-
Notifications
You must be signed in to change notification settings - Fork 0
/
Copy pathDMD_brainSpan_exons.m
553 lines (516 loc) · 22.8 KB
/
DMD_brainSpan_exons.m
1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
44
45
46
47
48
49
50
51
52
53
54
55
56
57
58
59
60
61
62
63
64
65
66
67
68
69
70
71
72
73
74
75
76
77
78
79
80
81
82
83
84
85
86
87
88
89
90
91
92
93
94
95
96
97
98
99
100
101
102
103
104
105
106
107
108
109
110
111
112
113
114
115
116
117
118
119
120
121
122
123
124
125
126
127
128
129
130
131
132
133
134
135
136
137
138
139
140
141
142
143
144
145
146
147
148
149
150
151
152
153
154
155
156
157
158
159
160
161
162
163
164
165
166
167
168
169
170
171
172
173
174
175
176
177
178
179
180
181
182
183
184
185
186
187
188
189
190
191
192
193
194
195
196
197
198
199
200
201
202
203
204
205
206
207
208
209
210
211
212
213
214
215
216
217
218
219
220
221
222
223
224
225
226
227
228
229
230
231
232
233
234
235
236
237
238
239
240
241
242
243
244
245
246
247
248
249
250
251
252
253
254
255
256
257
258
259
260
261
262
263
264
265
266
267
268
269
270
271
272
273
274
275
276
277
278
279
280
281
282
283
284
285
286
287
288
289
290
291
292
293
294
295
296
297
298
299
300
301
302
303
304
305
306
307
308
309
310
311
312
313
314
315
316
317
318
319
320
321
322
323
324
325
326
327
328
329
330
331
332
333
334
335
336
337
338
339
340
341
342
343
344
345
346
347
348
349
350
351
352
353
354
355
356
357
358
359
360
361
362
363
364
365
366
367
368
369
370
371
372
373
374
375
376
377
378
379
380
381
382
383
384
385
386
387
388
389
390
391
392
393
394
395
396
397
398
399
400
401
402
403
404
405
406
407
408
409
410
411
412
413
414
415
416
417
418
419
420
421
422
423
424
425
426
427
428
429
430
431
432
433
434
435
436
437
438
439
440
441
442
443
444
445
446
447
448
449
450
451
452
453
454
455
456
457
458
459
460
461
462
463
464
465
466
467
468
469
470
471
472
473
474
475
476
477
478
479
480
481
482
483
484
485
486
487
488
489
490
491
492
493
494
495
496
497
498
499
500
501
502
503
504
505
506
507
508
509
510
511
512
513
514
515
516
517
518
519
520
521
522
523
524
525
526
527
528
529
530
531
532
533
534
535
536
537
538
539
540
541
542
543
544
545
546
%%% 13 Jan 2015
%%% Read the exon expression data of DMD
%% Define directories
if ispc
atlasDir = 'C:/Users/amahfouz/SURFdrive/Projects/DMD/Data/ALLEN BRAIN ATLASES/exons_matrix_csv/';
dataDir = 'C:/Users/amahfouz/SURFdrive/Projects/DMD/Data/';
end
%% read data
dmdGene = 'DMD';
% read rows meta data
[num,txt] = xlsread([atlasDir 'rows_metadata.xlsx']);
transcript.gene_symbol = txt(2:end,4);
transcript.ensembl_gene_id = txt(2:end,3);
