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DREAM Module Identification Challenge – Consensus modules

PPI-STRING_Consensus_mod241

Assigned name NA Network PPI-STRING Module ID PPI-STRING_Consensus_mod241 Module size 40 genes

Module genes

This module comprises the following genes:

Gene ID Gene Symbol Gene Name 55811 ADCY10 adenylate cyclase 10 256006 ANKRD31 ankyrin repeat domain 31 339829 CCDC39 coiled-coil domain containing 39 1259 CNGA1 cyclic nucleotide gated channel alpha 1 1261 CNGA3 cyclic nucleotide gated channel alpha 3 1258 CNGB1 cyclic nucleotide gated channel beta 1 54714 CNGB3 cyclic nucleotide gated channel beta 3 26507 CNNM1 cyclin and CBS domain divalent metal cation transport mediator 1 54805 CNNM2 cyclin and CBS domain divalent metal cation transport mediator 2 26505 CNNM3 cyclin and CBS domain divalent metal cation transport mediator 3 23333 DPY19L1 dpy-19 like C-mannosyltransferase 1 283417 DPY19L2 dpy-19 like 2 147991 DPY19L3 dpy-19 like C-mannosyltransferase 3 286148 DPY19L4 dpy-19 like 4 390212 GPR152 G protein-coupled receptor 152 2980 GUCA2A guanylate cyclase activator 2A 2981 GUCA2B guanylate cyclase activator 2B 2984 GUCY2C guanylate cyclase 2C 3000 GUCY2D guanylate cyclase 2D, retinal 2986 GUCY2F guanylate cyclase 2F, retinal 4881 NPR1 natriuretic peptide receptor 1 363138 NPR2 NPR2-like, GATOR1 complex subunit 10846 PDE10A phosphodiesterase 10A 50940 PDE11A phosphodiesterase 11A 5138 PDE2A phosphodiesterase 2A 5141 PDE4A phosphodiesterase 4A 5142 PDE4B phosphodiesterase 4B 5143 PDE4C phosphodiesterase 4C 5144 PDE4D phosphodiesterase 4D 8654 PDE5A phosphodiesterase 5A 5145 PDE6A phosphodiesterase 6A 5158 PDE6B phosphodiesterase 6B 5146 PDE6C phosphodiesterase 6C 5148 PDE6G phosphodiesterase 6G 5149 PDE6H phosphodiesterase 6H 5150 PDE7A phosphodiesterase 7A 27115 PDE7B phosphodiesterase 7B 5152 PDE9A phosphodiesterase 9A 84457 PHYHIPL phytanoyl-CoA 2-hydroxylase interacting protein like 5592 PRKG1 protein kinase cGMP-dependent 1

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 4.54e-01 2.45e-30 GO cGMP binding molecular_function 4.04e-01 7.33e-13 GO guanylate cyclase activity molecular_function 2.99e-01 1.72e-21 GO 3',5'-cyclic-AMP phosphodiesterase activity molecular_function 1.46e-01 8.75e-12 Reactome Activation of the phototransduction cascade Signal Transduction 1.34e-01 1.80e-08 GO mannosyltransferase activity molecular_function 9.54e-02 1.60e-11 GO receptor guanylyl cyclase signaling pathway biological_process 6.82e-02 5.17e-23 GO 3',5'-cyclic-GMP phosphodiesterase activity molecular_function 3.63e-02 1.95e-12 GO 3',5'-cyclic-nucleotide phosphodiesterase activity molecular_function 2.77e-02 3.97e-14 GO regulation of rhodopsin mediated signaling pathway biological_process 6.41e-03 2.45e-04 GO positive regulation of guanylate cyclase activity biological_process 4.60e-03 2.47e-12 GO cGMP-mediated signaling biological_process 8.23e-04 1.38e-05 Reactome Digestion Digestion and absorption

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 purine nucleotide metabolic process 0e+00 0e+00 purine ribonucleotide catabolic process 0e+00 0e+00 nucleotide metabolic process 0e+00 0e+00 cGMP metabolic process 0e+00 0e+00 nucleotide catabolic process 0e+00 0e+00 ribonucleotide metabolic process 0e+00 0e+00 cyclic nucleotide catabolic process 0e+00 0e+00 organophosphate catabolic process 0e+00 0e+00 nucleoside phosphate catabolic process 0e+00 0e+00 nucleobase-containing small molecule metabolic process 0e+00 0e+00 cyclic nucleotide metabolic process 0e+00 0e+00 purine nucleotide catabolic process 0e+00 0e+00 cAMP catabolic process 0e+00 0e+00 cAMP metabolic process 0e+00 0e+00 regulation of rhodopsin mediated signaling pathway 0e+00 0e+00 sensory perception of light stimulus 0e+00 0e+00 visual perception 0e+00 0e+00 non-motile cilium 0e+00 0e+00 photoreceptor cell cilium 0e+00 0e+00 photoreceptor outer segment

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 CGMP EFFECTS 0.00e+00 0.00e+00 NITRIC OXIDE STIMULATES GUANYLATE CYCLASE 0.00e+00 0.00e+00 PLATELET HOMEOSTASIS 0.00e+00 0.00e+00 G ALPHA S SIGNALLING EVENTS 0.00e+00 0.00e+00 CGMP EFFECTS 0.00e+00 0.00e+00 NITRIC OXIDE STIMULATES GUANYLATE CYCLASE 0.00e+00 0.00e+00 PLATELET HOMEOSTASIS 8.57e-10 2.85e-07 G ALPHA S SIGNALLING EVENTS 9.41e-07 1.64e-04 DARPP 32 EVENTS 1.27e-06 2.83e-04 DARPP 32 EVENTS 7.94e-06 1.54e-03 OPIOID SIGNALLING 1.84e-05 2.64e-03 OPIOID SIGNALLING 1.21e-02 9.26e-01 RAP1 SIGNALLING 1.64e-02 1.00e+00 RAP1 SIGNALLING

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

²FDR corrected p-value (Benjamini-Hochberg)

Mouse mutant phenotypes

P-value1 FDR2 Term 7.36e-08 1.10e-03 salt-resistant hypertension 1.46e-06 1.16e-02 abnormal retinal cone cell outer segment morphology 2.35e-06 1.66e-02 abnormal eye electrophysiology 2.36e-06 1.66e-02 decreased retinal photoreceptor cell number 3.42e-06 2.21e-02 abnormal cone electrophysiology 2.76e-05 9.76e-02 decreased retinal cone cell number 4.57e-05 1.34e-01 retinal cone cell degeneration 1.07e-03 9.34e-01 abnormal eye physiology 1.37e-03 1.00e+00 impaired muscle relaxation 1.37e-03 1.00e+00 absent photoreceptor outer segment 2.20e-03 1.00e+00 abnormal retinal cone cell morphology 2.33e-03 1.00e+00 disorganized photoreceptor outer segment 2.59e-03 1.00e+00 abnormal ocular fundus morphology 2.84e-03 1.00e+00 brain vacuoles 3.22e-03 1.00e+00 retinal degeneration 3.71e-03 1.00e+00 abnormal rod electrophysiology 4.51e-03 1.00e+00 abnormal systemic arterial blood pressure 5.01e-03 1.00e+00 increased systemic arterial diastolic blood pressure 5.02e-03 1.00e+00 increased mean systemic arterial blood pressure 5.65e-03 1.00e+00 thin uterine horn

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

²FDR corrected p-value (Benjamini-Hochberg)