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DREAM Module Identification Challenge – Consensus modules

PPI-STRING_Consensus_mod25

Assigned name NA Network PPI-STRING Module ID PPI-STRING_Consensus_mod25 Module size 63 genes

Module genes

This module comprises the following genes:

Gene ID Gene Symbol Gene Name 23529 CLCF1 cardiotrophin like cytokine factor 1 1271 CNTFR ciliary neurotrophic factor receptor 64109 CRLF2 cytokine receptor like factor 2 1440 CSF3 colony stimulating factor 3 1441 CSF3R colony stimulating factor 3 receptor 1442 CSH1 chorionic somatomammotropin hormone 1 1443 CSH2 chorionic somatomammotropin hormone 2 1489 CTF1 cardiotrophin 1 2689 GH2 growth hormone 2 3439 IFNA1 interferon alpha 1 3446 IFNA10 interferon alpha 10 3447 IFNA13 interferon alpha 13 3448 IFNA14 interferon alpha 14 3449 IFNA16 interferon alpha 16 3451 IFNA17 interferon alpha 17 3440 IFNA2 interferon alpha 2 3452 IFNA21 interferon alpha 21 3441 IFNA4 interferon alpha 4 3442 IFNA5 interferon alpha 5 3443 IFNA6 interferon alpha 6 3444 IFNA7 interferon alpha 7 3445 IFNA8 interferon alpha 8 3454 IFNAR1 interferon alpha and beta receptor subunit 1 3455 IFNAR2 interferon alpha and beta receptor subunit 2 338376 IFNE interferon epsilon 116465 IFNGR1 interferon gamma receptor 1 3460 IFNGR2 interferon gamma receptor 2 56832 IFNK interferon kappa 3467 IFNW1 interferon omega 1 25325 IL10 interleukin 10 3587 IL10RA interleukin 10 receptor subunit alpha 3588 IL10RB interleukin 10 receptor subunit beta 3592 IL12A interleukin 12A 3597 IL13RA1 interleukin 13 receptor subunit alpha 1 25670 IL15 interleukin 15 3601 IL15RA interleukin 15 receptor subunit alpha 29949 IL19 interleukin 19 50604 IL20 interleukin 20 53832 IL20RA interleukin 20 receptor subunit alpha 53833 IL20RB interleukin 20 receptor subunit beta 59067 IL21 interleukin 21 50615 IL21R interleukin 21 receptor 50616 IL22 interleukin 22 58985 IL22RA1 interleukin 22 receptor subunit alpha 1 116379 IL22RA2 interleukin 22 receptor subunit alpha 2 11009 IL24 interleukin 24 55801 IL26 interleukin 26 282616 IL28A interferon lambda 2 282617 IL28B interferon lambda 3 163702 IL28RA interferon lambda receptor 1 282618 IL29 interferon lambda 1 3563 IL3RA interleukin 3 receptor subunit alpha 3566 IL4R interleukin 4 receptor 3568 IL5RA interleukin 5 receptor subunit alpha 3570 IL6R interleukin 6 receptor 116558 IL7 interleukin 9 3575 IL7R interleukin 7 receptor 3578 IL9 interleukin 9 3581 IL9R interleukin 9 receptor 3953 LEPR leptin receptor 3977 LIFR LIF receptor alpha 9180 OSMR oncostatin M receptor 85480 TSLP thymic stromal lymphopoietin

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 5.18e-01 1.87e-37 GO type I interferon receptor binding molecular_function 2.44e-01 4.33e-19 Reactome Interleukin-20 family signaling Immune System 1.83e-01 3.38e-22 GO cytokine receptor activity molecular_function 1.15e-01 1.12e-15 GO cytokine receptor binding molecular_function 9.54e-02 4.31e-06 GO positive regulation of growth biological_process 7.36e-02 3.93e-35 GO B cell proliferation biological_process 5.69e-02 9.49e-36 GO natural killer cell activation involved in immune response biological_process 4.99e-02 5.11e-19 GO cytokine binding molecular_function 4.34e-02 3.13e-20 GO positive regulation of tyrosine phosphorylation of STAT protein biological_process 3.76e-02 3.10e-04 GO positive regulation of immunoglobulin production biological_process 3.73e-02 6.27e-34 GO T cell activation involved in immune response biological_process 3.51e-02 1.80e-34 GO positive regulation of peptidyl-serine phosphorylation of STAT protein biological_process 1.46e-02 9.90e-70 Reactome Cytokine Signaling in Immune system Immune System 9.53e-03 3.03e-06 GO growth hormone receptor binding molecular_function 8.03e-03 1.65e-12 Reactome Interleukin-2 family signaling Immune System 5.73e-03 2.65e-41 Reactome Signaling by Interleukins Immune System 4.10e-03 3.41e-05 GO positive regulation of chemokine production biological_process 3.31e-03 2.13e-10 GO growth factor activity molecular_function