transcript.entrez_id = num(:,5);
transcript.start = num(:,6);
transcript.end = num(:,7);
clear num; clear txt;
save([dataDir 'transcript.mat'],'transcript');
% read columns meta data
[num,txt] = xlsread([atlasDir 'columns_metadata.xlsx']);
sample.donor_id = num(:,2);
sample.donor_name = txt(2:end,3);
sample.age = txt(2:end,4);
sample.gender = txt(2:end,5);
sample.structure_acronym = txt(2:end,7);
clear num; clear txt;
save([dataDir 'exon_sample.mat'],'sample');
% select only DMD data
gene_idx = find(strcmpi(transcript.gene_symbol,dmdGene));
data = csvread([atlasDir 'expression_matrix.csv']);
dmd_data = data(gene_idx,2:end);
clear data;
save([dataDir 'dmd_exon_data.mat'],'dmd_data','gene_idx');
%% load data
load([dataDir 'dmd_exon_data.mat']);
load([dataDir 'transcript.mat']);
load([dataDir 'exon_sample.mat']);
%% save data to xlsx
xlswrite([dataDir 'dmd_exon_data.xlsx'], sample.donor_name', 1, 'C1');
xlswrite([dataDir 'dmd_exon_data.xlsx'], sample.gender', 1, 'C2');
xlswrite([dataDir 'dmd_exon_data.xlsx'], sample.age', 1, 'C3');
xlswrite([dataDir 'dmd_exon_data.xlsx'], sample.structure_acronym', 1, 'C4');
xlswrite([dataDir 'dmd_exon_data.xlsx'], dmd_data, 1, 'C5');
transcript_info(1,:) = transcript.start(gene_idx);
transcript_info(2,:) = transcript.end(gene_idx);
xlswrite([dataDir 'dmd_exon_data.xlsx'], transcript_info', 1, 'A5');
xlswrite([dataDir 'dmd_exon_data.xlsx'], [{'transcript_start'},{'transcript_end'}], 1, 'A4');
%% developmental stages
devStages = {'8 pcw','9 pcw','12 pcw',... % early fetal
'13 pcw','16 pcw','17 pcw',... % early-mid fetal
'19 pcw','21 pcw',... % late-mid fetal
'24 pcw','25 pcw','26 pcw','35 pcw','37 pcw',... % late fetal
'4 mos',... % Neonatal & early enfancy
'10 mos',... % late enfancy
'1 yrs','2 yrs','3 yrs','4 yrs',... % early childhood
'8 yrs','11 yrs',... % middle & late childhood
'13 yrs','15 yrs','18 yrs','19 yrs',... % adolescence
'21 yrs','23 yrs','30 yrs','36 yrs','37 yrs',... % young adulthood
'40 yrs'}; % middle adulthood
devStagesNum = [1,1,1,2,2,2,3,3,4,4,4,4,4,5,6,7,7,7,7,8,8,9,9,9,9,10,10,10,10,10,...
11];
devStagesName = {'early_fetal','early_fetal','early_fetal',...
'early_mid_fetal','early_mid_fetal','early_mid_fetal',...
'late_mid_fetal','late_mid_fetal',...
'late_fetal','late_fetal','late_fetal','late_fetal','late_fetal',...
'Neonatal/early_enfancy',...
'late_enfancy',...
'early_childhood','early_childhood','early_childhood','early_childhood',...
'middle/late_childhood','middle/late_childhood',...
'adolescence','adolescence','adolescence','adolescence',...
'young_adulthood','young_adulthood','young_adulthood','young_adulthood','young_adulthood',...
