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DREAM Module Identification Challenge – Consensus modules

PPI-STRING_Consensus_mod20

Assigned name NA Network PPI-STRING Module ID PPI-STRING_Consensus_mod20 Module size 42 genes

Module genes

This module comprises the following genes:

Gene ID Gene Symbol Gene Name 55107 ANO1 anoctamin 1 57101 ANO2 anoctamin 2 196527 ANO6 anoctamin 6 7439 BEST1 bestrophin 1 54831 BEST2 bestrophin 2 144453 BEST3 bestrophin 3 266675 BEST4 bestrophin 4 1180 CLCN1 chloride voltage-gated channel 1 1181 CLCN2 chloride voltage-gated channel 2 1187 CLCNKA chloride voltage-gated channel Ka 1188 CLCNKB chloride voltage-gated channel Kb 9022 CLIC3 chloride intracellular channel 3 5348 FXYD1 FXYD domain containing ion transport regulator 1 5349 FXYD3 FXYD domain containing ion transport regulator 3 2554 GABRA1 gamma-aminobutyric acid type A receptor alpha1 subunit 2555 GABRA2 gamma-aminobutyric acid type A receptor alpha2 subunit 2556 GABRA3 gamma-aminobutyric acid type A receptor alpha3 subunit 2557 GABRA4 gamma-aminobutyric acid type A receptor alpha4 subunit 2558 GABRA5 gamma-aminobutyric acid type A receptor alpha5 subunit 2559 GABRA6 gamma-aminobutyric acid type A receptor alpha6 subunit 2560 GABRB1 gamma-aminobutyric acid type A receptor beta1 subunit 2561 GABRB2 gamma-aminobutyric acid type A receptor beta2 subunit 2562 GABRB3 gamma-aminobutyric acid type A receptor beta3 subunit 2563 GABRD gamma-aminobutyric acid type A receptor delta subunit 2564 GABRE gamma-aminobutyric acid type A receptor epsilon subunit 2565 GABRG1 gamma-aminobutyric acid type A receptor gamma1 subunit 2566 GABRG2 gamma-aminobutyric acid type A receptor gamma2 subunit 2567 GABRG3 gamma-aminobutyric acid type A receptor gamma3 subunit 2568 GABRP gamma-aminobutyric acid type A receptor pi subunit 55879 GABRQ gamma-aminobutyric acid type A receptor theta subunit 2569 GABRR1 gamma-aminobutyric acid type A receptor rho1 subunit 2570 GABRR2 gamma-aminobutyric acid type A receptor rho2 subunit 200959 GABRR3 gamma-aminobutyric acid type A receptor rho3 subunit (gene/pseudogene) 2741 GLRA1 glycine receptor alpha 1 2742 GLRA2 glycine receptor alpha 2 8001 GLRA3 glycine receptor alpha 3 441509 GLRA4 glycine receptor alpha 4 2743 GLRB glycine receptor beta 65010 SLC26A6 solute carrier family 26 member 6 66008 TRAK2 trafficking kinesin protein 2 94015 TTYH2 tweety family member 2 80727 TTYH3 tweety family member 3

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 4.05e-01 5.57e-98 GO chloride channel complex cellular_component 3.93e-01 6.83e-14 GO extracellularly glycine-gated chloride channel activity molecular_function 1.83e-01 1.89e-52 GO GABA-A receptor activity molecular_function 1.79e-01 1.89e-52 GO GABA-A receptor complex cellular_component 8.96e-02 1.22e-90 GO chloride transmembrane transport biological_process 7.34e-02 1.35e-13 GO voltage-gated chloride channel activity molecular_function 9.32e-03 1.62e-53 GO extracellular ligand-gated ion channel activity 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 0e+00 0e+00 inorganic anion transport 0e+00 0e+00 chloride transmembrane transport 0e+00 0e+00 anion transport 0e+00 0e+00 chloride transport 0e+00 0e+00 anion transmembrane transport 0e+00 0e+00 gamma-aminobutyric acid signaling pathway 0e+00 0e+00 neuron-neuron synaptic transmission 0e+00 0e+00 chemical synaptic transmission 0e+00 0e+00 chloride channel complex 0e+00 0e+00 transmembrane transporter complex 0e+00 0e+00 ion channel complex 0e+00 0e+00 postsynapse 0e+00 0e+00 postsynaptic membrane 0e+00 0e+00 GABA receptor complex 0e+00 0e+00 GABA-A receptor complex 0e+00 0e+00 receptor complex 0e+00 0e+00 synaptic membrane 0e+00 0e+00 synapse 0e+00 0e+00 ion channel activity 0e+00 0e+00 channel activity

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

²FDR corrected p-value (Benjamini-Hochberg)

Reactome

P-value1 FDR2 Term 0e+00 0e+00 GABA A RECEPTOR ACTIVATION 0e+00 0e+00 TRANSMEMBRANE TRANSPORT OF SMALL MOLECULES 0e+00 0e+00 ION CHANNEL TRANSPORT 0e+00 0e+00 NEUROTRANSMITTER RECEPTOR BINDING AND DOWNSTREAM TRANSMISSION IN THE POSTSYNAPTIC CELL 0e+00 0e+00 NEURONAL SYSTEM 0e+00 0e+00 LIGAND GATED ION CHANNEL TRANSPORT 0e+00 0e+00 GABA RECEPTOR ACTIVATION 0e+00 0e+00 TRANSMISSION ACROSS CHEMICAL SYNAPSES 0e+00 0e+00 GABA A RECEPTOR ACTIVATION 0e+00 0e+00 ION CHANNEL TRANSPORT 0e+00 0e+00 NEUROTRANSMITTER RECEPTOR BINDING AND DOWNSTREAM TRANSMISSION IN THE POSTSYNAPTIC CELL 0e+00 0e+00 NEURONAL SYSTEM 0e+00 0e+00 LIGAND GATED ION CHANNEL TRANSPORT 0e+00 0e+00 GABA RECEPTOR ACTIVATION 0e+00 0e+00 TRANSMISSION ACROSS CHEMICAL SYNAPSES

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

²FDR corrected p-value (Benjamini-Hochberg)

Mouse mutant phenotypes

P-value1 FDR2 Term 0.00e+00 0.00e+00 abnormal GABA-mediated receptor currents 2.98e-11 1.94e-06 abnormal inhibitory postsynaptic currents 2.24e-07 2.72e-03 impaired behavioral response to xenobiotic 8.04e-07 7.36e-03 type IV spiral ligament fibrocyte degeneration 1.21e-06 1.01e-02 abnormal cochlear OHC efferent innervation pattern 6.14e-06 3.32e-02 muscle hypertonia 1.33e-05 5.71e-02 altered righting response 3.01e-05 1.03e-01 absence seizures 4.27e-05 1.29e-01 hyperactivity 4.36e-05 1.30e-01 abnormal behavioral response to xenobiotic 6.93e-05 1.78e-01 muscle spasm 8.67e-05 2.07e-01 abnormal miniature inhibitory postsynaptic currents 8.74e-05 2.08e-01 sensorineural hearing loss 9.40e-05 2.17e-01 abnormal single cell response 1.05e-04 2.33e-01 abnormal auditory brainstem response waveform shape 1.37e-04 2.80e-01 impaired righting response 1.45e-04 2.90e-01 abnormal cochlea morphology 1.62e-04 3.10e-01 hyperekplexia 1.63e-04 3.10e-01 abnormal distortion product otoacoustic emission 1.85e-04 3.32e-01 limb grasping

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

²FDR corrected p-value (Benjamini-Hochberg)