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DREAM Module Identification Challenge – Consensus modules

PPI-STRING_Consensus_mod111

Assigned name NA Network PPI-STRING Module ID PPI-STRING_Consensus_mod111 Module size 59 genes

Module genes

This module comprises the following genes:

Gene ID Gene Symbol Gene Name 282679 AQP11 aquaporin 11 590 BCHE butyrylcholinesterase 359710 BPIFB3 BPI fold containing family B member 3 151888 BTLA B and T lymphocyte associated 868 CBLB Cbl proto-oncogene B 939 CD27 CD27 molecule 924 CD7 CD7 molecule 57585 CRAMP1L cramped chromatin regulator homolog 1 1774 DNASE1L1 deoxyribonuclease 1 like 1 9046 DOK2 docking protein 2 10148 EBI3 Epstein-Barr virus induced 3 83417 FCRL4 Fc receptor like 4 4616 GADD45B growth arrest and DNA damage inducible beta 10912 GADD45G growth arrest and DNA damage inducible gamma 11147 HHLA3 HERV-H LTR-associating 3 3142 HLX H2.0 like homeobox 100423062 IGLL5 immunoglobulin lambda like polypeptide 5 22806 IKZF3 IKAROS family zinc finger 3 112744 IL17F interleukin 17F 3606 IL18 interleukin 18 8809 IL18R1 interleukin 18 receptor 1 8807 IL18RAP interleukin 18 receptor accessory protein 8808 IL1RL2 interleukin 1 receptor like 2 56005 IL27 myeloid derived growth factor 9466 IL27RA interleukin 27 receptor subunit alpha 8660 IRS2 insulin receptor substrate 2 3716 JAK1 Janus kinase 1 3717 JAK2 Janus kinase 2 3718 JAK3 Janus kinase 3 152789 JAKMIP1 janus kinase and microtubule interacting protein 1 10128 LRPPRC leucine rich pentatricopeptide repeat containing 4353 MPO myeloperoxidase 9111 NMI N-myc and STAT interactor 22932 POMZP3 POM121 and ZP3 fusion 5971 RELB RELB proto-oncogene, NF-kB subunit 84666 RETNLB resistin like beta 79589 RNF128 ring finger protein 128, E3 ubiquitin protein ligase 10603 SH2B2 SH2B adaptor protein 2 10019 SH2B3 SH2B adaptor protein 3 8778 SIGLEC5 sialic acid binding Ig like lectin 5 9306 SOCS6 suppressor of cytokine signaling 6 55620 STAP2 signal transducing adaptor family member 2 6772 STAT1 signal transducer and activator of transcription 1 6774 STAT3 signal transducer and activator of transcription 3 6775 STAT4 signal transducer and activator of transcription 4 6776 STAT5A signal transducer and activator of transcription 5A 6777 STAT5B signal transducer and activator of transcription 5B 6778 STAT6 signal transducer and activator of transcription 6 30009 TBX21 T-box 21 7032 TFF2 trefoil factor 2 7033 TFF3 trefoil factor 3 7066 THPO thrombopoietin 9220 TIAF1 TGFB1-induced anti-apoptotic factor 1 8784 TNFRSF18 TNF receptor superfamily member 18 7293 TNFRSF4 TNF receptor superfamily member 4 8995 TNFSF18 TNF superfamily member 18 7252 TSHB thyroid stimulating hormone beta 7297 TYK2 tyrosine kinase 2 79679 VTCN1 V-set domain containing T cell activation inhibitor 1

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 3.41e-01 3.09e-07 Reactome Interleukin-18 signaling Immune System 2.47e-01 2.77e-16 Reactome Interleukin-21 signaling Immune System 1.74e-01 1.06e-18 GO interleukin-27-mediated signaling pathway biological_process 1.68e-01 1.06e-18 Reactome Interleukin-27 signaling Immune System 1.07e-01 3.18e-18 Reactome Interleukin-35 Signalling Immune System 7.46e-02 6.70e-06 GO transmembrane receptor protein tyrosine kinase adaptor activity molecular_function 6.90e-02 6.78e-14 Reactome Interleukin-9 signaling Immune System 6.59e-02 1.27e-10 Reactome Signaling by Leptin Signal Transduction 5.65e-02 6.70e-06 GO negative regulation of T cell activation biological_process 5.15e-02 1.38e-14 GO JAK-STAT cascade biological_process 3.59e-02 2.11e-06 Reactome TNFs bind their physiological receptors Immune System 3.24e-02 1.69e-05 Reactome Regulation of KIT signaling Signal Transduction 2.81e-02 9.58e-03 Reactome STAT6-mediated induction of chemokines Immune System 2.48e-02 5.33e-17 Reactome Interleukin-20 family signaling Immune System 1.28e-02 3.53e-10 GO JAK-STAT cascade involved in growth hormone signaling pathway biological_process 7.45e-03 6.51e-04 GO positive regulation of leukocyte migration biological_process 6.58e-03 7.68e-04 GO response to stress biological_process 3.29e-03 8.64e-13 Reactome Signaling by SCF-KIT Signal Transduction 1.80e-04 2.14e-11 GO interleukin-7-mediated signaling pathway biological_process