'middle_adulthood'};
%% select transcripts of each isoform
transcript_ranges = [31150000,31300000; 31600000,32000000; 32200000,33000000];
for i = 1 : size(transcript_ranges,1)
% find transcripts within the curent range
R1 = find(transcript.start(gene_idx) > transcript_ranges(i,1));
R2 = find(transcript.end(gene_idx) < transcript_ranges(i,2));
isoform_transcripts{i} = intersect(R1,R2);
trans_exp(i,:) = mean(dmd_data(isoform_transcripts{i},:));
L{i} = ['exons: ' num2str(transcript_ranges(i,1)) '-' num2str(transcript_ranges(i,2))];
clear R1; clear R2;
end
%% plot the average expression of exon groups
C = [1,0,0;0,1,0;0,0,1];
for i = 1 : length(devStages)
xTicks(i) = find(ismember(sample.age, devStages{i})==1, 1, 'first');
end
figure, hold on
for i = 1 : length(isoform_transcripts)
plot(trans_exp(i,:),'color',C(i,:),'linewidth',2);
end
hold off
grid on
ylabel('Expression (RPKM)', 'FontWeight', 'bold', 'FontSize', 15);
set(gca, 'XTickLabel', devStages, 'XTick', xTicks, 'xlim', [0 size(trans_exp,2)]);
rotateXLabels(gca, 45)
legend(L);
%% plot an image of the probe
% create sample labels
for i = 1 : length(sample.age)
sampleLabel{i} = [sample.structure_acronym{i} ' _ ' sample.age{i}];
end
for i = 1 : size(dmd_data,1)
transcriptLabel{i} = [num2str(i) ':' num2str(transcript.start(gene_idx(i))) ' - ' num2str(transcript.end(gene_idx(i)))];
end
for i = 1 : length(devStages)
xTicks(i) = find(ismember(sample.age, devStages{i})==1, 1, 'first');
end
% figure,
% imagesc(log10(dmd_data+1)), colormap('hot'), colorbar
% set(gca, 'XTickLabel', sampleLabel, 'XTick', 1:numel(sampleLabel));
% set(gca, 'YTickLabel', transcriptLabel, 'YTick', 1:numel(transcriptLabel));
% rotateXLabels(gca, 45)
figure,
imagesc(fliplr(log10(dmd_data+1)')), colormap('hot'), colorbar
set(gca, 'XTickLabel', fliplr(transcriptLabel), 'XTick', 1:numel(transcriptLabel));
set(gca, 'YTickLabel', devStages, 'YTick', xTicks);
% for i = 1 : length(isoform_transcripts)
% line([size(dmd_data,1)-isoform_transcripts{i}(end) size(dmd_data,1)-isoform_transcripts{i}(end)],...
% [0 524], 'Color', 'w', 'LineWidth', 5);
% end
% XYrotalabel
% set(gca, 'YTickLabel', sample.age, 'YTick', 1:numel(sampleLabel), 'FontSize', 5);
rotateXLabels(gca, 45)
figure,
boxplot(fliplr(log2(dmd_data+1)'))
ylabel('Expression (RPKM)', 'FontWeight', 'bold', 'FontSize', 15)
set(gca, 'XTickLabel', fliplr(1:length(transcriptLabel)), 'XTick', 1:numel(transcriptLabel));
for i = 1 : length(isoform_transcripts)
line([size(dmd_data,1)-isoform_transcripts{i}(end) size(dmd_data,1)-isoform_transcripts{i}(end)],...
[0 524], 'Color', 'black', 'LineWidth', 5);
end
% ylim([-0.1 6])
XYrotalabel
rotateXLabels(gca, 45)
%% exclude some exons
exon_exclude = [92,91,89,88,87,46,40,22];
dmd_data_updated = dmd_data;
dmd_data_updated(exon_exclude,:) = [];
transcriptLabel_updated = transcriptLabel;
transcriptLabel_updated(exon_exclude) = [];
custom_map = csvread('redblue_256_rgb.txt');
custom_map = custom_map / 255;
custom_map = flipud(custom_map);
figure,
imagesc(fliplr(log2(dmd_data_updated+1)')), colormap(custom_map), colorbar
% imagesc(fliplr(dmd_data_updated')), colormap(custom_map), colorbar
X = fliplr(log10(dmd_data_updated+1)');
hold on;
% for i = 1:size(X,1)
% plot([.5,size(X,2)+.5],[i-.5,i-.5],'k-');
% end
for i = 1:size(X,2)
plot([i-.5,i-.5],[.5,size(X,1)+.5],'k-');
end
hold off
set(gca, 'XTickLabel', fliplr(transcriptLabel_updated), 'XTick', 1:numel(transcriptLabel_updated));
set(gca, 'YTickLabel', devStages, 'YTick', xTicks);
rotateXLabels(gca, 45)
%% probe selection
exon_select = [19,41,86];
dmd_sub = dmd_data(exon_select,:);
xlswrite('individual_exons.xlsx', dmd_sub, 1, 'B4')
xlswrite('individual_exons.xlsx', sample.donor_name', 1, 'B1');
xlswrite('individual_exons.xlsx', sample.age', 1, 'B2');
xlswrite('individual_exons.xlsx', sample.structure_acronym', 1, 'B3');
xlswrite('individual_exons.xlsx', [{'Name'},{'Age'},{'Structure'},...
