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DREAM Module Identification Challenge – Consensus modules

PPI-STRING_Consensus_mod202

Assigned name NA Network PPI-STRING Module ID PPI-STRING_Consensus_mod202 Module size 23 genes

Module genes

This module comprises the following genes:

Gene ID Gene Symbol Gene Name 390259 BSX brain specific homeobox 54596 L1TD1 LINE1 type transposase domain containing 1 79923 NANOG Nanog homeobox 404635 NANOGP1 Nanog homeobox pseudogene 1 25833 POU2F3 POU class 2 homeobox 3 5453 POU3F1 POU class 3 homeobox 1 5454 POU3F2 POU class 3 homeobox 2 5455 POU3F3 POU class 3 homeobox 3 5456 POU3F4 POU class 3 homeobox 4 5457 POU4F1 POU class 4 homeobox 1 5458 POU4F2 POU class 4 homeobox 2 5459 POU4F3 POU class 4 homeobox 3 5460 POU5F1 POU class 5 homeobox 1 5462 POU5F1B POU class 5 homeobox 1B 134187 POU5F2 POU domain class 5, transcription factor 2 5463 POU6F1 POU class 6 homeobox 1 11281 POU6F2 POU class 6 homeobox 2 27164 SALL3 spalt like transcription factor 3 57167 SALL4 spalt like transcription factor 4 6664 SOX11 SRY-box 11 9580 SOX13 SRY-box 13 11166 SOX21 SRY-box 21 619279 ZNF704 zinc finger protein 704

Functional annotation

Modules were tested for enrichment in functional and pathway annotations using two complementary approaches:
1. To select a small number of specific / non-redundant annotations for each module, a regression-based approach was used;
2. To obtain the complete set of enriched annotations, an extension of Fisher’s exact test that takes annotation bias into account was employed (Wallenius’ non-central hypergeometric distribution).

Most specific annotations for this module

Coeff.1 P-value.2 Source.3 Term.4 Class.5 2.66e-02 5.76e-05 Reactome POU5F1 (OCT4), SOX2, NANOG repress genes related to differentiation Developmental Biology 1.46e-02 7.04e-05 Reactome POU5F1 (OCT4), SOX2, NANOG activate genes related to proliferation Developmental Biology 2.18e-03 1.16e-04 GO myelination in peripheral nervous system biological_process 2.18e-03 1.16e-04 Reactome Regulation of TP53 Activity through Association with Co-factors Gene expression (Transcription)

¹Regression coefficient

²Fisher’s exact test nominal P-value

³Annotation source (Reactome, GO biological process (BP), molecular function (MF) and cellular component (CC))

⁴GO category or Reactome pathway

⁵High-level branch of annotation tree

Gene membership

All enriched annotations

Gene Ontology

P-value1 FDR2 Term 0.00e+00 0.00e+00 transcription from RNA polymerase II promoter 2.43e-08 1.04e-05 transcription regulatory region DNA binding 2.45e-08 1.05e-05 regulatory region DNA binding 1.24e-06 3.86e-04 transcription regulatory region sequence-specific DNA binding 3.38e-06 9.69e-04 double-stranded DNA binding 5.16e-05 1.16e-02 transcriptional activator activity, RNA polymerase II core promoter proximal region sequence-specific binding 5.30e-05 1.19e-02 RNA polymerase II regulatory region sequence-specific DNA binding 5.44e-05 1.22e-02 RNA polymerase II regulatory region DNA binding 5.54e-05 1.75e-02 endodermal cell fate specification 6.60e-05 2.04e-02 forebrain development 6.96e-05 2.13e-02 neuromuscular process controlling balance 1.25e-04 3.53e-02 brain development 1.73e-04 4.64e-02 head development 1.82e-04 4.84e-02 forebrain ventricular zone progenitor cell division 2.04e-04 5.33e-02 regulation of transcription regulatory region DNA binding 2.18e-04 4.06e-02 transcriptional activator activity, RNA polymerase II transcription regulatory region sequence-specific binding 2.33e-04 5.96e-02 epidermis development 2.44e-04 6.19e-02 endodermal cell fate commitment 2.71e-04 6.77e-02 peripheral nervous system development 3.17e-04 5.66e-02 transcription factor activity, RNA polymerase II core promoter proximal region sequence-specific binding

¹1Nominal enrichment p-value (Wallenius’ noncentral hypergeometric distribution)

²FDR corrected p-value (Benjamini-Hochberg)

Mouse mutant phenotypes

P-value1 FDR2 Term 9.35e-04 8.68e-01 abnormal pinna reflex 1.24e-03 1.00e+00 conductive hearing loss 1.64e-03 1.00e+00 abnormal vestibular system physiology 2.69e-03 1.00e+00 increased circulating potassium level 3.60e-03 1.00e+00 abnormal stapes morphology 3.93e-03 1.00e+00 head tossing 5.61e-03 1.00e+00 abnormal spiral ligament fibrocyte morphology 6.51e-03 1.00e+00 abnormal inner cell mass morphology 7.51e-03 1.00e+00 abnormal calcaneum morphology 8.56e-03 1.00e+00 head bobbing 9.33e-03 1.00e+00 abnormal neurohypophysis morphology 9.36e-03 1.00e+00 abnormal stapes footplate morphology 9.36e-03 1.00e+00 absent primitive endoderm 1.12e-02 1.00e+00 abnormal pituicyte morphology 1.12e-02 1.00e+00 delayed blastocyst hatching from the zona pellucida 1.12e-02 1.00e+00 abnormal autonomic nervous system physiology 1.12e-02 1.00e+00 abnormal organ of Corti supporting cell differentiation 1.24e-02 1.00e+00 absent pinna reflex 1.31e-02 1.00e+00 barrel chest 1.31e-02 1.00e+00 abnormal spiral limbus morphology

¹1Nominal enrichment p-value (Wallenius’ noncentral hypergeometric distribution)

²FDR corrected p-value (Benjamini-Hochberg)