Output files

Overview of the switches

spada provides a overview of the switches in the file switches_spada.tsv. It is created for both the switches calculated by spada and those provided by the user. It is created by commands spada switches, summary and simulate.

• Experiment: identifier of the experiment, as indicated with the flag -N/--name to spada init.
• GeneId: gene identifier (e.g. ENSG00000141510.15).
• Symbol: gene symbol (e.g. TP53).
• Control_transcript: transcript identifier of the control transcript (e.g. ENST00000619485.4). This is the transcript that is deemed as best representative of the control samples specified under the Samples column.
• Case_transcript: transcript identifier of the control transcript (e.g. ENST00000445888.6). This is the transcript that is deemed as best representative of the case samples specified under the Samples column.
• CDS_control: 1 if the control transcript contains at least a CDS, 0 otherwise.
• CDS_case: 1 if the control transcript contains at least a CDS, 0 otherwise.
• CDS_change: 1 if the CDS changes between case and control transcripts, 0 otherwise.
• UTR_change: 1 if the UTR changes between case and control transcripts, 0 otherwise.
• Samples: identifiers of the samples where the switch occurs.

Structural features

Pfam and ProSite features

• Experiment: see above.
• GeneId: see above.
• Control_transcript: see above.
• Case_transcript: see above.
• Feature_type
• Feature
• What
• Index
• Control_start
• Control_end
• Case_start
• Case_end
• Control_MacroScore
• Control_MicroScore
• Control_Jaccard
• Case_MacroScore
• Case_MicroScore
• Case_Jaccard

Protein-protein interactions

• Experiment: see above.
• GeneId: see above.
• Control_transcript: see above.
• Case_transcript: see above.
• Other_gene
• Other_symbol
• Other_transcript
• What
• #nDDIs
• #tDDIs
• #BothDDIs
• nDDIs
• tDDIs
• BothDDIs

Intrinsecally disordered regions

Other

Proteome features

spada provides an overlook of the proteome in the controls. It takes the most expressed transcript in a gene as representative of the contribution of that gene to the proteome. spada only considers those transcripts under those above the specified minimum expression. Then, it lists information about the features on those transcripts. This provides information about which, genes, transcripts and protein features are expressed. This information is provided by spada summary.

• Experiment: see above.
• GeneId: see above.
• Transcript: transcript identifier of the most expressed transcript for this gene (e.g. ENST00000619485.4).
• Expression
• Feature_type
• Feature: (Empty when Feature_type is Transcript.)
• Index: (Empty when Feature_type is Transcript.)
• Length: (Empty when Feature_type is Transcript.)
• Start: (Empty when Feature_type is Transcript.)
• End: (Empty when Feature_type is Transcript.)