{'probe#19'},{'probe#41'},{'probe#86'}]', 1, 'A1');
%% Plot the expression of selected exons across development for different structures
exon_select = [19,41,86];
dmd_sub = dmd_data(exon_select,:);
% dmd_sub = log2(sum(dmd_data)+1);
isoforms = {'Dp71-Dp40', 'Dp140', 'Dp427'};
figure, hold on
% cortex
subplot(2,2,1), plot(dmd_sub(:,ismember(sample.structure_acronym,{'VFC','DFC','ITC','STC','MFC','OFC','M1C','IPC','A1C','V1C','S1C'}))')
legend(isoforms)
% cerebellum
subplot(2,2,2), plot(dmd_sub(:,ismember(sample.structure_acronym,{'CB','CBC'}))')
legend(isoforms)
% hippocampus
subplot(2,2,3), plot(dmd_sub(:,ismember(sample.structure_acronym,{'HIP'}))')
legend(isoforms)
% Amygdala
subplot(2,2,4), plot(dmd_sub(:,ismember(sample.structure_acronym,{'AMY'}))')
legend(isoforms)
hold off
figure, plot(sum(dmd_data))
%% cluster the DMD transcripts
% clustergram((log10(dmd_data+1)'))
%% group ages into developmental stages and define structures
% assign developmental stage label to each sample
for i = 1 : length(sample.age)
age_idx = find(strcmpi(devStages,sample.age{i})==1);
devStageLabel(i) = devStagesNum(age_idx);
devStageLabel_name{i} = devStagesName{age_idx};
end
structures = {'AMY','HIP','STR','MD','CBC',...
'VFC','DFC','ITC','STC','MFC','OFC','M1C','IPC','A1C','V1C','S1C'};
%% plot different transcripts across age for different stuctures
strLabelsModified = sample.structure_acronym;
strLabelsModified(find(ismember(sample.structure_acronym,structures(6:end))==1)) = {'CTX'};
strOfInterest = find(ismember(sample.structure_acronym,structures)==1);
for i = 1 : length(isoform_transcripts)
figure,
boxplot(nanmean(dmd_data(isoform_transcripts{i},strOfInterest)), ...
{strLabelsModified(strOfInterest),devStageLabel_name(strOfInterest)}, ...
'colorgroup',strLabelsModified(strOfInterest), 'factorgap',5, ...
'factorseparator',1, 'labelorientation', 'inline', 'plotstyle', 'compact')
grid on
ylabel('Expression (RPKM)', 'FontWeight', 'bold', 'FontSize', 15)
ylim([0 20])
title(['Probes: ' num2str(transcript_ranges(i,1)) ' - ' num2str(transcript_ranges(i,2))],...
'FontWeight', 'bold', 'FontSize', 15);
figure,
boxplot(nanmean(dmd_data(isoform_transcripts{i},strOfInterest)), ...
{devStageLabel_name(strOfInterest),strLabelsModified(strOfInterest)}, ...
'colorgroup',strLabelsModified(strOfInterest), 'factorgap',5, ...
'factorseparator',1, 'labelorientation', 'inline', 'plotstyle', 'compact')
grid on
ylabel('Expression (RPKM)', 'FontWeight', 'bold', 'FontSize', 15)
ylim([0 20])
title(['Probes: ' num2str(transcript_ranges(i,1)) ' - ' num2str(transcript_ranges(i,2))],...
'FontWeight', 'bold', 'FontSize', 15);
end
% plot the expression across cortical structures
strOfInterest = find(ismember(sample.structure_acronym,structures(6:end))==1);
for i = 1 : length(isoform_transcripts)
figure,
% boxplot(nanmean(dmd_data(isoform_transcripts{i},strOfInterest)), ...
% {sample.structure_acronym(strOfInterest),devStageLabel_name(strOfInterest)}, ...
% 'colorgroup',sample.structure_acronym(strOfInterest), 'factorgap',5, ...
