + Adds a new task and their associated reactions and genes to the database. Parameters ---------- @@ -145,7 +146,7 @@ def add_new_task(task_by_rxn, task_by_gene, rxn_by_gene, task_info, rxn_info, def combine_and_sort_dataframes(df1, df2, preference='max'): """ - Combine two DataFrames and sort the rows and columns alphabetically. + Combines two DataFrames and sort the rows and columns alphabetically. Parameters ---------- @@ -205,12 +206,12 @@ def handle_duplicate_indexes(df, value_column=None, operation='first'): df : pandas.DataFrame DataFrame with duplicated indexes. - value_column : str, optional (default=None) + value_column : str, optional (default: None) Name of the column containing values to make a decision when handling duplicated indexes. This value is optional only when operation is 'first' or 'last'. - operation : str, optional (default='first') + operation : str, optional (default: 'first') Operation to perform when handling duplicated indexes. Options: 'min', 'max', 'mean', 'first', 'last'. diff --git a/sccellfie/preprocessing/gpr_rules.py b/sccellfie/preprocessing/gpr_rules.py index 2f41f5f..a7e5c45 100644 --- a/sccellfie/preprocessing/gpr_rules.py +++ b/sccellfie/preprocessing/gpr_rules.py @@ -4,7 +4,7 @@ def clean_gene_names(gpr_rule): """ - Remove spaces between parentheses and gene IDs in a GPR rule. + Removes spaces between parentheses and gene IDs in a GPR rule. Parameters ---------- @@ -23,7 +23,7 @@ def clean_gene_names(gpr_rule): def find_genes_gpr(gpr_rule): """ - Find all gene IDs in a GPR rule. + Finds all gene IDs in a GPR rule. Parameters ---------- @@ -42,7 +42,7 @@ def find_genes_gpr(gpr_rule): def replace_gene_ids_in_gpr(gpr_rule, gene_id_mapping): """ - Replace gene IDs in a GPR rule with new IDs (different nomenclature). + Replaces gene IDs in a GPR rule with new IDs (different nomenclature). Parameters ---------- @@ -68,7 +68,7 @@ def replace_gene_ids_in_gpr(gpr_rule, gene_id_mapping): def convert_gpr_nomenclature(gpr_rules, id_mapping): """ - Convert gene IDs in multiple GPR rules to a different nomenclature. + Converts gene IDs in multiple GPR rules to a different nomenclature. Parameters ---------- diff --git a/sccellfie/preprocessing/prepare_inputs.py b/sccellfie/preprocessing/prepare_inputs.py index 89f705b..445841f 100644 --- a/sccellfie/preprocessing/prepare_inputs.py +++ b/sccellfie/preprocessing/prepare_inputs.py @@ -31,25 +31,25 @@ def preprocess_inputs(adata, gpr_info, task_by_gene, rxn_by_gene, task_by_rxn, c task_by_rxn : pandas.DataFrame DataFrame representing the relationship between tasks and reactions. - correction_organism : str, optional (default='human') + correction_organism : str, optional (default: 'human') Organism of the input data. This is important to correct gene names that are present in scCellFie's or custom database. Check options in `sccellfie.preprocessing.prepare_inputs.CORRECT_GENES.keys()` - gene_fraction_threshold : float, optional (default=0.0) + gene_fraction_threshold : float, optional (default: 0.0) The minimum fraction of genes in a reaction's GPR that must be present in adata to keep the reaction. Range is 0 to 1. 1.0 means all genes must be present. Any value > 0 and < 1 keeps reactions with at least that fraction of genes present. 0 means keep reactions with at least one gene present. - reaction_fraction_threshold : float, optional (default=0.0) + reaction_fraction_threshold : float, optional (default: 0.0) The minimum fraction of reactions in a task that must be present after gene filtering to keep the task. Range is 0 to 1. 1.0 means all reactions must be present. Any value > 0 and < 1 keeps tasks with at least that fraction of reactions present. 