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DREAM Module Identification Challenge – Consensus modules

PPI-STRING_Consensus_mod179

Assigned name NA Network PPI-STRING Module ID PPI-STRING_Consensus_mod179 Module size 49 genes

Module genes

This module comprises the following genes:

Gene ID Gene Symbol Gene Name 146 ADRA1A adrenoceptor alpha 1D 146 ADRA1D adrenoceptor alpha 1D 886 CCKAR cholecystokinin A receptor 887 CCKBR cholecystokinin B receptor 1131 CHRM3 cholinergic receptor muscarinic 3 1133 CHRM5 cholinergic receptor muscarinic 5 10800 CYSLTR1 cysteinyl leukotriene receptor 1 57105 CYSLTR2 cysteinyl leukotriene receptor 2 1907 EDN2 endothelin 2 1908 EDN3 endothelin 3 2864 FFAR1 free fatty acid receptor 1 2867 FFAR2 free fatty acid receptor 2 2865 FFAR3 free fatty acid receptor 3 2693 GHSR growth hormone secretagogue receptor 2797 GNRH2 gonadotropin releasing hormone 2 29933 GPR132 G protein-coupled receptor 132 2828 GPR4 G protein-coupled receptor 4 8111 GPR68 G protein-coupled receptor 68 222545 GPRC6A G protein-coupled receptor class C group 6 member A 2925 GRPR gastrin releasing peptide receptor 3060 HCRT hypocretin neuropeptide precursor 3062 HCRTR2 hypocretin receptor 2 1659 HRH1 DEAH-box helicase 8 84634 KISS1R KISS1 receptor 1241 LTB4R leukotriene B4 receptor 56413 LTB4R2 leukotriene B4 receptor 2 4295 MLN motilin 10457 NMB glycoprotein nmb 4829 NMBR neuromedin B receptor 8620 NPFF neuropeptide FF-amide peptide precursor 64106 NPFFR1 neuropeptide FF receptor 1 10886 NPFFR2 neuropeptide FF receptor 2 23620 NTSR2 neurotensin receptor 2 94233 OPN4 opsin 4 5028 P2RY1 purinergic receptor P2Y1 27334 P2RY10 P2Y receptor family member 10 84432 PROK1 prokineticin 1 60675 PROK2 prokineticin 2 10887 PROKR1 prokineticin receptor 1 128674 PROKR2 prokineticin receptor 2 347148 QRFP pyroglutamylated RFamide peptide 84109 QRFPR pyroglutamylated RFamide peptide receptor 6866 TAC3 tachykinin 3 25569 TRH thyrotropin releasing hormone 7201 TRHR thyrotropin releasing hormone receptor 10911 UTS2 urotensin 2 257313 UTS2D urotensin 2B 2837 UTS2R urotensin 2 receptor 6846 XCL2 X-C motif chemokine ligand 2

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 4.62e-01 6.73e-18 Reactome Orexin and neuropeptides FF and QRFP bind to their respective receptors Signal Transduction 3.51e-01 2.68e-10 Reactome Leukotriene receptors Signal Transduction 1.99e-01 2.04e-07 Reactome Free fatty acid receptors Signal Transduction 1.37e-01 1.71e-95 Reactome G alpha (q) signalling events Signal Transduction 4.54e-02 1.36e-81 Reactome Class A/1 (Rhodopsin-like receptors) Signal Transduction 4.08e-02 7.61e-05 Reactome Muscarinic acetylcholine receptors Signal Transduction 1.09e-02 4.11e-29 GO neuropeptide signaling pathway biological_process 3.41e-03 1.60e-07 GO positive regulation of smooth muscle contraction biological_process 2.43e-03 2.59e-18 GO phospholipase C-activating G-protein coupled receptor signaling pathway 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 neuropeptide signaling pathway 0.00e+00 0.00e+00 circulatory system process 0.00e+00 0.00e+00 calcium ion homeostasis 0.00e+00 0.00e+00 cellular cation homeostasis 0.00e+00 0.00e+00 cellular chemical homeostasis 0.00e+00 0.00e+00 metal ion homeostasis 0.00e+00 0.00e+00 regulation of cytosolic calcium ion concentration 0.00e+00 0.00e+00 phospholipase C-activating G-protein coupled receptor signaling pathway 0.00e+00 0.00e+00 cellular metal ion homeostasis 0.00e+00 0.00e+00 cellular 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 ion homeostasis 0.00e+00 0.00e+00 G-protein coupled receptor activity 0.00e+00 0.00e+00 G-protein coupled peptide receptor activity 0.00e+00 0.00e+00 neuropeptide receptor activity 0.00e+00 0.00e+00 G-protein coupled receptor binding 1.15e-11 7.61e-09 hormone activity 7.29e-11 6.14e-08 blood circulation 8.69e-11 7.25e-08 feeding behavior