% 'factorseparator',1, 'labelorientation', 'inline')
boxplot(nanmean(dmd_data(isoform_transcripts{i},strOfInterest)), ...
{devStageLabel_name(strOfInterest),sample.structure_acronym(strOfInterest)}, ...
'colorgroup',sample.structure_acronym(strOfInterest), 'factorgap',5, ...
'factorseparator',1, 'labelorientation', 'inline')
grid on
ylabel('Expression (RPKM)', 'FontWeight', 'bold', 'FontSize', 15)
ylim([0 20])
title(['Probes: ' num2str(transcript_ranges(i,1)) ' - ' num2str(transcript_ranges(i,2))],...
'FontWeight', 'bold', 'FontSize', 15);
end
%% OLD plot different transcripts across age for different stuctures
structures = {'AMY','HIP','STR','MD','CBC',...
'VFC','DFC','ITC','STC','MFC','OFC','M1C','IPC','A1C','V1C','S1C'};
ages = {'12 pcw','13 pcw','16 pcw','17 pcw','19 pcw','21 pcw','24 pcw','37 pcw',...
'4 mos','1 yrs','2 yrs','3 yrs','4 yrs','8 yrs','11 yrs','13 yrs','18 yrs',...
'19 yrs','21 yrs','23 yrs','30 yrs','36 yrs','37 yrs','40 yrs'};
% ages = unique(sample.age);
for i = 1 : length(structures)
str_samples = find(strcmpi(sample.structure_acronym,structures{i})==1);
for j = 1 : length(ages)
str_age_samples = find(strcmpi(sample.age(str_samples),ages{j})==1);
if isempty(str_age_samples)
dmd_data_reshaped(:,i,j) = NaN;
else
dmd_data_reshaped(:,i,j) = nanmean(dmd_data(:,str_samples(str_age_samples)),2);
end
end
end
% average the cortical samples
dmd_ctx = squeeze(nanmean(dmd_data_reshaped(:,6:end,:),2));
% colors = jet(length(structures));
colors = lines(6);
for i = 1 : length(isoform_transcripts)
figure, hold on
for j = 1 : 5
plot(nanmean(squeeze(dmd_data_reshaped(isoform_transcripts{i},j,:)))', ...
'LineWidth', 2, 'Color', colors(j,:))
end
plot(nanmean(dmd_ctx(isoform_transcripts{i},:)), ...
'LineWidth', 2, 'Color', colors(6,:))
hold off
grid on
legend([structures(1:5) 'CTX'])
set(gca, 'XTickLabel', ages, 'XTick', 1:numel(ages), 'FontWeight', 'bold');
ylim([0 18])
ylabel('Expression (RPKM)', 'FontWeight', 'bold', 'FontSize', 15)
title(['Probes: ' num2str(transcript_ranges(i,1)) ' - ' num2str(transcript_ranges(i,2))],...
'FontWeight', 'bold', 'FontSize', 15);
end
%% plot the expression of each isofom's transcripts
for i = 1 : 3
figure, plot(dmd_data(isoform_transcripts{i},:)');
end
%% co-expression analysis
dataDir = '/tudelft.net/staff-bulk/ewi/insy/DBL/amahfouz/MATLAB/Data/exons_matrix_csv/';
resDir = '/tudelft.net/staff-bulk/ewi/insy/DBL/amahfouz/MATLAB/Results/DMD/';
geneName = 'DMD';
% read probe info
T = readtable([dataDir 'rows_metadata.xlsx']);
transcript.gene_symbol = T.gene_symbol;
transcript.entrez_id = T.entrez_id;
transcript.start = T.start;
transcript.end = T.xEnd;
clear T;
% remove pobes with no entrez_id
removedProbes = find(isnan(transcript.entrez_id));
transcript.gene_symbol(removedProbes) = [];
transcript.entrez_id(removedProbes) = [];
transcript.start(removedProbes) = [];
transcript.end(removedProbes) = [];
gene_idx = find(strcmpi(transcript.gene_symbol,geneName));
% read expression data
data = csvread([dataDir 'expression_matrix.csv']);
data(removedProbes,:) = [];
data(:,1) = [];
% create expression profile of isoforms