0 means keep tasks with at least one reaction present. - verbose : bool, optional (default=True) + verbose : bool, optional (default: True) If True, prints information about the preprocessing results. Returns: @@ -188,10 +188,10 @@ def stratified_subsample_adata(adata, group_column, target_fraction=0.20, random group_column : str Column name in adata.obs containing the group information. - target_fraction : float, optional (default=0.20) + target_fraction : float, optional (default: 0.20) Fraction of cells to sample from each group. - random_state : int, optional (default=0) + random_state : int, optional (default: 0) Random seed for reproducibility. Returns @@ -239,13 +239,13 @@ def normalize_adata(adata, target_sum=10_000, n_counts_key='n_counts', copy=Fals adata : AnnData Annotated data matrix containing the expression data. - target_sum : int, optional (default=10_000) + target_sum : int, optional (default: 10_000) The target sum to which the data will be normalized. - n_counts_key : str, optional (default='n_counts') + n_counts_key : str, optional (default: 'n_counts') The key in adata.obs containing the total counts for each cell. - copy : bool, optional (default=False) + copy : bool, optional (default: False) If True, returns a copy of adata with the normalized data. """ if copy: @@ -303,13 +303,13 @@ def transform_adata_gene_names(adata, filename=None, organism='human', copy=True The file path to a custom CSV file containing Ensembl IDs and gene symbols. One column must be 'ensembl_id' and the other 'symbol'. - organism : str, optional (default='human') + organism : str, optional (default: 'human') The organism to retrieve data for. Choose 'human' or 'mouse'. - copy : bool, optional (default=True) + copy : bool, optional (default: True) If True, return a copy of the AnnData object. If False, modify the object in place. - drop_unmapped : bool, optional (default=False) + drop_unmapped : bool, optional (default: False) If True, drop genes that could not be mapped to symbols. Returns diff --git a/sccellfie/reaction_activity.py b/sccellfie/reaction_activity.py index 0a0bfb1..a2a483c 100644 --- a/sccellfie/reaction_activity.py +++ b/sccellfie/reaction_activity.py @@ -1,4 +1,3 @@ -import cobra import scanpy as sc import numpy as np import pandas as pd @@ -10,7 +9,7 @@ def compute_reaction_activity(adata, gpr_dict, use_specificity=True, layer='gene_scores', disable_pbar=False): - ''' + """ Computes reaction activity from gene scores and GPRs. Parameters @@ -52,7 +51,7 @@ def compute_reaction_activity(adata, gpr_dict, use_specificity=True, layer='gene form of a string, e.g., '(gene1 and gene2) or gene3'. This score is computed as previously indicated in the CellFie paper (https://doi.org/10.1016/j.crmeth.2021.100040). - ''' + """ genes = adata.var_names gene_scores = adata.layers[layer] rxns = gpr_dict.keys() diff --git a/sccellfie/sccellfie_pipeline.py b/sccellfie/sccellfie_pipeline.py index 282cee4..a677cc7 100644 --- a/sccellfie/sccellfie_pipeline.py +++ b/sccellfie/sccellfie_pipeline.py @@ -23,14 +23,14 @@ def run_sccellfie_pipeline(adata, organism='human', sccellfie_data_folder=None, Annotated data matrix containing the expression data and nearest neighbor graph. The .X matrix must contain raw counts. If neighbors are not present, they will be computed. - organism : str, optional (default='human') + organism : str, optional (default: 'human') Organism for the analysis. Options are 'human' or 'mouse'. - sccellfie_data_folder : str, optional (default=None) + sccellfie_data_folder : str, optional (default: None) Path to the folder containing the files of the scCellFie database (reactions, GPR rules, metabolic tasks, etc.). - sccellfie_db : dict, optional (default=None) + sccellfie_db : dict, optional (default: None) Dictionary containing the scCellFie database information. If this information is provided, the sccellfie_data_folder