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DREAM Module Identification Challenge – Consensus modules

PPI-STRING_Consensus_mod323

Assigned name NA Network PPI-STRING Module ID PPI-STRING_Consensus_mod323 Module size 38 genes

Module genes

This module comprises the following genes:

Gene ID Gene Symbol Gene Name 388407 C17orf82 chromosome 17 open reading frame 82 958 CD40 CD40 molecule 959 CD40LG CD40 ligand 922 CD5L CD5 molecule like 1418 CRYGA crystallin gamma A 10913 EDAR ectodysplasin A receptor 128178 EDARADD EDAR associated death domain 4049 LTA lymphotoxin alpha 4050 LTB lymphotoxin beta 4055 LTBR lymphotoxin beta receptor 27018 NGFRAP1 brain expressed X-linked 3 11105 PRDM7 PR/SET domain 7 147138 TMC8 transmembrane channel like 8 298566 TNF complement C1q A chain 8792 TNFRSF11A TNF receptor superfamily member 11a 51330 TNFRSF12A TNF receptor superfamily member 12A 23495 TNFRSF13B TNF receptor superfamily member 13B 115650 TNFRSF13C TNF receptor superfamily member 13C 8764 TNFRSF14 TNF receptor superfamily member 14 608 TNFRSF17 TNF receptor superfamily member 17 55504 TNFRSF19 TNF receptor superfamily member 19 7133 TNFRSF1B TNF receptor superfamily member 1B 8771 TNFRSF6B TNF receptor superfamily member 6b 943 TNFRSF8 TNF receptor superfamily member 8 3604 TNFRSF9 TNF receptor superfamily member 9 8742 TNFSF12 TNF superfamily member 12 8741 TNFSF13 TNF superfamily member 13 10673 TNFSF13B TNF superfamily member 13b 8740 TNFSF14 TNF superfamily member 14 9966 TNFSF15 TNF superfamily member 15 7292 TNFSF4 TNF superfamily member 4 8744 TNFSF9 TNF superfamily member 9 7185 TRAF1 TNF receptor associated factor 1 7186 TRAF2 TNF receptor associated factor 2 7187 TRAF3 TNF receptor associated factor 3 10758 TRAF3IP2 TRAF3 interacting protein 2 7188 TRAF5 TNF receptor associated factor 5 10293 TRAIP TRAF interacting protein

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 3.76e-01 3.02e-33 Reactome TNF receptor superfamily (TNFSF) members mediating non-canonical NF-kB pathway Immune System 2.33e-01 1.80e-37 Reactome TNFs bind their physiological receptors Immune System 1.06e-01 1.22e-33 GO tumor necrosis factor receptor binding molecular_function 8.41e-02 2.98e-61 GO tumor necrosis factor-mediated signaling pathway biological_process 5.46e-02 5.31e-09 GO thioesterase binding molecular_function 2.77e-02 1.20e-54 Reactome TNFR2 non-canonical NF-kB pathway Immune System

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 response to cytokine 0.00e+00 0.00e+00 tumor necrosis factor-mediated signaling pathway 0.00e+00 0.00e+00 cytokine-mediated signaling pathway 0.00e+00 0.00e+00 cellular response to tumor necrosis factor 0.00e+00 0.00e+00 cellular response to cytokine stimulus 0.00e+00 0.00e+00 response to tumor necrosis factor 0.00e+00 0.00e+00 tumor necrosis factor receptor superfamily binding 0.00e+00 0.00e+00 tumor necrosis factor receptor binding 0.00e+00 0.00e+00 cytokine activity 0.00e+00 0.00e+00 cytokine receptor binding 0.00e+00 0.00e+00 tumor necrosis factor-activated receptor activity 0.00e+00 0.00e+00 death receptor activity 8.41e-10 4.52e-07 thioesterase binding 8.50e-10 3.86e-07 CD40 receptor complex 1.99e-09 8.64e-07 external side of plasma membrane 1.11e-08 7.18e-06 positive regulation of adaptive immune response 5.72e-08 2.05e-05 cell surface 6.00e-08 3.51e-05 regulation of immunoglobulin secretion 6.73e-08 2.65e-05 ubiquitin protein ligase binding 7.32e-08 2.87e-05 ubiquitin-like protein ligase binding

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

²FDR corrected p-value (Benjamini-Hochberg)

Reactome

P-value1 FDR2 Term 3.83e-05 5.24e-03 EXTRINSIC PATHWAY FOR APOPTOSIS 1.56e-03 1.73e-01 EXTRINSIC PATHWAY FOR APOPTOSIS 3.28e-03 2.87e-01 RIG I MDA5 MEDIATED INDUCTION OF IFN ALPHA BETA PATHWAYS 5.92e-03 4.74e-01 APOPTOSIS 1.22e-02 8.65e-01 IMMUNOREGULATORY INTERACTIONS BETWEEN A LYMPHOID AND A NON LYMPHOID CELL 1.26e-02 8.86e-01 TRAF6 MEDIATED NFKB ACTIVATION 1.62e-02 1.00e+00 TRAF3 DEPENDENT IRF ACTIVATION PATHWAY 1.62e-02 1.00e+00 ACTIVATION OF IRF3 IRF7 MEDIATED BY TBK1 IKK EPSILON 2.03e-02 1.00e+00 REGULATION OF MRNA STABILITY BY PROTEINS THAT BIND AU RICH ELEMENTS 2.21e-02 1.00e+00 INNATE IMMUNE SYSTEM 2.36e-02 1.00e+00 IMMUNOREGULATORY INTERACTIONS BETWEEN A LYMPHOID AND A NON LYMPHOID CELL 3.77e-02 1.00e+00 RIG I MDA5 MEDIATED INDUCTION OF IFN ALPHA BETA PATHWAYS 3.96e-02 1.00e+00 ACTIVATED TLR4 SIGNALLING 4.13e-02 1.00e+00 COSTIMULATION BY THE CD28 FAMILY 4.33e-02 1.00e+00 TRAF6 MEDIATED IRF7 ACTIVATION 4.90e-02 1.00e+00 NEGATIVE REGULATORS OF RIG I MDA5 SIGNALING

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

²FDR corrected p-value (Benjamini-Hochberg)

Mouse mutant phenotypes

P-value1 FDR2 Term 1.20e-08 2.91e-04 absent spleen germinal center 1.81e-08 3.81e-04 decreased IgG level 7.81e-07 7.32e-03 decreased IgA level 2.70e-06 1.88e-02 abnormal humoral immune response 5.64e-06 3.17e-02 decreased IgG2a level 6.33e-06 3.39e-02 decreased IgG1 level 6.56e-06 3.45e-02 absent peripheral lymph nodes 7.56e-06 3.85e-02 absent follicular dendritic cells 9.95e-06 4.71e-02 decreased interferon-gamma secretion 1.32e-05 5.70e-02 abnormal lymph node primary follicle morphology 1.32e-05 5.70e-02 absent marginal zone B cells 1.81e-05 7.03e-02 absent Peyer's patches 2.98e-05 1.02e-01 abnormal thymus epithelium morphology 3.22e-05 1.07e-01 absent lymph node germinal center 3.74e-05 1.17e-01 decreased IgM level 5.89e-05 1.59e-01 abnormal class switch recombination 7.35e-05 1.84e-01 increased lymphocyte cell number 7.84e-05 1.93e-01 decreased spleen white pulp amount 8.69e-05 2.07e-01 lymph node hypoplasia 1.00e-04 2.26e-01 decreased interleukin-10 secretion

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

²FDR corrected p-value (Benjamini-Hochberg)