transcript_ranges = [31150000,31300000; 31600000,32000000; 32200000,33000000];
for i = 1 : size(transcript_ranges,1)
% find transcripts within the curent range
R1 = find(transcript.start(gene_idx) > transcript_ranges(i,1));
R2 = find(transcript.end(gene_idx) < transcript_ranges(i,2));
isoform_transcripts{i} = intersect(R1,R2);
clear R1; clear R2;
end
trans1_exp = mean(data(gene_idx(isoform_transcripts{1}),:));
trans2_exp = mean(data(gene_idx(isoform_transcripts{2}),:));
trans3_exp = mean(data(gene_idx(isoform_transcripts{3}),:));
% calculate the correlation
[corrMat pVal] = corr([trans1_exp;trans2_exp;trans3_exp]', data');
save([resDir 'corrMat_exonArray.mat'],'corrMat','pVal','transcript');
%% coexpression of individual exons
exon_select = [19,41,86];
dataDir = '/tudelft.net/staff-bulk/ewi/insy/DBL/amahfouz/MATLAB/Data/exons_matrix_csv/';
resDir = '/tudelft.net/staff-bulk/ewi/insy/DBL/amahfouz/MATLAB/Results/DMD/';
geneName = 'DMD';
% read probe info
T = readtable([dataDir 'rows_metadata.xlsx']);
transcript.gene_symbol = T.gene_symbol;
transcript.entrez_id = T.entrez_id;
transcript.start = T.start;
transcript.end = T.xEnd;
clear T;
% remove pobes with no entrez_id
removedProbes = find(isnan(transcript.entrez_id));
transcript.gene_symbol(removedProbes) = [];
transcript.entrez_id(removedProbes) = [];
transcript.start(removedProbes) = [];
transcript.end(removedProbes) = [];
gene_idx = find(strcmpi(transcript.gene_symbol,geneName));
% read expression data
data = csvread([dataDir 'expression_matrix.csv']);
data(removedProbes,:) = [];
data(:,1) = [];
% log-transform the data
data = log2(data+1);
% create expression profile of isoforms
trans1_exp = (data(gene_idx(exon_select(1)),:));
trans2_exp = (data(gene_idx(exon_select(2)),:));
trans3_exp = (data(gene_idx(exon_select(3)),:));
% calculate the correlation
[corrMat pVal] = corr([trans1_exp;trans2_exp;trans3_exp]', data');
save([resDir 'corrMat_exonArray_individual_exons_log2.mat'],'corrMat','pVal','transcript');
%% Analyze the combined donor correlation list
geneName = 'DMD';
transcript_ranges = [31150000,31300000; 31600000,32000000; 32200000,33000000];
dataDir = 'C:/Users/amahfouz/SURFdrive/Projects/DMD/Data/';
resultsDir = 'C:/Users/amahfouz/SURFdrive/Projects/DMD/Results/';
% load([dataDir 'corrMat_exonArray.mat']);
load([dataDir 'corrMat_exonArray_individual_exons_log2.mat']);
removedRows = logical(prod(double(isnan(corrMat))));
corrMat(:,removedRows) = [];
transcript.gene_symbol(removedRows) = [];
transcript.entrez_id(removedRows) = [];
transcript.start(removedRows) = [];
transcript.end(removedRows) = [];
pVal(:,removedRows) = [];
% f = figure; hold on
for i = 1 : size(corrMat,1)
% sort the data
[sortedCorrMat IX] = sort(corrMat(i,:),2,'descend');
rankedGenes = transcript.gene_symbol(IX);
[b,m,~] = unique(rankedGenes, 'stable');
[~,IX2] = sort(m);
sortedG = b(IX2);
sortedCorr = sortedCorrMat(m(IX2));
sortedPval = pVal(i,IX);
sortedPval = sortedPval(m(IX2));
sotredEntrez = transcript.entrez_id(IX);
sotredEntrez = sotredEntrez(m(IX2));
% save to excel
