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DREAM Module Identification Challenge – Consensus modules

PPI-STRING_Consensus_mod231

Assigned name NA Network PPI-STRING Module ID PPI-STRING_Consensus_mod231 Module size 34 genes

Module genes

This module comprises the following genes:

Gene ID Gene Symbol Gene Name 51554 CCBP2 atypical chemokine receptor 4 6346 CCL1 C-C motif chemokine ligand 1 6357 CCL13 C-C motif chemokine ligand 13 6358 CCL14 C-C motif chemokine ligand 14 348249 CCL15-CCL14 CCL15-CCL14 readthrough (NMD candidate) 6361 CCL17 C-C motif chemokine ligand 17 6362 CCL18 C-C motif chemokine ligand 18 6347 CCL2 C-C motif chemokine ligand 2 6367 CCL22 C-C motif chemokine ligand 22 6368 CCL23 C-C motif chemokine ligand 23 6348 CCL3 C-C motif chemokine ligand 3 6351 CCL4 C-C motif chemokine ligand 4 6352 CCL5 C-C motif chemokine ligand 5 6354 CCL7 C-C motif chemokine ligand 7 6355 CCL8 C-C motif chemokine ligand 8 1230 CCR1 C-C motif chemokine receptor 1 51554 CCR10 atypical chemokine receptor 4 729230 CCR2 C-C motif chemokine receptor 2 1232 CCR3 C-C motif chemokine receptor 3 57472 CCR4 CCR4-NOT transcription complex subunit 6 1234 CCR5 C-C motif chemokine receptor 5 (gene/pseudogene) 9034 CCR6 C-C motif chemokine receptor like 2 1236 CCR7 C-C motif chemokine receptor 7 1237 CCR8 C-C motif chemokine receptor 8 1238 CCR9 atypical chemokine receptor 2 51554 CCRL1 atypical chemokine receptor 4 6376 CX3CL1 C-X3-C motif chemokine ligand 1 1524 CX3CR1 C-X3-C motif chemokine receptor 1 9547 CXCL14 C-X-C motif chemokine ligand 14 3579 CXCR2 C-X-C motif chemokine receptor 2 2833 CXCR3 C-X-C motif chemokine receptor 3 7852 CXCR4 C-X-C motif chemokine receptor 4 643 CXCR5 C-X-C motif chemokine receptor 5 131890 GRK7 G protein-coupled receptor kinase 7

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 3.33e-01 1.62e-14 GO CCR1 chemokine receptor binding molecular_function 1.94e-01 1.08e-37 GO C-C chemokine receptor activity molecular_function 1.45e-01 4.79e-29 GO eosinophil chemotaxis biological_process 1.39e-01 2.89e-37 GO chemokine binding molecular_function 1.30e-01 2.89e-37 GO C-C chemokine binding molecular_function 9.43e-02 1.24e-34 GO lymphocyte chemotaxis biological_process 7.27e-02 1.71e-35 GO CCR chemokine receptor binding molecular_function 4.84e-02 4.70e-69 GO chemokine-mediated signaling pathway biological_process 2.56e-02 5.72e-35 GO monocyte chemotaxis biological_process 2.34e-02 1.35e-18 GO dendritic cell chemotaxis biological_process 1.61e-02 3.93e-58 GO chemotaxis 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 0e+00 0e+00 response to cytokine 0e+00 0e+00 cellular chemical homeostasis 0e+00 0e+00 cellular homeostasis 0e+00 0e+00 calcium ion homeostasis 0e+00 0e+00 metal ion homeostasis 0e+00 0e+00 cellular metal ion homeostasis 0e+00 0e+00 cellular ion homeostasis 0e+00 0e+00 cellular calcium ion homeostasis 0e+00 0e+00 positive regulation of cytosolic calcium ion concentration 0e+00 0e+00 chemotaxis 0e+00 0e+00 chemokine-mediated signaling pathway 0e+00 0e+00 cytokine-mediated signaling pathway 0e+00 0e+00 ion homeostasis 0e+00 0e+00 cellular response to cytokine stimulus 0e+00 0e+00 cellular cation homeostasis 0e+00 0e+00 inflammatory response 0e+00 0e+00 response to tumor necrosis factor 0e+00 0e+00 neutrophil chemotaxis 0e+00 0e+00 leukocyte migration 0e+00 0e+00 leukocyte chemotaxis

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 G ALPHA I SIGNALLING EVENTS 0.00e+00 0.00e+00 CHEMOKINE RECEPTORS BIND CHEMOKINES 0.00e+00 0.00e+00 CLASS A1 RHODOPSIN LIKE RECEPTORS 0.00e+00 0.00e+00 GPCR LIGAND BINDING 0.00e+00 0.00e+00 PEPTIDE LIGAND BINDING RECEPTORS 0.00e+00 0.00e+00 G ALPHA I SIGNALLING EVENTS 0.00e+00 0.00e+00 CHEMOKINE RECEPTORS BIND CHEMOKINES 0.00e+00 0.00e+00 PEPTIDE LIGAND BINDING RECEPTORS 1.89e-05 2.71e-03 BINDING AND ENTRY OF HIV VIRION 1.53e-04 2.27e-02 BINDING AND ENTRY OF HIV VIRION 6.89e-04 7.21e-02 EARLY PHASE OF HIV LIFE CYCLE 3.75e-03 3.60e-01 BETA DEFENSINS 3.78e-03 3.24e-01 BETA DEFENSINS 3.92e-03 3.74e-01 EARLY PHASE OF HIV LIFE CYCLE 4.03e-03 3.82e-01 DEFENSINS 9.81e-03 7.22e-01 DEFENSINS 1.52e-02 1.00e+00 HIV LIFE CYCLE 3.00e-02 1.00e+00 HIV INFECTION 4.97e-02 1.00e+00 ACTIVATION OF GENES BY ATF4

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

²FDR corrected p-value (Benjamini-Hochberg)

Mouse mutant phenotypes

P-value1 FDR2 Term 3.20e-08 5.96e-04 increased length of allograft survival 9.57e-07 8.52e-03 impaired macrophage chemotaxis 1.06e-06 9.10e-03 decreased macrophage cell number 2.07e-06 1.50e-02 retinal deposits 3.84e-06 2.36e-02 abnormal cellular extravasation 5.49e-06 3.15e-02 choroidal neovascularization 7.67e-06 3.87e-02 decreased susceptibility to experimental autoimmune encephalomyelitis 2.70e-05 9.64e-02 abnormal dendritic cell chemotaxis 3.55e-05 1.14e-01 decreased susceptibility to viral infection 3.66e-05 1.16e-01 decreased monocyte cell number 6.21e-05 1.64e-01 increased alcohol consumption 6.59e-05 1.72e-01 increased interferon-gamma secretion 6.66e-05 1.72e-01 abnormal chemokine secretion 7.18e-05 1.81e-01 abnormal conditioned taste aversion behavior 7.34e-05 1.84e-01 abnormal leukocyte migration 1.14e-04 2.46e-01 altered response to myocardial infarction 1.21e-04 2.55e-01 abnormal leukocyte physiology 1.50e-04 2.95e-01 decreased susceptibility to induced colitis 1.73e-04 3.21e-01 decreased susceptibility to type IV hypersensitivity reaction 1.84e-04 3.31e-01 decreased airway responsiveness

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

²FDR corrected p-value (Benjamini-Hochberg)