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DREAM Module Identification Challenge – Consensus modules

PPI-STRING_Consensus_mod182

Assigned name NA Network PPI-STRING Module ID PPI-STRING_Consensus_mod182 Module size 24 genes

Module genes

This module comprises the following genes:

Gene ID Gene Symbol Gene Name 107 ADCY1 adenylate cyclase 1 108 ADCY2 adenylate cyclase 2 114 ADCY3 adenylate cyclase 8 196883 ADCY4 adenylate cyclase 4 111 ADCY5 adenylate cyclase 5 112 ADCY6 adenylate cyclase 6 113 ADCY7 adenylate cyclase 7 114 ADCY8 adenylate cyclase 8 2768 GNA12 G protein subunit alpha 12 10672 GNA13 G protein subunit alpha 13 2770 GNAI1 G protein subunit alpha i1 2771 GNAI2 G protein subunit alpha i2 2773 GNAI3 G protein subunit alpha i3 2775 GNAO1 G protein subunit alpha o1 2779 GNAT1 G protein subunit alpha transducin 1 2780 GNAT2 G protein subunit alpha transducin 2 346562 GNAT3 G protein subunit alpha transducin 3 2781 GNAZ G protein subunit alpha z 2783 GNB2 G protein subunit beta 2 59345 GNB4 G protein subunit beta 4 NA GNG5P2 347404 LANCL3 LanC like 3 8622 PDE8B phosphodiesterase 8B 388531 RGS9BP regulator of G protein signaling 9 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 2.08e-01 8.96e-35 Reactome Adenylate cyclase inhibitory pathway Neuronal System#Signal Transduction 2.07e-01 8.96e-35 Reactome Inhibition of adenylate cyclase pathway Neuronal System 1.83e-01 3.42e-25 GO G-protein beta/gamma-subunit complex binding molecular_function 1.70e-01 1.17e-22 GO adenylate cyclase activity molecular_function 1.12e-01 2.41e-23 Reactome G-protein activation Signal Transduction 6.40e-02 2.36e-38 Reactome PLC beta mediated events Signal Transduction 1.71e-02 1.30e-15 GO cellular response to forskolin biological_process 6.51e-03 1.29e-21 GO cAMP biosynthetic process biological_process 6.03e-03 1.41e-06 GO detection of light stimulus involved in visual perception biological_process 5.16e-03 3.30e-25 GO adenylate cyclase-modulating G-protein coupled receptor signaling pathway biological_process 2.43e-03 2.68e-21 Reactome Cooperation of PDCL (PhLP1) and TRiC/CCT in G-protein beta folding Metabolism of proteins

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 G-protein coupled receptor signaling pathway, coupled to cyclic nucleotide second messenger 0e+00 0e+00 adenylate cyclase-modulating G-protein coupled receptor signaling pathway 0e+00 0e+00 protein folding 0e+00 0e+00 adenylate cyclase-inhibiting G-protein coupled receptor signaling pathway 0e+00 0e+00 renal water homeostasis 0e+00 0e+00 activation of protein kinase A activity 0e+00 0e+00 positive regulation of adenylate cyclase activity 0e+00 0e+00 cyclic purine nucleotide metabolic process 0e+00 0e+00 cGMP metabolic process 0e+00 0e+00 cellular response to glucagon stimulus 0e+00 0e+00 cyclic nucleotide biosynthetic process 0e+00 0e+00 regulation of cyclase activity 0e+00 0e+00 cAMP biosynthetic process 0e+00 0e+00 adenylate cyclase-activating G-protein coupled receptor signaling pathway 0e+00 0e+00 regulation of cAMP metabolic process 0e+00 0e+00 regulation of cAMP biosynthetic process 0e+00 0e+00 response to glucagon 0e+00 0e+00 cGMP biosynthetic process 0e+00 0e+00 multicellular organismal water homeostasis 0e+00 0e+00 activation of adenylate cyclase 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 G ALPHA I SIGNALLING EVENTS 0.00e+00 0.00e+00 OPIOID SIGNALLING 0.00e+00 0.00e+00 PLC BETA MEDIATED EVENTS 0.00e+00 0.00e+00 ADENYLATE CYCLASE INHIBITORY PATHWAY 0.00e+00 0.00e+00 ADENYLATE CYCLASE ACTIVATING PATHWAY 0.00e+00 0.00e+00 G ALPHA S SIGNALLING EVENTS 0.00e+00 0.00e+00 G ALPHA Z SIGNALLING EVENTS 0.00e+00 0.00e+00 GABA B RECEPTOR ACTIVATION 0.00e+00 0.00e+00 GABA RECEPTOR ACTIVATION 0.00e+00 0.00e+00 G ALPHA I SIGNALLING EVENTS 0.00e+00 0.00e+00 OPIOID SIGNALLING 0.00e+00 0.00e+00 PLC BETA MEDIATED EVENTS 0.00e+00 0.00e+00 ADENYLATE CYCLASE INHIBITORY PATHWAY 0.00e+00 0.00e+00 ADENYLATE CYCLASE ACTIVATING PATHWAY 0.00e+00 0.00e+00 G ALPHA S SIGNALLING EVENTS 0.00e+00 0.00e+00 G ALPHA Z SIGNALLING EVENTS 0.00e+00 0.00e+00 GABA B RECEPTOR ACTIVATION 0.00e+00 0.00e+00 GABA RECEPTOR ACTIVATION 0.00e+00 0.00e+00 INTEGRATION OF ENERGY METABOLISM 5.96e-11 1.67e-08 NEUROTRANSMITTER RECEPTOR BINDING AND DOWNSTREAM TRANSMISSION IN THE POSTSYNAPTIC CELL

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

²FDR corrected p-value (Benjamini-Hochberg)

Mouse mutant phenotypes

P-value1 FDR2 Term 4.38e-04 5.61e-01 abnormal cone electrophysiology 1.47e-03 1.00e+00 increased chemical nociceptive threshold 2.54e-03 1.00e+00 abnormal enzyme/coenzyme activity 3.06e-03 1.00e+00 taste/olfaction phenotype 3.75e-03 1.00e+00 abnormal somatosensory cortex physiology 5.64e-03 1.00e+00 chronic diarrhea 5.65e-03 1.00e+00 decreased urine urea nitrogen level 7.51e-03 1.00e+00 increased circulating interleukin-5 level 8.38e-03 1.00e+00 abnormal eye physiology 9.33e-03 1.00e+00 absent barrels in primary somatosensory cortex 9.34e-03 1.00e+00 disorganized barrel cortex 9.35e-03 1.00e+00 abnormal heart left ventricle pressure 9.36e-03 1.00e+00 abnormal renal water reabsorbtion 9.36e-03 1.00e+00 abnormal body size 1.12e-02 1.00e+00 unidirectional circling 1.49e-02 1.00e+00 increased circulating interleukin-4 level 1.49e-02 1.00e+00 decreased brown fat cell size 1.49e-02 1.00e+00 decreased urine chloride ion level 1.68e-02 1.00e+00 abnormal large intestine morphology 1.68e-02 1.00e+00 hyperalgesia

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

²FDR corrected p-value (Benjamini-Hochberg)