will be ignored. This dictionary must contain the keys 'rxn_info', 'task_by_gene', 'rxn_by_gene', 'task_by_rxn', 'thresholds', and @@ -38,34 +38,34 @@ def run_sccellfie_pipeline(adata, organism='human', sccellfie_data_folder=None, Examples of dataframes can be found at https://github.com/earmingol/scCellFie/raw/refs/heads/main/task_data/homo_sapiens/ - n_counts_col : str, optional (default='n_counts') + n_counts_col : str, optional (default: 'n_counts') Column name in adata.obs containing the total counts per cell. If None or not present, the total counts will be computed. - process_by_group : bool, optional (default=False) + process_by_group : bool, optional (default: False) Whether to process data by groups (e.g., cell types). This is intended to be memory efficient for huge datasets. Results will be not outputted and will be saved to the disk instead. If True, `groupby` must be specified, as well as `save_folder`. - groupby : str, optional (default=None) + groupby : str, optional (default: None) Column name in adata.obs for the groups to process. Required if process_by_group is True. - neighbors_key : str, optional (default='neighbors') + neighbors_key : str, optional (default: 'neighbors') Key in adata.uns for neighbor data. If not present, neighbors will be computed. - n_neighbors : int, optional (default=10) + n_neighbors : int, optional (default: 10) Number of neighbors to find (if `neighbors_key` is not present). This number of neighbors will be used in the KNN smoothing too, if `smooth_cells` is True. - batch_key : str, optional (default=None) + batch_key : str, optional (default: None) Column name in adata.obs for batch information. If present, Harmony will be used to integrate the data before computing neighbors (when neighbors are not present in the AnnData object). - threshold_key : str, optional (default='sccellfie_threshold') + threshold_key : str, optional (default: 'sccellfie_threshold') Key for the threshold to use in gene score computation. This key is present in the threshold file of the scCellFie (or custom) database. - smooth_cells : bool, optional (default=True) + smooth_cells : bool, optional (default: True) Whether to perform a smoothing for the expression values based on the nearest neighbors. If True, KNN smoothing will be performed. @@ -74,14 +74,14 @@ def run_sccellfie_pipeline(adata, organism='human', sccellfie_data_folder=None, The final expression matrix is computed as (1 - alpha) * X + alpha * (S @ X), where X is the original expression matrix and S is the smoothed matrix. - chunk_size : int, optional (default=5000) + chunk_size : int, optional (default: 5000) Size of chunks for smoothing the expression of large datasets. This is used to split the data into smaller parts to reduce memory usage. - disable_pbar : bool, optional (default=False) + disable_pbar : bool, optional (default: False) Whether to disable the progress bar. - save_folder : str, optional (default=None) + save_folder : str, optional (default: None) Folder to save results. The AnnData object is saved to folder/save_filename.h5ad. The scCellFie attributes are saved to: - reactions: folder/save_filename_reactions.h5ad. @@ -89,10 +89,10 @@ def run_sccellfie_pipeline(adata, organism='human', sccellfie_data_folder=None, If process_by_group is True, file names will include cell type name as in save_filename_celltype.h5ad. - save_filename : str, optional (default=None) + save_filename : str, optional (default: None) Filename to save results. If None, the filename will be 'sccellfie'. - verbose : bool, optional (default=True) + verbose : bool, optional (default: True) Whether to print messages during the processing. Returns: @@ -260,16 +260,16 @@ def process_chunk(adata, sccellfie_db, n_counts_col, smooth_cells, alpha, chunk_ organism : str