xlswrite([resultsDir geneName '_exonArray_coexpressed_genes_individual_exons_log2.xlsx'], sortedG(2:end), i, 'A1');
xlswrite([resultsDir geneName '_exonArray_coexpressed_genes_individual_exons_log2.xlsx'], sotredEntrez(2:end), i, 'B1');
xlswrite([resultsDir geneName '_exonArray_coexpressed_genes_individual_exons_log2.xlsx'], sortedCorr(2:end)', i, 'C1');
clear IXl clear IX2; clear b; clear m;
% % flip the list for negaive correlations
% [sortedCorrMat IX] = sort(corrMat(i,:),2);
% rankedGenes = transcript.gene_symbol(IX);
% [b,m,~] = unique(rankedGenes, 'first');
% [~,IX2] = sort(m);
% sortedG = b(IX2);
% sortedCorr = sortedCorrMat(m(IX2));
% sotredEntrez = transcript.entrez_id(IX);
% sotredEntrez = sotredEntrez(m(IX2));
% xlswrite([resultsDir geneName '_exonArray_coexpressed_genes.xlsx'], sortedG(1:end-1), i, 'A1');
% xlswrite([resultsDir geneName '_exonArray_coexpressed_genes.xlsx'], sotredEntrez(1:end-1), i, 'B1');
% xlswrite([resultsDir geneName '_exonArray_coexpressed_genes.xlsx'], sortedCorr(1:end-1)', i, 'C1');
% clear IXl; clear IX2; clear b; clear m;
% % plot correlation and p-value
% subplot(2,3,i), hold on
% line([0 length(sortedCorr)-1], [0 0],'LineStyle','--','Color',[0.5,0.5,0.5],'LineWidth',2)
% plot(2:201,sortedCorr(2:201),'LineWidth',3,'Color','r'),
% plot(202:numel(sortedCorr)-200,sortedCorr(202:end-200),'LineWidth',3),
% plot(numel(sortedCorr)-199:numel(sortedCorr),sortedCorr(end-199:end),'LineWidth',3,'Color','r'),
% grid on, hold off
% ylabel('Correlation', 'FontWeight', 'bold', 'FontSize', 15)
% xlabel('Genes sorted on corrleation')
% set(gca,'XTick',[],'XTickLabel',[],'xlim',[0 numel(sortedCorr)],'ylim',[-1 1])
% title([{['Correlation to ' geneName]},...
% {['Probes: ' num2str(transcript_ranges(i,1)) ' - ' num2str(transcript_ranges(i,2))]}],...
% 'FontWeight', 'bold', 'FontSize', 15)
% subplot(2,3,i+3), bar(-log10(sortedPval(2:end)),'b','EdgeColor','w'), grid on
% ylabel('-log_1_0 (p-value)', 'FontWeight', 'bold', 'FontSize', 15)
% xlabel('Genes sorted on corrleation')
% set(gca,'XTick',[],'XTickLabel',[],'xlim',[0 numel(sortedCorr)],'ylim',[0 200])
end
% hold off
% saveas(f, [resultsDir 'corelationPlot_BrainSpan_exons_individual_exons.fig']);
% saveas(f, [resultsDir 'corelationPlot_BrainSpan_exons_individual_exons.png']);
%% build a coexpression netwok between the top 25 genes correalted with DMD in the adult brain
N = 25;
exon_select = [19,41,86];
dataDir = '/tudelft.net/staff-bulk/ewi/insy/DBL/amahfouz/MATLAB/Data/exons_matrix_csv/';
resDir = '/tudelft.net/staff-bulk/ewi/insy/DBL/amahfouz/MATLAB/Results/DMD/';
geneName = 'DMD';
% read probe info
T = readtable([dataDir 'rows_metadata.xlsx']);
origTranscript.gene_symbol = T.gene_symbol;
origTranscript.entrez_id = T.entrez_id;
origTranscript.start = T.start;
origTranscript.end = T.xEnd;
clear T;
% remove pobes with no entrez_id
removedProbes = find(isnan(origTranscript.entrez_id));
origTranscript.gene_symbol(removedProbes) = [];
origTranscript.entrez_id(removedProbes) = [];
origTranscript.start(removedProbes) = [];
origTranscript.end(removedProbes) = [];
% read expression data
