Back to main page

DREAM Module Identification Challenge – Consensus modules

PPI-STRING_Consensus_mod268

Assigned name NA Network PPI-STRING Module ID PPI-STRING_Consensus_mod268 Module size 48 genes

Module genes

This module comprises the following genes:

Gene ID Gene Symbol Gene Name 8038 ADAM12 ADAM metallopeptidase domain 12 8728 ADAM19 ADAM metallopeptidase domain 19 56899 AIDA ankyrin repeat and sterile alpha motif domain containing 1B 28990 ASTE1 asteroid homolog 1 685 BTC betacellulin 64115 C10orf54 V-set immunoregulatory receptor 342510 CD300E CD300e molecule 124599 CD300LB CD300 molecule like family member b 963 CD53 CD53 molecule 968 CD68 CD68 molecule 160364 CLEC12A C-type lectin domain family 12 member A 23601 CLEC5A C-type lectin domain containing 5A 1535 CYBA cytochrome b-245 alpha chain 1536 CYBB cytochrome b-245 beta chain 192262 EGF complement C1s 1956 EGFR epidermal growth factor receptor 2015 EMR1 adhesion G protein-coupled receptor E1 84658 EMR3 adhesion G protein-coupled receptor E3 2065 ERBB3 erb-b2 receptor tyrosine kinase 3 2066 ERBB4 erb-b2 receptor tyrosine kinase 4 2069 EREG epiregulin 685433 EVI2A ecotropic viral integration site 2A 2124 EVI2B ecotropic viral integration site 2B 84467 FBN3 fibrillin 3 10457 GPNMB glycoprotein nmb 1839 HBEGF heparin binding EGF like growth factor 10261 IGSF6 immunoglobulin superfamily member 6 7805 LAPTM5 lysosomal protein transmembrane 5 219972 MPEG1 macrophage expressed 1 653361 NCF1 neutrophil cytosolic factor 1 4688 NCF2 neutrophil cytosolic factor 2 9436 NCR2 natural cytotoxicity triggering receptor 2 27035 NOX1 NADPH oxidase 1 50508 NOX3 NADPH oxidase 3 50507 NOX4 NADPH oxidase 4 10811 NOXA1 NADPH oxidase activator 1 124056 NOXO1 NADPH oxidase organizer 1 3084 NRG1 neuregulin 1 9542 NRG2 neuregulin 2 10718 NRG3 neuregulin 3 145957 NRG4 neuregulin 4 6039 RNASE6 ribonuclease A family member k6 6402 SELL selectin L 6404 SELPLG selectin P ligand 56833 SLAMF8 SLAM family member 8 54210 TREM1 triggering receptor expressed on myeloid cells 1 285852 TREML4 triggering receptor expressed on myeloid cells like 4 7305 TYROBP TYRO protein tyrosine kinase binding 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 4.11e-01 2.14e-22 GO NADPH oxidase complex cellular_component 4.00e-01 2.56e-28 Reactome ERBB2 Activates PTK6 Signaling Signal Transduction 2.20e-01 3.33e-05 Reactome Invadopodia formation Extracellular matrix organization 1.61e-01 4.47e-27 Reactome ERBB2 Regulates Cell Motility Signal Transduction 1.23e-01 6.50e-19 Reactome RHO GTPases Activate NADPH Oxidases Signal Transduction 1.22e-01 2.28e-20 Reactome PI3K events in ERBB4 signaling Signal Transduction 1.06e-01 4.37e-16 GO superoxide anion generation biological_process 4.51e-02 1.43e-26 Reactome PI3K events in ERBB2 signaling Signal Transduction 4.18e-02 8.34e-10 Reactome DAP12 interactions Immune System 1.75e-02 5.56e-06 Reactome Signaling by Overexpressed Wild-Type EGFR in Cancer Disease 5.88e-03 5.56e-06 Reactome Inhibition of Signaling by Overexpressed EGFR Disease