Organism for the analysis. Options are 'human' or 'mouse'. - first_group : bool, optional (default=True) + first_group : bool, optional (default: True) Whether this is the first group to process. - preprocessed_db : dict, optional (default=None) + preprocessed_db : dict, optional (default: None) Dictionary containing the processed data from previous groups. - met_genes : list, optional (default=None) + met_genes : list, optional (default: None) List of genes to filter for subsequent groups. - verbose : bool, optional (default=True) + verbose : bool, optional (default: True) Whether to print messages during the processing. Returns @@ -378,10 +378,10 @@ def compute_neighbors(adata, batch_key, n_neighbors=10, verbose=True): Column name in adata.obs for batch information. This is used for Harmony integration if neighbors are not present. - n_neighbors : int, optional (default=10) + n_neighbors : int, optional (default: 10) Number of neighbors to find. - verbose : bool, optional (default=True) + verbose : bool, optional (default: True) Whether to print messages during the processing. Returns diff --git a/sccellfie/spatial/assortativity.py b/sccellfie/spatial/assortativity.py index 8018d7f..75ec2bc 100644 --- a/sccellfie/spatial/assortativity.py +++ b/sccellfie/spatial/assortativity.py @@ -7,7 +7,7 @@ def compute_var_assortativity(adata, var_name, spatial_network_key='spatial_network', use_raw=False): - ''' + """ Computes the assortativity of a variable (e.g., a gene, a metabolic tasks, etc.) in a spatial network. Parameters @@ -28,7 +28,7 @@ def compute_var_assortativity(adata, var_name, spatial_network_key='spatial_netw ------- assortativity: float The assortativity of the variable in the spatial network. - ''' + """ if spatial_network_key not in adata.uns.keys(): raise ValueError(f'{spatial_network_key} not found in adata.uns. Run sccellfie.spatial.knn_network.create_knn_network() first.') H = adata.uns[spatial_network_key]['graph'].copy() @@ -56,7 +56,7 @@ def compute_var_assortativity(adata, var_name, spatial_network_key='spatial_netw def compute_assortativity(adata, spatial_network_key='spatial_network', use_raw=False): - ''' + """ Computes the assortativity of all variables (e.g., genes, metabolic tasks, etc.) in a spatial network. Parameters @@ -75,7 +75,7 @@ def compute_assortativity(adata, spatial_network_key='spatial_network', use_raw= None A pandas.DataFrame object containing the assortativity of each variable in the spatial network is added to adata.uns['spatial_network']['assortativity']. - ''' + """ records = [] for var_ in tqdm(adata.var_names): assort = compute_var_assortativity(adata, var_name=var_, spatial_network_key=spatial_network_key, use_raw=use_raw) diff --git a/sccellfie/spatial/hotspots.py b/sccellfie/spatial/hotspots.py index 997a9ee..5b1d929 100644 --- a/sccellfie/spatial/hotspots.py +++ b/sccellfie/spatial/hotspots.py @@ -11,8 +11,8 @@ def obtain_hotspots(adata, spatial_key='X_spatial', use_raw=False): - ''' - Obtain hotspots for each variable in adata.var_names. + """ + Obtains hotspots for each variable in adata.var_names. It uses the Getis-Ord Gi* statistic from PySAL. Parameters @@ -30,7 +30,7 @@ def obtain_hotspots(adata, spatial_key='X_spatial', use_raw=False): ------- hotspots: dict A dictionary with variable names as keys and Getis-Ord Gi* statistics as values. - ''' + """ assert spatial_key in adata.obsm.keys(), "obsm_key must be a key in adata.obsm." hotspots = dict() @@ -59,7 +59,7 @@ def obtain_hotspots(adata, spatial_key='X_spatial', use_raw=False): def calculate_aggregate_metric(z_scores, z_threshold=1.96): - ''' + """ Aggregates the Getis-Ord Gi* statistics for a variable. Parameters @@ -86,7 +86,7 @@ def calculate_aggregate_metric(z_scores, z_threshold=1.96): significant_proportion: float The