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DREAM Module Identification Challenge – Consensus modules

PPI-STRING_Consensus_mod351

Assigned name NA Network PPI-STRING Module ID PPI-STRING_Consensus_mod351 Module size 88 genes

Module genes

This module comprises the following genes:

Gene ID Gene Symbol Gene Name 134 ADORA1 adenosine A1 receptor 140 ADORA3 adenosine A3 receptor 150 ADRA2A adrenoceptor alpha 2A 151 ADRA2B adrenoceptor alpha 2B 152 ADRA2C adrenoceptor alpha 2C 8862 APLN apelin 187 APLNR apelin receptor 719 C3AR1 complement C3a receptor 1 728 C5AR1 complement C5a receptor 1 6360 CCL16 C-C motif chemokine ligand 16 6363 CCL19 C-C motif chemokine ligand 19 6364 CCL20 C-C motif chemokine ligand 20 6366 CCL21 C-C motif chemokine ligand 21 6370 CCL25 C-C motif chemokine ligand 25 10850 CCL27 C-C motif chemokine ligand 27 56477 CCL28 C-C motif chemokine ligand 28 1132 CHRM4 cholinergic receptor muscarinic 4 56142 CNR2 protocadherin alpha 6 10563 CXCL13 C-X-C motif chemokine ligand 13 58191 CXCL16 C-X-C motif chemokine ligand 16 2921 CXCL3 C-X-C motif chemokine ligand 3 6374 CXCL5 C-X-C motif chemokine ligand 5 6372 CXCL6 C-X-C motif chemokine ligand 6 2359 FPR3 formyl peptide receptor 3 2587 GALR1 galanin receptor 1 8811 GALR2 galanin receptor 2 8484 GALR3 galanin receptor 3 2852 GPER G protein-coupled estrogen receptor 1 2841 GPR18 G protein-coupled receptor 18 9290 GPR55 G protein-coupled receptor 55 2912 GRM2 glutamate metabotropic receptor 2 2913 GRM3 glutamate metabotropic receptor 3 2916 GRM6 glutamate metabotropic receptor 6 2918 GRM8 glutamate metabotropic receptor 8 27198 HCAR1 hydroxycarboxylic acid receptor 1 338442 HCAR2 hydroxycarboxylic acid receptor 2 8843 HCAR3 hydroxycarboxylic acid receptor 3 50865 HEBP1 heme binding protein 1 11255 HRH3 histamine receptor H3 59340 HRH4 histamine receptor H4 3351 HTR1B 5-hydroxytryptamine receptor 1B 3352 HTR1D 5-hydroxytryptamine receptor 1D 3354 HTR1E 5-hydroxytryptamine receptor 1E 3355 HTR1F 5-hydroxytryptamine receptor 1F 3361 HTR5A 5-hydroxytryptamine receptor 5A 256933 NPB neuropeptide B 2831 NPBWR1 neuropeptides B and W receptor 1 2832 NPBWR2 neuropeptides B and W receptor 2 283869 NPW neuropeptide W 4852 NPY neuropeptide Y 4886 NPY1R neuropeptide Y receptor Y1 4887 NPY2R neuropeptide Y receptor Y2 4889 NPY5R neuropeptide Y receptor Y5 4985 OPRD1 opioid receptor delta 1 4986 OPRK1 opioid receptor kappa 1 4987 OPRL1 opioid related nociceptin receptor 1 165140 OXER1 oxoeicosanoid receptor 1 27199 OXGR1 oxoglutarate receptor 1 64805 P2RY12 purinergic receptor P2Y12 53829 P2RY13 purinergic receptor P2Y13 9934 P2RY14 purinergic receptor P2Y14 5030 P2RY4 pyrimidinergic receptor P2Y4 5173 PDYN prodynorphin 5179 PENK proenkephalin 5368 PNOC prepronociceptin 5539 PPY pancreatic polypeptide 11251 PTGDR2 prostaglandin D2 receptor 2 5733 PTGER3 prostaglandin E receptor 3 339403 RXFP4 relaxin family peptide/INSL5 receptor 4 1903 S1PR3 sphingosine-1-phosphate receptor 3 53637 S1PR5 sphingosine-1-phosphate receptor 5 6750 SST somatostatin 6751 SSTR1 somatostatin receptor 1 6752 SSTR2 somatostatin receptor 2 6754 SSTR4 somatostatin receptor 4 6755 SSTR5 somatostatin receptor 5 56670 SUCNR1 succinate receptor 1 50834 TAS2R1 taste 2 receptor member 1 50833 TAS2R16 taste 2 receptor member 16 50831 TAS2R3 taste 2 receptor member 3 259285 TAS2R39 taste 2 receptor member 39 50832 TAS2R4 taste 2 receptor member 4 259286 TAS2R40 taste 2 receptor member 40 259287 TAS2R41 taste 2 receptor member 41 353164 TAS2R42 taste 2 receptor member 42 259289 TAS2R43 taste 2 receptor member 43 54429 TAS2R5 taste 2 receptor member 5 338398 TAS2R60 taste 2 receptor member 60

