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DREAM Module Identification Challenge – Consensus modules

PPI-STRING_Consensus_mod310

Assigned name NA Network PPI-STRING Module ID PPI-STRING_Consensus_mod310 Module size 39 genes

Module genes

This module comprises the following genes:

Gene ID Gene Symbol Gene Name 554 AVPR2 arginine vasopressin receptor 2 718 C3 complement C3 727 C5 complement C5 6356 CCL11 C-C motif chemokine ligand 11 6359 CCL15 C-C motif chemokine ligand 15 6349 CCL3L1 C-C motif chemokine ligand 3 like 1 414062 CCL3L3 C-C motif chemokine ligand 3 like 3 388372 CCL4L1 C-C motif chemokine ligand 4 like 1 9560 CCL4L2 C-C motif chemokine ligand 4 like 2 9034 CCRL2 C-C motif chemokine receptor like 2 8763 CD164 CD164 molecule 10878 CFHR3 complement factor H related 3 10877 CFHR4 complement factor H related 4 1240 CMKLR1 chemerin chemokine-like receptor 1 2532 DARC atypical chemokine receptor 1 (Duffy blood group) 1669 DEFA4 defensin alpha 4 1670 DEFA5 defensin alpha 5 1672 DEFB1 defensin beta 1 414325 DEFB103A defensin beta 103A 55894 DEFB103B defensin beta 103B 1803 DPP4 dipeptidyl peptidase 4 115350 FCRL1 Fc receptor like 1 2825 GPR1 G protein-coupled receptor 1 134391 GPR151 G protein-coupled receptor 151 1902 GPR26 lysophosphatidic acid receptor 1 9248 GPR50 G protein-coupled receptor 50 27202 GPR77 complement component 5a receptor 2 6011 GRK1 G protein-coupled receptor kinase 1 2868 GRK4 G protein-coupled receptor kinase 4 2870 GRK6 G protein-coupled receptor kinase 6 3358 HTR2C 5-hydroxytryptamine receptor 2C 117194 MRGPRX2 MAS related GPR family member X2 4489 MT1A metallothionein 1A 5197 PF4V1 platelet factor 4 variant 1 5473 PPBP pro-platelet basic protein 8460 TPST1 tyrosylprotein sulfotransferase 1 8459 TPST2 tyrosylprotein sulfotransferase 2 7275 TUB tubby bipartite transcription factor 11326 VSIG4 V-set and immunoglobulin domain containing 4

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 1.19e-01 3.84e-03 Reactome Defective AVP causes neurohypophyseal diabetes insipidus (NDI) Disease 7.21e-02 5.34e-05 Reactome Activation of C3 and C5 Immune System 6.96e-02 3.76e-14 GO chemokine activity molecular_function 5.75e-02 1.82e-06 GO complement activation, alternative pathway biological_process 4.39e-02 9.95e-05 GO membrane disruption in other organism biological_process 2.07e-02 6.13e-06 GO innate immune response in mucosa biological_process 7.51e-03 7.26e-13 GO chemokine-mediated signaling pathway biological_process 1.19e-03 1.60e-04 Reactome Alpha-defensins 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 chemokine-mediated signaling pathway 0.00e+00 0.00e+00 G-protein coupled receptor binding 0.00e+00 0.00e+00 chemokine receptor binding 2.50e-11 1.61e-08 chemokine activity 1.87e-10 1.10e-07 CCR chemokine receptor binding 2.65e-09 1.87e-06 inflammatory response 5.35e-09 2.53e-06 cytokine receptor binding 6.31e-08 3.68e-05 chemotaxis 1.13e-07 6.33e-05 cell chemotaxis 1.20e-07 6.70e-05 humoral immune response 2.80e-07 1.47e-04 neutrophil chemotaxis 3.18e-07 1.65e-04 innate immune response 3.29e-07 1.15e-04 G-protein coupled receptor activity 3.82e-07 1.96e-04 leukocyte chemotaxis 4.16e-07 2.12e-04 granulocyte chemotaxis 5.59e-07 2.79e-04 neutrophil migration 6.65e-07 2.18e-04 G-protein coupled receptor kinase activity 1.53e-06 4.70e-04 cytokine activity 2.35e-06 1.04e-03 complement activation, alternative pathway 2.65e-06 1.16e-03 monocyte chemotaxis

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

²FDR corrected p-value (Benjamini-Hochberg)

Reactome

P-value1 FDR2 Term 2.98e-09 9.20e-07 PEPTIDE LIGAND BINDING RECEPTORS 8.47e-09 1.87e-06 DEFENSINS 1.12e-08 2.44e-06 PEPTIDE LIGAND BINDING RECEPTORS 1.92e-08 5.43e-06 CLASS A1 RHODOPSIN LIKE RECEPTORS 2.40e-08 6.72e-06 DEFENSINS 3.52e-08 7.27e-06 INNATE IMMUNE SYSTEM 2.53e-07 6.21e-05 INNATE IMMUNE SYSTEM 3.27e-07 7.88e-05 GPCR LIGAND BINDING 1.15e-05 1.70e-03 BETA DEFENSINS 4.00e-05 6.85e-03 CHEMOKINE RECEPTORS BIND CHEMOKINES 5.82e-05 7.72e-03 CHEMOKINE RECEPTORS BIND CHEMOKINES 6.39e-05 1.04e-02 BETA DEFENSINS 1.52e-04 2.26e-02 COMPLEMENT CASCADE 2.30e-04 2.69e-02 COMPLEMENT CASCADE 1.08e-03 1.08e-01 REGULATION OF COMPLEMENT CASCADE 1.33e-03 1.50e-01 REGULATION OF COMPLEMENT CASCADE 1.74e-02 1.00e+00 G ALPHA I SIGNALLING EVENTS 2.54e-02 1.00e+00 G ALPHA I SIGNALLING EVENTS 3.16e-02 1.00e+00 SYNTHESIS SECRETION AND INACTIVATION OF GIP 3.35e-02 1.00e+00 REGULATION OF WATER BALANCE BY RENAL AQUAPORINS

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

²FDR corrected p-value (Benjamini-Hochberg)

Mouse mutant phenotypes

P-value1 FDR2 Term 3.28e-05 1.08e-01 increased food intake 3.55e-04 4.95e-01 increased circulating insulin level 8.89e-04 8.41e-01 increased susceptibility to age related obesity 1.87e-03 1.00e+00 abnormal growth hormone level 2.83e-03 1.00e+00 abnormal postnatal growth/weight/body size 3.76e-03 1.00e+00 abnormal induced morbidity/mortality 3.82e-03 1.00e+00 increased susceptibility to diet-induced obesity 5.28e-03 1.00e+00 abnormal retinal apoptosis 5.47e-03 1.00e+00 abnormal immune system morphology 5.49e-03 1.00e+00 retinal photoreceptor degeneration 6.01e-03 1.00e+00 abnormal tumor necrosis factor level 7.40e-03 1.00e+00 polyphagia 9.33e-03 1.00e+00 decreased circulating ghrelin level 9.38e-03 1.00e+00 increased circulating ghrelin level 1.12e-02 1.00e+00 retinal deposits 1.12e-02 1.00e+00 enhanced spatial learning 1.13e-02 1.00e+00 impaired complement alternative pathway 1.25e-02 1.00e+00 decreased susceptibility to injury 1.49e-02 1.00e+00 abnormal hypersensitivity reaction 1.55e-02 1.00e+00 decreased neutrophil cell number

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

²FDR corrected p-value (Benjamini-Hochberg)