proportion of significant pixels for the variable. - ''' + """ mean_z = np.mean(z_scores) median_z = np.median(z_scores) hotspot_proportion = np.sum(z_scores > z_threshold) / len(z_scores) @@ -96,7 +96,7 @@ def calculate_aggregate_metric(z_scores, z_threshold=1.96): def summarize_hotspots(hotspots, z_threshold=1.96): - ''' + """ Summarizes hotspots for each variable in adata.var_names. It computes the mean, median, and proportion of hotspots, coldspots, and significant pixels. @@ -122,7 +122,7 @@ def summarize_hotspots(hotspots, z_threshold=1.96): Hotspot-Proportion: The proportion of hotspots for the variable. Coldspot-Proportion: The proportion of coldspots for the variable. Significant-Proportion: The proportion of significant pixels for the variable. - ''' + """ records = [] for k, v in hotspots.items(): @@ -137,7 +137,7 @@ def summarize_hotspots(hotspots, z_threshold=1.96): def compute_hotspots(adata, spatial_key='X_spatial', use_raw=False, z_threshold=1.96): - ''' + """ Computes hotspots for each variable in adata.var_names. Hotspots are computed using the Getis-Ord Gi* statistic. @@ -163,7 +163,7 @@ def compute_hotspots(adata, spatial_key='X_spatial', use_raw=False, z_threshold= A pandas.DataFrame object containing the aggregate metrics for each variable in adata.var_names is added to adata.uns['hotspots']['hotspot_df']. - ''' + """ hotspots = obtain_hotspots(adata, spatial_key=spatial_key, use_raw=use_raw) hotspot_df = summarize_hotspots(hotspots, z_threshold=z_threshold) adata.uns['hotspots'] = {'hotspots': hotspots, 'hotspot_df': hotspot_df} \ No newline at end of file diff --git a/sccellfie/spatial/knn_network.py b/sccellfie/spatial/knn_network.py index c2ce504..f7062e2 100644 --- a/sccellfie/spatial/knn_network.py +++ b/sccellfie/spatial/knn_network.py @@ -5,9 +5,8 @@ import networkx as nx - def find_spatial_neighbors(adata, n_neighbors=10, spatial_key='X_spatial'): - ''' + """ Finds the spatial neighbors of each cell in adata. Parameters @@ -26,12 +25,12 @@ def find_spatial_neighbors(adata, n_neighbors=10, spatial_key='X_spatial'): None The spatial neighbors are added to adata.uns['spatial_neighbors'] and the spatial connectivities are added to adata.obsp['spatial_connectivities']. - ''' + """ sq.gr.spatial_neighbors(adata, spatial_key=spatial_key, n_neighs=n_neighbors, key_added='spatial') def create_knn_network(adata, n_neighbors=10, spatial_key='X_spatial', added_key='spatial_network'): - ''' + """ Creates a k-nearest neighbor network from the spatial coordinates in adata.obsm[obsm_key]. Parameters @@ -52,7 +51,7 @@ def create_knn_network(adata, n_neighbors=10, spatial_key='X_spatial', added_key ------- None The k-nearest neighbor network is added to adata.uns['spatial_network']. - ''' + """ if 'spatial_connectivities' not in adata.obsp.keys(): warnings.warn('spatial_connectivities not found in adata.uns. Creating spatial_neighbors.') sq.gr.spatial_neighbors(adata, spatial_key=spatial_key, n_neighs=n_neighbors, key_added='spatial') diff --git a/sccellfie/stats/markers_from_task.py b/sccellfie/stats/markers_from_task.py index cc02bed..48fe705 100644 --- a/sccellfie/stats/markers_from_task.py +++ b/sccellfie/stats/markers_from_task.py @@ -3,7 +3,7 @@ def get_task_determinant_genes(adata, metabolic_task, task_by_rxn, groupby=None, group=None, min_activity=0.0): - ''' + """ Finds the genes that determine the activity of all reactions in a metabolic task. Returns determinant genes for each reaction and their activity across specified cell groups. If no groups are specified, the analysis is performed across all cells. @@ -53,7 +53,7 @@ def get_task_determinant_genes(adata, metabolic_task, task_by_rxn, groupby=None, sccellfie.reaction_activity.compute_reaction_activity() and are stored in adata.reactions.X. Scores are