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DREAM Module Identification Challenge – Consensus modules

PPI-STRING_Consensus_mod56

Assigned name NA Network PPI-STRING Module ID PPI-STRING_Consensus_mod56 Module size 20 genes

Module genes

This module comprises the following genes:

Gene ID Gene Symbol Gene Name 9568 GABBR2 gamma-aminobutyric acid type B receptor subunit 2 10681 GNB5 G protein subunit beta 5 2790 GNG10 G protein subunit gamma 10 2791 GNG11 G protein subunit gamma 11 55970 GNG12 G protein subunit gamma 12 51764 GNG13 G protein subunit gamma 13 2785 GNG3 G protein subunit gamma 3 2786 GNG4 G protein subunit gamma 4 2787 GNG5 G protein subunit gamma 5 2788 GNG7 G protein subunit gamma 7 94235 GNG8 G protein subunit gamma 8 2793 GNGT2 G protein subunit gamma transducin 2 3760 KCNJ3 potassium voltage-gated channel subfamily J member 3 3762 KCNJ5 potassium voltage-gated channel subfamily J member 5 3763 KCNJ6 potassium voltage-gated channel subfamily J member 6 3765 KCNJ9 potassium voltage-gated channel subfamily J member 9 57580 PREX1 phosphatidylinositol-3,4,5-trisphosphate dependent Rac exchange factor 1 8786 RGS11 regulator of G protein signaling 11 388531 RGS9 regulator of G protein signaling 9 binding protein 6323 SCN1A sodium voltage-gated channel alpha subunit 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 1.09e-01 1.32e-29 Reactome Prostacyclin signalling through prostacyclin receptor Hemostasis 8.50e-02 2.22e-34 Reactome Inhibition of voltage gated Ca2+ channels via Gbeta/gamma subunits Neuronal System 8.47e-02 2.22e-34 Reactome G protein gated Potassium channels Neuronal System 8.39e-02 2.22e-34 Reactome Activation of G protein gated Potassium channels Neuronal System 6.04e-02 2.93e-29 Reactome G beta:gamma signalling through PLC beta Signal Transduction 4.30e-02 1.08e-30 Reactome Cooperation of PDCL (PhLP1) and TRiC/CCT in G-protein beta folding Metabolism of proteins 2.60e-02 2.36e-28 Reactome Thromboxane signalling through TP receptor Hemostasis 2.48e-02 6.15e-29 Reactome Presynaptic function of Kainate receptors Neuronal System 1.51e-02 1.23e-28 Reactome ADP signalling through P2Y purinoceptor 12 Hemostasis 1.10e-02 7.76e-28 Reactome G beta:gamma signalling through PI3Kgamma Signal Transduction 2.09e-03 7.76e-28 Reactome ADP signalling through P2Y purinoceptor 1 Hemostasis

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 cellular response to peptide 0.00e+00 0.00e+00 cellular response to glucagon stimulus 0.00e+00 0.00e+00 cellular response to peptide hormone stimulus 0.00e+00 0.00e+00 response to glucagon 0.00e+00 0.00e+00 cytoplasmic side of plasma membrane 0.00e+00 0.00e+00 cytoplasmic side of membrane 0.00e+00 0.00e+00 heterotrimeric G-protein complex 0.00e+00 0.00e+00 plasma membrane protein complex 0.00e+00 0.00e+00 extrinsic component of cytoplasmic side of plasma membrane 0.00e+00 0.00e+00 extrinsic component of membrane 0.00e+00 0.00e+00 extrinsic component of plasma membrane 3.53e-11 3.06e-08 response to peptide hormone 8.99e-11 7.50e-08 response to peptide 2.19e-10 1.76e-07 cellular response to organonitrogen compound 1.46e-09 1.06e-06 cellular response to hormone stimulus 1.65e-09 8.45e-07 GTPase activity 3.38e-08 2.05e-05 response to organonitrogen compound 3.40e-08 2.06e-05 response to hormone 3.44e-08 1.43e-05 G-protein activated inward rectifier potassium channel activity 1.11e-07 6.23e-05 potassium ion import

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

²FDR corrected p-value (Benjamini-Hochberg)

Reactome

P-value1 FDR2 Term 0e+00 0e+00 NEUROTRANSMITTER RECEPTOR BINDING AND DOWNSTREAM TRANSMISSION IN THE POSTSYNAPTIC CELL 0e+00 0e+00 POTASSIUM CHANNELS 0e+00 0e+00 NEURONAL SYSTEM 0e+00 0e+00 INWARDLY RECTIFYING K CHANNELS 0e+00 0e+00 GABA B RECEPTOR ACTIVATION 0e+00 0e+00 GABA RECEPTOR ACTIVATION 0e+00 0e+00 TRANSMISSION ACROSS CHEMICAL SYNAPSES 0e+00 0e+00 INHIBITION OF VOLTAGE GATED CA2 CHANNELS VIA GBETA GAMMA SUBUNITS 0e+00 0e+00 G ALPHA I SIGNALLING EVENTS 0e+00 0e+00 GPCR LIGAND BINDING 0e+00 0e+00 ACTIVATION OF KAINATE RECEPTORS UPON GLUTAMATE BINDING 0e+00 0e+00 REGULATION OF INSULIN SECRETION BY GLUCAGON LIKE PEPTIDE1 0e+00 0e+00 THROMBIN SIGNALLING THROUGH PROTEINASE ACTIVATED RECEPTORS PARS 0e+00 0e+00 AQUAPORIN MEDIATED TRANSPORT 0e+00 0e+00 SIGNAL AMPLIFICATION 0e+00 0e+00 GLUCAGON TYPE LIGAND RECEPTORS 0e+00 0e+00 ADP SIGNALLING THROUGH P2RY12 0e+00 0e+00 G PROTEIN BETA GAMMA SIGNALLING 0e+00 0e+00 CLASS B 2 SECRETIN FAMILY RECEPTORS 0e+00 0e+00 G BETA GAMMA SIGNALLING THROUGH PI3KGAMMA

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

²FDR corrected p-value (Benjamini-Hochberg)

Mouse mutant phenotypes

P-value1 FDR2 Term 2.55e-07 3.00e-03 abnormal synaptic transmission 5.18e-05 1.46e-01 tonic-clonic seizures 2.17e-04 3.66e-01 clonic seizures 5.00e-04 6.05e-01 environmentally induced seizures 7.60e-04 7.67e-01 convulsive seizures 1.87e-03 1.00e+00 abnormal cardiogenic mesoderm morphology 2.13e-03 1.00e+00 abnormal brain wave pattern 3.56e-03 1.00e+00 abnormal myocardial fiber physiology 5.30e-03 1.00e+00 abnormal rod electrophysiology 5.61e-03 1.00e+00 abnormal inhibitory postsynaptic potential 5.61e-03 1.00e+00 abnormal vomeronasal sensory neuron morphology 5.63e-03 1.00e+00 bundle branch block 5.63e-03 1.00e+00 abnormal RR interval 5.63e-03 1.00e+00 ventricular fibrillation 5.63e-03 1.00e+00 dilated aortic sac 7.49e-03 1.00e+00 maximal tonic hindlimb extension seizures 7.51e-03 1.00e+00 weaving 7.51e-03 1.00e+00 absent cerebellar lobules 8.39e-03 1.00e+00 abnormal nervous system electrophysiology 9.37e-03 1.00e+00 abnormal hippocampus granule cell morphology

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

²FDR corrected p-value (Benjamini-Hochberg)