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 4.02e-01 1.26e-07 Reactome Hydroxycarboxylic acid-binding receptors Signal Transduction 3.97e-01 1.26e-07 Reactome Adrenaline signalling through Alpha-2 adrenergic receptor Hemostasis 1.85e-01 1.56e-150 Reactome G alpha (i) signalling events Signal Transduction 1.83e-01 2.12e-08 GO adenylate cyclase-inhibiting G-protein coupled glutamate receptor signaling pathway biological_process 1.65e-01 8.03e-23 GO neuropeptide binding molecular_function 1.20e-01 1.34e-09 GO serotonin binding molecular_function 1.20e-01 1.23e-19 GO bitter taste receptor activity molecular_function 9.42e-02 1.09e-10 Reactome Nucleotide-like (purinergic) receptors Signal Transduction 7.13e-02 1.64e-10 GO opioid receptor signaling pathway biological_process 6.85e-02 3.34e-112 Reactome Class A/1 (Rhodopsin-like receptors) Signal Transduction 6.04e-02 1.51e-04 Reactome Histamine receptors Signal Transduction 5.36e-02 5.91e-07 GO positive regulation of chemotaxis biological_process 5.15e-02 6.66e-35 GO neuropeptide signaling pathway biological_process 2.10e-02 1.21e-141 Reactome GPCR ligand binding Signal Transduction 1.60e-02 4.25e-26 GO adenylate cyclase-inhibiting G-protein coupled receptor signaling pathway biological_process 9.24e-03 2.79e-25 GO G-protein coupled receptor signaling pathway, coupled to cyclic nucleotide second messenger biological_process 7.00e-03 1.35e-17 GO chemokine activity molecular_function 3.04e-03 3.78e-25 Reactome Class C/3 (Metabotropic glutamate/pheromone receptors) Signal Transduction 3.91e-04 6.90e-06 GO chemokine receptor binding molecular_function

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 negative regulation of cAMP biosynthetic process 0.00e+00 0.00e+00 sensory perception of taste 0.00e+00 0.00e+00 sensory perception of bitter taste 0.00e+00 0.00e+00 detection of chemical stimulus involved in sensory perception of bitter taste 0.00e+00 0.00e+00 detection of chemical stimulus involved in sensory perception of taste 0.00e+00 0.00e+00 taste receptor activity 0.00e+00 0.00e+00 bitter taste receptor activity 3.11e-65 2.27e-62 G-protein coupled receptor activity 2.27e-41 2.23e-38 G-protein coupled receptor signaling pathway, coupled to cyclic nucleotide second messenger 2.16e-30 2.12e-27 adenylate cyclase-modulating G-protein coupled receptor signaling pathway 1.25e-28 1.22e-25 neuropeptide signaling pathway 2.91e-28 2.85e-25 adenylate cyclase-inhibiting G-protein coupled receptor signaling pathway 2.33e-22 1.69e-19 G-protein coupled receptor binding 4.01e-21 3.88e-18 chemical synaptic transmission 3.50e-20 2.52e-17 neuropeptide binding 3.96e-18 3.78e-15 negative regulation of cAMP metabolic process 1.21e-16 8.52e-14 G-protein coupled peptide receptor activity 1.35e-16 9.50e-14 neuropeptide receptor activity 3.48e-16 3.29e-13 phospholipase C-activating G-protein coupled receptor signaling pathway 3.73e-16 2.62e-13 chemokine activity