computed as previously indicated in the CellFie paper (https://doi.org/10.1016/j.crmeth.2021.100040). - ''' + """ assert hasattr(adata, "metabolic_tasks"), "Please run scCellFie on your dataset before using this function." # Get list of rxns that belong to the metabolic task From f43968380b698f529ed3f137154ff81faa7247e7 Mon Sep 17 00:00:00 2001 From: Erick Armingol Date: Mon, 21 Oct 2024 15:56:19 +0100 Subject: [PATCH 14/18] Added one-command quickstart --- README.rst | 65 +++++++++++++++++++++++++++++++++++++++++++++++++++++- 1 file changed, 64 insertions(+), 1 deletion(-) diff --git a/README.rst b/README.rst index e1bd3e0..7f09ad0 100644 --- a/README.rst +++ b/README.rst @@ -12,7 +12,22 @@ .. |Downloads| image:: https://pepy.tech/badge/sccellfie/month :target: https://pepy.tech/project/sccellfie - +.. role:: graycode + :class: highlight-gray + +.. raw:: html + + Metabolic activity from single-cell and spatial transcriptomics with scCellFie ----------------------------------------------------------------------------------------- @@ -54,6 +69,54 @@ Features - **Organisms:** Metabolic database and analysis available for human and mouse. +Quick start +----------- +A quick example of how to use scCellFie with a single-cell dataset and generate results:: + + import sccellfie + import scanpy as sc + + # Load the dataset + adata = sc.read(filename='BALF-COVID19.h5ad', + backup_url='https://zenodo.org/record/7535867/files/BALF-COVID19-Liao_et_al-NatMed-2020.h5ad') + + # Run one-command scCellFie pipeline + results = sccellfie.run_sccellfie_pipeline(adata, + organism='human', + sccellfie_data_folder=None, + n_counts_col='n_counts', + process_by_group=False, + groupby=None, + neighbors_key='neighbors', + n_neighbors=10, + batch_key='sample', + threshold_key='sccellfie_threshold', + smooth_cells=True, + alpha=0.33, + chunk_size=5000, + disable_pbar=False, + save_folder=None, + save_filename=None + ) + +This will produce a dictionary with the results of the analysis. The keys of the dictionary includes the +single-cell data and metabolic activities (:graycode:`'adata'`) and the scCellFie database already filtered for the elements present +in the dataset (:graycode:`'gpr_rules'`, :graycode:`'task_by_gene'`, :graycode:`'rxn_by_gene'`, :graycode:`'task_by_rxn'`, :graycode:`'rxn_info'`, :graycode:`'task_info'`, :graycode:`'thresholds'`, :graycode:`'organism'`). + +To access metabolic activities, we need to inspect :graycode:`results['adata']`: + +- The processed single-cell data is located in the AnnData object :graycode:`results['adata']`. +- The reaction activities for each cell are located in the AnnData object :graycode:`results['adata'].reactions`. +- The metabolic task activities for each cell are located in the AnnData object :graycode:`results['adata'].metabolic_tasks`. + +In particular: + +- :graycode:`results['adata']`: contains gene expression in :graycode:`.X`. +- :graycode:`results['adata'].layers['gene_scores']`: contains gene scores as in the original CellFie paper. +- :graycode:`results['adata'].uns['Rxn-Max-Genes']`: contains determinant genes for each reaction per cell. +- :graycode:`results['adata'].reactions`: contains reaction scores in :graycode:`.X` so every scanpy function can be used on this object to visualize or compare values. +- :graycode:`results['adata'].metabolic_tasks`: contains metabolic task scores in :graycode:`.X` so every scanpy function can be used on this object to visualize or compare values. + How to cite ----------- From 57d7f2c6d705b62deceaf2fcc1ac1fd180cd091a Mon Sep 17 00:00:00 2001 From: Erick Armingol Date: Mon, 21 Oct 2024 15:59:09 +0100 Subject: [PATCH 15/18] Added one-command quickstart --- README.rst | 39 +++++++++++---------------------------- 1 file changed, 11 insertions(+), 28 deletions(-) diff --git a/README.rst b/README.rst index 7f09ad0..026dd3e 100644 --- a/README.rst +++ b/README.rst @@ -12,22 +12,6 @@ .. |Downloads| image:: https://pepy.tech/badge/sccellfie/month :target: https://pepy.tech/project/sccellfie -.. role:: graycode - :class: highlight-gray - -.. raw:: html - - Metabolic activity from single-cell and spatial transcriptomics with scCellFie ----------------------------------------------------------------------------------------- @@ -100,23 +84,22 @@ A quick example of how to use scCellFie with a single-cell dataset and generate ) This will produce a dictionary with the results of the analysis. The keys of the dictionary includes the -single-cell data and metabolic activities (:graycode:`'adata'`) and the scCellFie database already filtered for the elements present -in the dataset (:graycode:`'gpr_rules'`, :graycode:`'task_by_gene'`, :graycode:`'rxn_by_gene'`, :graycode:`'task_by_rxn'`, :graycode:`'rxn_info'`, :graycode:`'task_info'`, :graycode:`'thresholds'`, :graycode:`'organism'`). +single-cell data and metabolic activities (`'adata'`) and the scCellFie database already filtered for the elements present +in the dataset (`'gpr_rules'`, `'task_by_gene'`, `'rxn_by_gene'`, `'task_by_rxn'`, `'rxn_info'`, `'task_info'`, `'thresholds'`, `'organism'`). -To access metabolic activities, we need to inspect :graycode:`results['adata']`: +To access metabolic activities, we need to inspect `results['adata']`: -- The processed single-cell data is located in the AnnData object :graycode:`results['adata']`. -- The reaction activities for each cell are located in the AnnData object :graycode:`results['adata'].reactions`. -- The metabolic task activities for each cell are located in the AnnData object :graycode:`results['adata'].metabolic_tasks`. +- The processed single-cell data is located in the AnnData object `results['adata']`. +- The reaction activities for each cell are located in the AnnData object `results['adata'].reactions`. +- The metabolic task activities for each cell are located in the AnnData object `results['adata'].metabolic_tasks`. In particular: -- :graycode:`results['adata']`: contains gene expression in :graycode:`.X`. -- :graycode:`results['adata'].layers['gene_scores']`: contains gene scores as in the original CellFie paper. -- :graycode:`results['adata'].uns['Rxn-Max-Genes']`: contains determinant genes for each reaction per cell. -- :graycode:`results['adata'].reactions`: contains reaction scores in :graycode:`.X` so every scanpy function can be used on this object to visualize or compare values. -- :graycode:`results['adata'].metabolic_tasks`: contains metabolic task scores in :graycode:`.X` so every scanpy function can be used on this object to visualize or compare values. - +- `results['adata']`: contains gene expression in `.X`. +- `results['adata'].layers['gene_scores']`: contains gene scores as in the original CellFie paper. +- `results['adata'].uns['Rxn-Max-Genes']`: contains determinant genes for each reaction per cell. +- `results['adata'].reactions`: contains reaction scores in `.X` so every scanpy function can be used on this object to visualize or compare values. +- `results['adata'].metabolic_tasks`: contains metabolic task scores in `.X` so every scanpy function can be used on this object to visualize or compare values. How to cite ----------- From e3a4c6fbb8aecaaf45502f75ba655f0fbd6cd405 Mon Sep 17 00:00:00 2001 From: Erick Armingol Date: Mon, 21 Oct 2024 16:01:09 +0100 Subject: [PATCH 16/18] Added one-command quickstart --- README.rst | 1 + 1 file changed, 1 insertion(+) diff --git a/README.rst b/README.rst index 026dd3e..fc21dde 100644 --- a/README.rst +++ b/README.rst @@ -100,6 +100,7 @@ In particular: - `results['adata'].uns['Rxn-Max-Genes']`: contains determinant genes for each