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 adaptive immune response 7.49e-15 7.04e-12 cytokine-mediated signaling pathway 8.17e-13 7.58e-10 cellular response to cytokine stimulus 1.52e-12 1.40e-09 response to cytokine 5.81e-12 5.28e-09 regulation of lymphocyte activation 2.09e-11 1.85e-08 regulation of cell activation 3.52e-11 3.06e-08 JAK-STAT cascade 2.00e-09 1.43e-06 positive regulation of cell activation 6.24e-08 3.64e-05 JAK-STAT cascade involved in growth hormone signaling pathway 7.76e-08 3.03e-05 cytokine receptor binding 3.30e-07 1.71e-04 T-helper 1 type immune response 4.49e-07 2.28e-04 growth hormone receptor signaling pathway 6.50e-07 3.21e-04 cellular response to growth hormone stimulus 8.26e-07 3.99e-04 regulation of lymphocyte differentiation 9.49e-07 3.02e-04 growth hormone receptor binding 9.52e-07 4.54e-04 positive regulation of B cell activation 9.63e-07 4.59e-04 regulation of T cell activation 1.84e-06 8.32e-04 adaptive immune response based on somatic recombination of immune receptors built from immunoglobulin superfamily domains 1.98e-06 8.89e-04 regulation of cell-cell adhesion 2.03e-06 9.10e-04 regulation of T cell differentiation

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

²FDR corrected p-value (Benjamini-Hochberg)

Reactome

P-value1 FDR2 Term 3.48e-09 8.00e-07 IL 6 SIGNALING 1.29e-08 2.79e-06 GROWTH HORMONE RECEPTOR SIGNALING 2.02e-08 4.28e-06 SIGNALING BY ILS 3.79e-08 1.03e-05 IL 6 SIGNALING 9.23e-08 2.38e-05 GROWTH HORMONE RECEPTOR SIGNALING 1.10e-07 2.13e-05 SIGNALING BY SCF KIT 6.08e-07 1.10e-04 CYTOKINE SIGNALING IN IMMUNE SYSTEM 8.05e-07 1.42e-04 IL 7 SIGNALING 1.55e-06 3.39e-04 SIGNALING BY ILS 1.79e-06 3.86e-04 SIGNALING BY SCF KIT 2.64e-06 4.30e-04 SIGNALING BY FGFR1 FUSION MUTANTS 5.01e-06 1.00e-03 IL 7 SIGNALING 1.17e-05 2.21e-03 SIGNALING BY FGFR1 FUSION MUTANTS 1.47e-05 2.14e-03 IL 3 5 AND GM CSF SIGNALING 1.68e-05 2.43e-03 IL 2 SIGNALING 5.54e-05 7.39e-03 SIGNALING BY FGFR1 MUTANTS 6.65e-05 8.74e-03 REGULATION OF IFNG SIGNALING 7.16e-05 1.15e-02 CYTOKINE SIGNALING IN IMMUNE SYSTEM 1.31e-04 1.98e-02 IL 2 SIGNALING 1.34e-04 1.66e-02 REGULATION OF IFNA SIGNALING

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

²FDR corrected p-value (Benjamini-Hochberg)

Mouse mutant phenotypes

P-value1 FDR2 Term 0.00e+00 0.00e+00 decreased interferon-gamma secretion 4.77e-08 7.99e-04 abnormal T-helper 1 physiology 9.72e-08 1.38e-03 increased susceptibility to experimental autoimmune encephalomyelitis 3.69e-06 2.32e-02 impaired natural killer cell mediated cytotoxicity 6.66e-06 3.50e-02 increased interferon-gamma secretion 7.11e-06 3.69e-02 increased T cell proliferation 2.21e-05 8.23e-02 abnormal T-helper 1 cell differentiation 2.75e-05 9.75e-02 increased IgG1 level 2.83e-05 9.84e-02 decreased circulating interferon-gamma level 3.62e-05 1.15e-01 increased susceptibility to parasitic infection 4.05e-05 1.24e-01 abnormal CD4-positive T cell differentiation 7.46e-05 1.86e-01 abnormal T-helper 2 physiology 7.79e-05 1.92e-01 decreased NK cell number 8.30e-05 2.01e-01 decreased interleukin-4 secretion 1.61e-04 3.09e-01 increased interleukin-2 secretion 1.62e-04 3.10e-01 abnormal CD4-positive, alpha-beta T cell physiology 1.70e-04 3.18e-01 increased IgG2a level 2.94e-04 4.43e-01 increased circulating interleukin-12 level 4.90e-04 5.99e-01 increased circulating interleukin-12b level 5.65e-04 6.54e-01 abnormal leukocyte physiology

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

²FDR corrected p-value (Benjamini-Hochberg)