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DREAM Module Identification Challenge – Consensus modules

PPI-STRING_Consensus_mod221

Assigned name NA Network PPI-STRING Module ID PPI-STRING_Consensus_mod221 Module size 21 genes

Module genes

This module comprises the following genes:

Gene ID Gene Symbol Gene Name 301 ANXA1 annexin A1 623 BDKRB1 bradykinin receptor B1 623 BDKRB2 bradykinin receptor B1 846 CASR calcium sensing receptor 2358 FPR2 formyl peptide receptor 2 2840 GPR17 G protein-coupled receptor 17 1902 LPAR1 lysophosphatidic acid receptor 1 9170 LPAR2 lysophosphatidic acid receptor 2 23566 LPAR3 lysophosphatidic acid receptor 3 57121 LPAR5 lysophosphatidic acid receptor 5 2847 MCHR1 melanin concentrating hormone receptor 1 84539 MCHR2 melanin concentrating hormone receptor 2 100462981 MTRNR2L2 MT-RNR2 like 2 129521 NMS neuromedin S 63887 NMU neuromedin U 10316 NMUR1 neuromedin U receptor 1 56923 NMUR2 neuromedin U receptor 2 5367 PMCH pro-melanin concentrating hormone 64407 RGS18 regulator of G protein signaling 18 10287 RGS19 regulator of G protein signaling 19 6288 SAA1 serum amyloid A1

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 1.15e-01 1.64e-09 Reactome Lysosphingolipid and LPA receptors Signal Transduction 1.11e-01 1.32e-07 Reactome Formyl peptide receptors bind formyl peptides and many other ligands Signal Transduction 3.79e-02 1.60e-32 Reactome G alpha (q) signalling events Signal Transduction 8.97e-03 7.89e-28 Reactome G alpha (i) signalling events Signal Transduction 5.28e-03 3.14e-06 GO arachidonic acid secretion biological_process 4.73e-03 2.75e-06 GO feeding behavior biological_process 4.61e-03 2.07e-06 GO G-protein alpha-subunit binding molecular_function 2.79e-03 4.69e-16 GO positive regulation of cytosolic calcium ion concentration biological_process 9.11e-04 6.37e-05 GO bleb assembly 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 calcium ion homeostasis 0.00e+00 0.00e+00 cellular calcium ion homeostasis 0.00e+00 0.00e+00 positive regulation of cytosolic calcium ion concentration 0.00e+00 0.00e+00 G-protein coupled receptor activity 1.47e-11 9.65e-09 G-protein coupled peptide receptor activity 1.73e-11 1.54e-08 regulation of cytosolic calcium ion concentration 1.22e-10 1.00e-07 cellular metal ion homeostasis 1.25e-10 1.03e-07 neuropeptide signaling pathway 4.43e-10 3.44e-07 metal ion homeostasis 7.58e-10 5.73e-07 phospholipase C-activating G-protein coupled receptor signaling pathway 7.60e-10 5.74e-07 cellular cation homeostasis 9.52e-10 7.12e-07 cellular ion homeostasis 4.32e-09 2.95e-06 ion homeostasis 4.36e-09 2.97e-06 cellular chemical homeostasis 2.12e-08 1.32e-05 cellular homeostasis 9.26e-08 3.58e-05 lysophosphatidic acid receptor activity 3.14e-07 1.63e-04 regulation of phospholipase activity 2.37e-06 7.00e-04 bioactive lipid receptor activity 3.29e-06 9.46e-04 G-protein alpha-subunit binding 5.89e-06 2.40e-03 positive regulation of phospholipase activity

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

²FDR corrected p-value (Benjamini-Hochberg)

Reactome

P-value1 FDR2 Term 0.00e+00 0e+00 GASTRIN CREB SIGNALLING PATHWAY VIA PKC AND MAPK 0.00e+00 0e+00 G ALPHA I SIGNALLING EVENTS 0.00e+00 0e+00 CLASS A1 RHODOPSIN LIKE RECEPTORS 0.00e+00 0e+00 GPCR LIGAND BINDING 0.00e+00 0e+00 G ALPHA Q SIGNALLING EVENTS 0.00e+00 0e+00 PEPTIDE LIGAND BINDING RECEPTORS 0.00e+00 0e+00 GASTRIN CREB SIGNALLING PATHWAY VIA PKC AND MAPK 0.00e+00 0e+00 G ALPHA I SIGNALLING EVENTS 0.00e+00 0e+00 G ALPHA Q SIGNALLING EVENTS 0.00e+00 0e+00 PEPTIDE LIGAND BINDING RECEPTORS 2.41e-02 1e+00 CLASS C 3 METABOTROPIC GLUTAMATE PHEROMONE RECEPTORS 2.46e-02 1e+00 ADVANCED GLYCOSYLATION ENDPRODUCT RECEPTOR SIGNALING 2.69e-02 1e+00 TRAF6 MEDIATED NFKB ACTIVATION 2.89e-02 1e+00 RIP MEDIATED NFKB ACTIVATION VIA DAI 3.16e-02 1e+00 RIP MEDIATED NFKB ACTIVATION VIA DAI 3.38e-02 1e+00 CLASS C 3 METABOTROPIC GLUTAMATE PHEROMONE RECEPTORS 3.42e-02 1e+00 ADVANCED GLYCOSYLATION ENDPRODUCT RECEPTOR SIGNALING 3.89e-02 1e+00 TAK1 ACTIVATES NFKB BY PHOSPHORYLATION AND ACTIVATION OF IKKS COMPLEX 4.09e-02 1e+00 TAK1 ACTIVATES NFKB BY PHOSPHORYLATION AND ACTIVATION OF IKKS COMPLEX

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

²FDR corrected p-value (Benjamini-Hochberg)

Mouse mutant phenotypes

P-value1 FDR2 Term 9.32e-04 8.66e-01 decreased circulating leptin level 1.87e-03 1.00e+00 abnormal serotonin level 2.53e-03 1.00e+00 abnormal pain threshold 5.78e-03 1.00e+00 abnormal colon morphology 7.47e-03 1.00e+00 decreased respiratory mucosa goblet cell number 7.47e-03 1.00e+00 abnormal gonadotroph morphology 7.47e-03 1.00e+00 ectopic cranial bone growth 7.50e-03 1.00e+00 polyphagia 7.92e-03 1.00e+00 decreased food intake 9.33e-03 1.00e+00 enhanced spatial learning 9.33e-03 1.00e+00 abnormal corticotroph morphology 9.34e-03 1.00e+00 increased colonic adenoma incidence 9.34e-03 1.00e+00 calcinosis 9.50e-03 1.00e+00 abnormal response/metabolism to endogenous compounds 1.12e-02 1.00e+00 long incisors 1.12e-02 1.00e+00 abnormal juxtaglomerular cell morphology 1.24e-02 1.00e+00 abnormal social investigation 1.27e-02 1.00e+00 decreased response to stress-induced hyperthermia 1.29e-02 1.00e+00 increased thermal nociceptive threshold 1.30e-02 1.00e+00 abnormal mitochondrial chromosome morphology

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

²FDR corrected p-value (Benjamini-Hochberg)