reaction per cell. - `results['adata'].reactions`: contains reaction scores in `.X` so every scanpy function can be used on this object to visualize or compare values. - `results['adata'].metabolic_tasks`: contains metabolic task scores in `.X` so every scanpy function can be used on this object to visualize or compare values. + How to cite ----------- From 84f44d673fd765a33ed432c62b3c5558945e8872 Mon Sep 17 00:00:00 2001 From: Erick Armingol Date: Mon, 21 Oct 2024 16:03:18 +0100 Subject: [PATCH 17/18] Added one-command quickstart --- README.rst | 7 +++---- 1 file changed, 3 insertions(+), 4 deletions(-) diff --git a/README.rst b/README.rst index fc21dde..fa6b412 100644 --- a/README.rst +++ b/README.rst @@ -83,10 +83,6 @@ A quick example of how to use scCellFie with a single-cell dataset and generate save_filename=None ) -This will produce a dictionary with the results of the analysis. The keys of the dictionary includes the -single-cell data and metabolic activities (`'adata'`) and the scCellFie database already filtered for the elements present -in the dataset (`'gpr_rules'`, `'task_by_gene'`, `'rxn_by_gene'`, `'task_by_rxn'`, `'rxn_info'`, `'task_info'`, `'thresholds'`, `'organism'`). - To access metabolic activities, we need to inspect `results['adata']`: - The processed single-cell data is located in the AnnData object `results['adata']`. @@ -101,6 +97,9 @@ In particular: - `results['adata'].reactions`: contains reaction scores in `.X` so every scanpy function can be used on this object to visualize or compare values. - `results['adata'].metabolic_tasks`: contains metabolic task scores in `.X` so every scanpy function can be used on this object to visualize or compare values. +Other keys in the `results` dictionary are associated with the scCellFie database and are already filtered for the elements present +in the dataset (`'gpr_rules'`, `'task_by_gene'`, `'rxn_by_gene'`, `'task_by_rxn'`, `'rxn_info'`, `'task_info'`, `'thresholds'`, `'organism'`). + How to cite ----------- From 728952f23713c0a68ba153437d47fa37598f8eb8 Mon Sep 17 00:00:00 2001 From: Erick Armingol Date: Mon, 21 Oct 2024 16:12:25 +0100 Subject: [PATCH 18/18] Set default xticklabels --- sccellfie/plotting/distributions.py | 7 +++++-- 1 file changed, 5 insertions(+), 2 deletions(-) diff --git a/sccellfie/plotting/distributions.py b/sccellfie/plotting/distributions.py index 2d0b473..d4796d0 100644 --- a/sccellfie/plotting/distributions.py +++ b/sccellfie/plotting/distributions.py @@ -2,7 +2,7 @@ import matplotlib.pyplot as plt -def create_multi_violin_plots(adata, genes, groupby, n_cols=4, figsize=(5, 5), ylabel='Metabolic Activity', fontsize=10, save=None, dpi=300, **kwargs): +def create_multi_violin_plots(adata, genes, groupby, n_cols=4, figsize=(5, 5), ylabel='Metabolic Activity', fontsize=10, rotation=90, save=None, dpi=300, **kwargs): """ Plots a grid of violin plots for multiple genes in Scanpy, controlling the number of columns. @@ -33,6 +33,9 @@ def create_multi_violin_plots(adata, genes, groupby, n_cols=4, figsize=(5, 5), y be set to `fontsize`, while the title will be set to `fontsize + 4`. Ylabel will be set to `fontsize + 2`. + rotation : int, optional (default: 90) + Rotation of the x-axis tick labels + save : str, optional (default: None) Filepath to save the figure. If not provided, the figure will be displayed. @@ -56,7 +59,7 @@ def create_multi_violin_plots(adata, genes, groupby, n_cols=4, figsize=(5, 5), y col = i % n_cols ax = axes[row, col] - sc.pl.violin(adata, keys=gene, groupby=groupby, ax=ax, show=False, **kwargs) + sc.pl.violin(adata, keys=gene, groupby=groupby, ax=ax, show=False, rotation=rotation, **kwargs) ax.set_title(gene, fontsize=fontsize + 4) ax.set_ylabel(ylabel, fontsize=fontsize + 2) ax.tick_params(axis='x', labelsize=fontsize)