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 CHEMOKINE RECEPTORS BIND CHEMOKINES 0.00e+00 0.00e+00 G ALPHA I SIGNALLING EVENTS 0.00e+00 0.00e+00 PEPTIDE LIGAND BINDING RECEPTORS 1.54e-86 6.21e-84 G ALPHA I SIGNALLING EVENTS 1.52e-66 6.12e-64 GPCR LIGAND BINDING 3.03e-65 1.22e-62 CLASS A1 RHODOPSIN LIKE RECEPTORS 1.89e-37 7.58e-35 PEPTIDE LIGAND BINDING RECEPTORS 3.13e-11 8.97e-09 CHEMOKINE RECEPTORS BIND CHEMOKINES 8.45e-09 1.87e-06 NUCLEOTIDE LIKE PURINERGIC RECEPTORS 2.11e-08 4.46e-06 AMINE LIGAND BINDING RECEPTORS 3.90e-08 1.06e-05 AMINE LIGAND BINDING RECEPTORS 2.92e-07 5.43e-05 SEROTONIN RECEPTORS 5.48e-07 1.28e-04 NUCLEOTIDE LIKE PURINERGIC RECEPTORS 6.23e-07 1.12e-04 P2Y RECEPTORS 2.93e-06 6.09e-04 SEROTONIN RECEPTORS 8.05e-06 1.56e-03 CLASS C 3 METABOTROPIC GLUTAMATE PHEROMONE RECEPTORS 3.89e-05 5.30e-03 CLASS C 3 METABOTROPIC GLUTAMATE PHEROMONE RECEPTORS 7.54e-05 1.21e-02 P2Y RECEPTORS 3.36e-03 3.30e-01 G ALPHA Z SIGNALLING EVENTS 3.65e-03 3.14e-01 ADP SIGNALLING THROUGH P2RY12

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

²FDR corrected p-value (Benjamini-Hochberg)

Mouse mutant phenotypes

P-value1 FDR2 Term 1.48e-06 1.17e-02 abnormal anxiety-related response 2.81e-05 9.84e-02 increased circulating corticosterone level 3.29e-05 1.09e-01 increased anxiety-related response 3.44e-05 1.12e-01 decreased osteoclast cell number 5.90e-05 1.59e-01 increased circulating leptin level 8.81e-05 2.09e-01 hyperalgesia 1.07e-04 2.37e-01 polyphagia 1.85e-04 3.32e-01 abnormal excitatory postsynaptic potential 2.28e-04 3.78e-01 decreased oxygen consumption 2.91e-04 4.41e-01 impaired conditioned place preference behavior 4.28e-04 5.53e-01 decreased chemically-elicited antinociception 4.68e-04 5.84e-01 increased total body fat amount 6.72e-04 7.20e-01 abnormal synaptic norepinephrine release 9.83e-04 8.94e-01 altered righting response 1.08e-03 9.40e-01 abnormal locomotor behavior 1.11e-03 9.56e-01 increased circulating insulin level 1.21e-03 1.00e+00 abnormal chemically-elicited antinociception 1.22e-03 1.00e+00 decreased exploration in new environment 1.25e-03 1.00e+00 decreased circulating interleukin-6 level 1.46e-03 1.00e+00 decreased energy expenditure

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

²FDR corrected p-value (Benjamini-Hochberg)