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 GASTRIN CREB SIGNALLING PATHWAY VIA PKC AND MAPK 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 G ALPHA Q SIGNALLING EVENTS 0.00e+00 0.00e+00 PEPTIDE LIGAND BINDING RECEPTORS 0.00e+00 0.00e+00 GASTRIN CREB SIGNALLING PATHWAY VIA PKC AND MAPK 0.00e+00 0.00e+00 G ALPHA Q SIGNALLING EVENTS 0.00e+00 0.00e+00 PEPTIDE LIGAND BINDING RECEPTORS 3.65e-05 6.30e-03 EICOSANOID LIGAND BINDING RECEPTORS 9.37e-05 1.20e-02 AMINE LIGAND BINDING RECEPTORS 9.63e-05 1.23e-02 EICOSANOID LIGAND BINDING RECEPTORS 3.42e-04 4.61e-02 AMINE LIGAND BINDING RECEPTORS 7.22e-03 5.62e-01 P2Y RECEPTORS 9.72e-03 7.16e-01 NUCLEOTIDE LIKE PURINERGIC RECEPTORS 1.03e-02 8.15e-01 ADP SIGNALLING THROUGH P2RY1 1.32e-02 9.18e-01 G ALPHA1213 SIGNALLING EVENTS 1.45e-02 9.89e-01 REGULATION OF INSULIN SECRETION 1.81e-02 1.00e+00 ADP SIGNALLING THROUGH P2RY1 1.90e-02 1.00e+00 P2Y RECEPTORS 2.39e-02 1.00e+00 SIGNAL AMPLIFICATION

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

²FDR corrected p-value (Benjamini-Hochberg)

Mouse mutant phenotypes

P-value1 FDR2 Term 3.45e-06 2.22e-02 decreased body temperature 7.63e-06 3.87e-02 abnormal muscle tone 4.85e-05 1.39e-01 decreased susceptibility to type I hypersensitivity reaction 6.64e-05 1.72e-01 decreased circulating insulin level 1.30e-04 2.69e-01 decreased circulating glucagon level 1.63e-04 3.10e-01 abnormal non-rapid eye movement sleep pattern 1.63e-04 3.10e-01 narcolepsy 1.65e-04 3.13e-01 abnormal histamine physiology 4.07e-04 5.37e-01 fragmentation of sleep/wake states 4.09e-04 5.37e-01 abnormal paradoxical sleep pattern 6.82e-04 7.26e-01 abnormal response/metabolism to endogenous compounds 9.40e-04 8.70e-01 decreased insulin secretion 1.10e-03 9.51e-01 decreased circulating testosterone level 1.17e-03 9.85e-01 abnormal circadian temperature homeostasis 1.34e-03 1.00e+00 abnormal granulocyte physiology 1.42e-03 1.00e+00 abnormal digestive system physiology 1.53e-03 1.00e+00 decreased digestive secretion 1.67e-03 1.00e+00 decreased circulating triiodothyronine level 1.77e-03 1.00e+00 decreased luteinizing hormone level 2.21e-03 1.00e+00 abnormal rostral migratory stream morphology

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

²FDR corrected p-value (Benjamini-Hochberg)