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 0e+00 0e+00 response to cytokine 0e+00 0e+00 cytokine-mediated signaling pathway 0e+00 0e+00 cellular response to cytokine stimulus 0e+00 0e+00 regulation of tyrosine phosphorylation of Stat3 protein 0e+00 0e+00 regulation of JAK-STAT cascade 0e+00 0e+00 positive regulation of tyrosine phosphorylation of STAT protein 0e+00 0e+00 positive regulation of JAK-STAT cascade 0e+00 0e+00 regulation of peptidyl-serine phosphorylation 0e+00 0e+00 positive regulation of peptidyl-serine phosphorylation 0e+00 0e+00 B cell differentiation 0e+00 0e+00 B cell activation 0e+00 0e+00 positive regulation of peptidyl-serine phosphorylation of STAT protein 0e+00 0e+00 T cell activation involved in immune response 0e+00 0e+00 leukocyte proliferation 0e+00 0e+00 response to exogenous dsRNA 0e+00 0e+00 humoral immune response 0e+00 0e+00 natural killer cell activation 0e+00 0e+00 cellular response to type I interferon 0e+00 0e+00 mononuclear cell proliferation 0e+00 0e+00 response to type I interferon

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

²FDR corrected p-value (Benjamini-Hochberg)

Reactome

P-value1 FDR2 Term 0.00e+00 0.00e+00 TRAF6 MEDIATED IRF7 ACTIVATION 0.00e+00 0.00e+00 RIG I MDA5 MEDIATED INDUCTION OF IFN ALPHA BETA PATHWAYS 0.00e+00 0.00e+00 INTERFERON ALPHA BETA SIGNALING 0.00e+00 0.00e+00 REGULATION OF IFNA SIGNALING 0.00e+00 0.00e+00 FACTORS INVOLVED IN MEGAKARYOCYTE DEVELOPMENT AND PLATELET PRODUCTION 0.00e+00 0.00e+00 RIG I MDA5 MEDIATED INDUCTION OF IFN ALPHA BETA PATHWAYS 0.00e+00 0.00e+00 INTERFERON ALPHA BETA SIGNALING 0.00e+00 0.00e+00 REGULATION OF IFNA SIGNALING 0.00e+00 0.00e+00 TRAF6 MEDIATED IRF7 ACTIVATION 0.00e+00 0.00e+00 CYTOKINE SIGNALING IN IMMUNE SYSTEM 0.00e+00 0.00e+00 INTERFERON SIGNALING 1.13e-16 4.47e-14 CYTOKINE SIGNALING IN IMMUNE SYSTEM 1.13e-12 4.44e-10 INTERFERON SIGNALING 2.76e-09 8.56e-07 FACTORS INVOLVED IN MEGAKARYOCYTE DEVELOPMENT AND PLATELET PRODUCTION 4.73e-09 1.07e-06 INNATE IMMUNE SYSTEM 4.41e-06 8.90e-04 INNATE IMMUNE SYSTEM 4.35e-05 5.88e-03 SIGNALING BY ILS 3.07e-04 3.50e-02 IL 7 SIGNALING 6.50e-04 6.83e-02 REGULATION OF IFNG SIGNALING 1.82e-03 1.71e-01 PROLACTIN RECEPTOR SIGNALING

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

²FDR corrected p-value (Benjamini-Hochberg)

Mouse mutant phenotypes

P-value1 FDR2 Term 5.97e-10 2.39e-05 increased susceptibility to parasitic infection 3.56e-08 6.46e-04 colitis 6.03e-07 6.05e-03 impaired natural killer cell mediated cytotoxicity 2.27e-06 1.61e-02 altered susceptibility to infection 1.19e-05 5.31e-02 abnormal T-helper 2 physiology 1.75e-05 6.95e-02 increased interferon-gamma secretion 2.52e-05 9.14e-02 decreased NK cell number 5.51e-05 1.53e-01 abnormal CD4-positive, alpha-beta T cell physiology 6.95e-05 1.78e-01 abnormal chemokine level 9.11e-05 2.12e-01 abnormal immune system physiology 9.85e-05 2.24e-01 abnormal response to infection 1.10e-04 2.40e-01 respiratory system inflammation 1.17e-04 2.50e-01 abnormal cytotoxic T cell physiology 1.18e-04 2.51e-01 decreased motor neuron number 1.53e-04 2.98e-01 decreased CD4-positive, alpha beta T cell number 1.71e-04 3.19e-01 decreased memory T cell number 1.72e-04 3.20e-01 abnormal cytokine secretion 1.77e-04 3.24e-01 increased circulating interleukin-12 level 2.00e-04 3.50e-01 abnormal immunoglobulin level 2.53e-04 4.02e-01 decreased CD8-positive, gamma-delta intraepithelial T cell number

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

²FDR corrected p-value (Benjamini-Hochberg)