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DREAM Module Identification Challenge – Consensus modules

PPI-STRING_Consensus_mod355

Assigned name NA Network PPI-STRING Module ID PPI-STRING_Consensus_mod355 Module size 40 genes

Module genes

This module comprises the following genes:

Gene ID Gene Symbol Gene Name 130497 OSR1 odd-skipped related transciption factor 1 57786 RBAK RB associated KRAB zinc finger 9278 ZBTB22 zinc finger and BTB domain containing 22 140685 ZBTB46 zinc finger and BTB domain containing 46 7771 ZFP112 zinc finger protein 112 163071 ZNF114 zinc finger protein 114 7728 ZNF175 zinc finger protein 175 10168 ZNF197 zinc finger protein 197 7571 ZNF23 zinc finger protein 23 23036 ZNF292 zinc finger protein 292 7582 ZNF33B zinc finger protein 33B 84905 ZNF341 zinc finger protein 341 84671 ZNF347 zinc finger protein 347 117608 ZNF354B zinc finger protein 354B 140467 ZNF358 zinc finger protein 358 7592 ZNF41 zinc finger protein 41 147687 ZNF417 zinc finger protein 417 147923 ZNF420 zinc finger protein 420 256051 ZNF549 zinc finger protein 549 147741 ZNF560 zinc finger protein 560 374900 ZNF568 zinc finger protein 568 51276 ZNF571 zinc finger protein 571 147660 ZNF578 zinc finger protein 578 51157 ZNF580 zinc finger protein 580 92285 ZNF585B zinc finger protein 585B 100293516 ZNF587B zinc finger protein 587B 84622 ZNF594 zinc finger protein 594 80095 ZNF606 zinc finger protein 606 26149 ZNF658 zinc finger protein 658 79788 ZNF665 zinc finger protein 665 91120 ZNF682 zinc finger protein 682 115509 ZNF689 zinc finger protein 689 440519 ZNF724P zinc finger protein 724 100287226 ZNF729 zinc finger protein 729 342132 ZNF774 zinc finger protein 774 163049 ZNF791 zinc finger protein 791 347344 ZNF81 zinc finger protein 81 162962 ZNF836 zinc finger protein 836 91664 ZNF845 zinc finger protein 845 342892 ZNF850 zinc finger protein 850

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 3.93e-03 7.89e-25 Reactome Generic Transcription Pathway 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 1.68e-04 4.53e-02 embryonic forelimb morphogenesis 1.70e-04 4.57e-02 forelimb morphogenesis 3.94e-03 5.76e-01 negative regulation of dendritic cell differentiation 3.94e-03 5.76e-01 signal transduction by trans-phosphorylation 3.94e-03 5.76e-01 pattern specification involved in metanephros development 3.97e-03 5.79e-01 embryonic limb morphogenesis 3.99e-03 5.81e-01 mesonephric duct morphogenesis 3.99e-03 5.81e-01 embryonic skeletal limb joint morphogenesis 4.99e-03 6.94e-01 limb morphogenesis 5.54e-03 7.55e-01 limb development 5.88e-03 7.74e-01 negative regulation of monocyte differentiation 5.93e-03 7.79e-01 positive regulation of dendritic cell differentiation 5.98e-03 7.83e-01 ureter urothelium development 5.98e-03 7.83e-01 metanephric mesenchyme morphogenesis 5.98e-03 7.83e-01 metanephric mesenchymal cell differentiation 5.99e-03 7.83e-01 segment specification 7.92e-03 9.55e-01 regulation of dendritic cell differentiation 7.92e-03 9.55e-01 negative regulation of granulocyte differentiation 7.92e-03 9.55e-01 positive regulation of gastrulation 7.97e-03 9.58e-01 metanephric glomerulus vasculature development

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

²FDR corrected p-value (Benjamini-Hochberg)

Reactome

P-value1 FDR2 Term 0e+00 0e+00 GENERIC TRANSCRIPTION PATHWAY

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

²FDR corrected p-value (Benjamini-Hochberg)

Mouse mutant phenotypes

P-value1 FDR2 Term 1.87e-03 1e+00 gonadal ridge hypoplasia 1.87e-03 1e+00 abnormal pericardium morphology 1.87e-03 1e+00 absent adrenal gland 1.87e-03 1e+00 absent metanephric mesenchyme 1.87e-03 1e+00 abnormal nephrogenic mesenchyme morphogenesis 1.87e-03 1e+00 abnormal mesonephric mesenchyme morphology 3.74e-03 1e+00 abnormal mesonephros morphology 3.74e-03 1e+00 abnormal fetal atrioventricular canal morphology 3.74e-03 1e+00 abnormal interatrial septum morphology 3.74e-03 1e+00 absent ureteric bud 3.74e-03 1e+00 abnormal forelimb bud morphology 5.60e-03 1e+00 absent metanephros 5.60e-03 1e+00 absent testes 5.60e-03 1e+00 agonadal 5.61e-03 1e+00 abnormal Wolffian duct morphology 5.61e-03 1e+00 increased metanephric mesenchyme apoptosis 7.46e-03 1e+00 absent ovary 7.47e-03 1e+00 abnormal dendritic cell morphology 7.47e-03 1e+00 abnormal metanephric mesenchyme morphology 7.47e-03 1e+00 abnormal survival

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

²FDR corrected p-value (Benjamini-Hochberg)