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 superoxide anion generation 0.00e+00 0.00e+00 reactive oxygen species metabolic process 0.00e+00 0.00e+00 superoxide metabolic process 0.00e+00 0.00e+00 negative regulation of ERBB signaling pathway 0.00e+00 0.00e+00 ERBB2 signaling pathway 0.00e+00 0.00e+00 NADPH oxidase complex 0.00e+00 0.00e+00 oxidoreductase complex 0.00e+00 0.00e+00 superoxide-generating NADPH oxidase activity 0.00e+00 0.00e+00 phosphatidylinositol-4,5-bisphosphate 3-kinase activity 0.00e+00 0.00e+00 phosphatidylinositol 3-kinase activity 2.81e-11 2.46e-08 regulation of ERBB signaling pathway 2.81e-11 2.46e-08 phosphatidylinositol phosphorylation 3.12e-11 2.72e-08 ERBB signaling pathway 6.82e-11 5.76e-08 lipid phosphorylation 1.14e-09 5.99e-07 protein tyrosine kinase activity 2.77e-09 1.95e-06 transmembrane receptor protein tyrosine kinase signaling pathway 3.76e-09 2.59e-06 phosphatidylinositol-mediated signaling 3.88e-09 2.66e-06 inositol lipid-mediated signaling 4.40e-09 2.11e-06 Ras guanyl-nucleotide exchange factor activity 9.44e-09 6.16e-06 phosphatidylinositol metabolic process

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 SIGNALING BY ERBB4 0.00e+00 0.00e+00 SIGNALING BY ERBB2 0.00e+00 0.00e+00 PI3K EVENTS IN ERBB2 SIGNALING 0.00e+00 0.00e+00 GRB2 EVENTS IN ERBB2 SIGNALING 0.00e+00 0.00e+00 SHC1 EVENTS IN ERBB4 SIGNALING 0.00e+00 0.00e+00 SIGNALING BY ERBB4 0.00e+00 0.00e+00 SIGNALING BY ERBB2 0.00e+00 0.00e+00 PI3K EVENTS IN ERBB2 SIGNALING 0.00e+00 0.00e+00 GRB2 EVENTS IN ERBB2 SIGNALING 8.23e-12 2.41e-09 SHC1 EVENTS IN ERBB4 SIGNALING 7.21e-11 2.65e-08 PI3K EVENTS IN ERBB4 SIGNALING 2.02e-10 5.35e-08 NUCLEAR SIGNALING BY ERBB4 2.71e-10 7.06e-08 PI3K EVENTS IN ERBB4 SIGNALING 6.30e-10 2.12e-07 NUCLEAR SIGNALING BY ERBB4 1.49e-05 2.76e-03 DOWNREGULATION OF ERBB2 ERBB3 SIGNALING 2.22e-05 3.14e-03 DOWNREGULATION OF ERBB2 ERBB3 SIGNALING 7.72e-05 1.00e-02 LATENT INFECTION OF HOMO SAPIENS WITH MYCOBACTERIUM TUBERCULOSIS 7.42e-04 9.06e-02 LATENT INFECTION OF HOMO SAPIENS WITH MYCOBACTERIUM TUBERCULOSIS 1.17e-03 1.35e-01 SHC1 EVENTS IN EGFR SIGNALING 1.27e-03 1.24e-01 SHC1 EVENTS IN EGFR SIGNALING

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

²FDR corrected p-value (Benjamini-Hochberg)

Mouse mutant phenotypes

P-value1 FDR2 Term 3.04e-05 1.03e-01 absent otoliths 3.10e-05 1.05e-01 abnormal neutrophil physiology 5.73e-05 1.57e-01 cardiac hypertrophy 9.62e-05 2.21e-01 abnormal aortic valve morphology 3.03e-04 4.49e-01 enlarged aortic valve 4.03e-04 5.35e-01 head tilt 4.74e-04 5.90e-01 abnormal type IV hypersensitivity reaction 8.39e-04 8.16e-01 abnormal pulmonary valve morphology 1.09e-03 9.45e-01 thick aortic valve 1.24e-03 1.00e+00 pulmonary valve stenosis 1.26e-03 1.00e+00 decreased atrioventricular cushion size 1.56e-03 1.00e+00 abnormal maternal decidual layer morphology 2.05e-03 1.00e+00 aortic valve stenosis 2.07e-03 1.00e+00 abnormal redox activity 2.42e-03 1.00e+00 abnormal atrioventricular valve morphology 2.65e-03 1.00e+00 abnormal tricuspid valve morphology 3.64e-03 1.00e+00 increased acute inflammation 3.66e-03 1.00e+00 absent linear vestibular evoked potential 4.13e-03 1.00e+00 abnormal semilunar valve morphology 4.26e-03 1.00e+00 abnormal mitral valve morphology

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

²FDR corrected p-value (Benjamini-Hochberg)