data = csvread([dataDir 'expression_matrix.csv']);
data(removedProbes,:) = [];
data(:,1) = [];
% log-transform the data
data = log2(data+1);
% read the coexpression results and clean the data
load([resDir 'corrMat_exonArray_individual_exons_log2.mat']);
removedRows = logical(prod(double(isnan(corrMat))));
corrMat(:,removedRows) = [];
transcript.gene_symbol(removedRows) = [];
transcript.entrez_id(removedRows) = [];
transcript.start(removedRows) = [];
transcript.end(removedRows) = [];
pVal(:,removedRows) = [];
data(removedRows,:) = [];
% loop on the different isoform-specific exons
for i = 1 : size(corrMat,1)
% sort the data
[sortedCorrMat IX] = sort(corrMat(i,:),2,'descend');
rankedGenes = transcript.gene_symbol(IX);
[b,m,~] = unique(rankedGenes, 'stable');
[~,IX2] = sort(m);
sortedG = b(IX2);
sortedData = data(IX,:);
sortedData = sortedData(m(IX2),:);
% select the top N genes and calculate the correlation between them
topN_genes{i} = sortedG(1:N+1); % N + DMD
[corrMat_topN(:,:,i),~] = corr(sortedData(1:N+1,:)');
end
save([resDir 'corrMat_exonArray_individual_exons_log2_topN.mat'],'corrMat_topN','topN_genes');
%% load the topN corelations and save to excel
load([dataDir 'corrMat_exonArray_individual_exons_log2_topN.mat'])
for k = 1 : size(corrMat_topN,3)
corrMat_curr = corrMat_topN(:,:,k) .* abs(eye(size(corrMat_topN,1))-1);
corr_topN = squareform(corrMat_curr,'tovector');
count = 0;
for i = 1 : length(topN_genes{k})
for j = i+1 : length(topN_genes{k})
count = count + 1;
top200_pair(count,1) = topN_genes{k}(j);
top200_pair(count,2) = topN_genes{k}(i);
end
end
T = table(top200_pair(:,1), top200_pair(:,2), corr_topN', 'VariableNames',{'Gene1','Gene2','correlation'});
writetable(T, [dataDir 'DMD_exons_individual_topN_log2' num2str(k) '.xls']);
end
%% read the GOElite results and plot a graph
resDir = 'C:\Users\amahfouz\SURFdrive\Projects\DMD\Results\BrainSpan_exons\GO_elite\';
T_Dp71_Dp40 = readtable([resDir 'pruned-results_combination_elite_Dp71_Dp40.txt'],'Delimiter','\t');
T_Dp140 = readtable([resDir 'pruned-results_combination_elite_Dp140.txt'],'Delimiter','\t');
T_Dp427 = readtable([resDir 'pruned-results_combination_elite_Dp427.txt'],'Delimiter','\t');
tableList = {T_Dp71_Dp40, T_Dp140, T_Dp427};
for ii = 1 : length(tableList)
currT = tableList{ii};
% select GO terms related to "biological_processes" and "molecular_function"
GOtype_idx = find(ismember(currT.GOType,{'biological_process','molecular_function'})==1);
% select GO terms with a Z-score > 4
zScore_idx = find(currT.ZScore >= 4);
% select the GO terms fulfilling bith criteria
selection_idx = intersect(GOtype_idx, zScore_idx);
go_selected = currT.GOName_GOID_(selection_idx);
% plot the GO terms enrichment
f = figure;
hold on
set(f,'Position',[200, 200, 1024, 300])
barh(flipud(currT.ZScore(selection_idx)),'FaceColor',[0 0 153/255],'EdgeColor',[0 0 153/255])
set(gca,'YTick',1:length(selection_idx),'YTickLabel',flipud(go_selected))
ylim([0 9])
xlim([0 12])
line([4 4],[0.5 length(selection_idx)+0.5],'Color','r','LineWidth',2,'LineStyle','--');
grid on
grid minor
hold off
end