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DREAM Module Identification Challenge – Consensus modules

PPI-STRING_Consensus_mod167

Assigned name NA Network PPI-STRING Module ID PPI-STRING_Consensus_mod167 Module size 16 genes

Module genes

This module comprises the following genes:

Gene ID Gene Symbol Gene Name 1135 CHRNA2 cholinergic receptor nicotinic alpha 2 subunit 1136 CHRNA3 cholinergic receptor nicotinic alpha 3 subunit 1137 CHRNA4 cholinergic receptor nicotinic alpha 4 subunit 1138 CHRNA5 cholinergic receptor nicotinic alpha 5 subunit 8973 CHRNA6 cholinergic receptor nicotinic alpha 6 subunit 1139 CHRNA7 cholinergic receptor nicotinic alpha 7 subunit 55584 CHRNA9 cholinergic receptor nicotinic alpha 9 subunit 1140 CHRNB1 cholinergic receptor nicotinic beta 1 subunit 1141 CHRNB2 cholinergic receptor nicotinic beta 2 subunit 1142 CHRNB3 cholinergic receptor nicotinic beta 3 subunit 1143 CHRNB4 cholinergic receptor nicotinic beta 4 subunit 1144 CHRND cholinergic receptor nicotinic delta subunit 1145 CHRNE cholinergic receptor nicotinic epsilon subunit 1146 CHRNG cholinergic receptor nicotinic gamma subunit 116372 LYPD1 LY6/PLAUR domain containing 1 134957 STXBP5 syntaxin binding protein 5

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 3.76e-01 8.57e-49 GO acetylcholine-gated channel complex cellular_component 1.19e-01 4.33e-42 Reactome Postsynaptic nicotinic acetylcholine receptors Neuronal System 1.17e-01 4.33e-42 Reactome Acetylcholine binding and downstream events Neuronal System 1.17e-01 4.33e-42 Reactome Activation of Nicotinic Acetylcholine Receptors Neuronal System 4.00e-02 1.31e-22 Reactome Highly sodium permeable acetylcholine nicotinic receptors Neuronal System 2.66e-02 3.53e-37 GO synaptic transmission, cholinergic biological_process 1.13e-03 1.73e-40 GO acetylcholine receptor 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 regulation of postsynaptic membrane potential 0e+00 0e+00 excitatory postsynaptic potential 0e+00 0e+00 chemical synaptic transmission 0e+00 0e+00 response to alkaloid 0e+00 0e+00 regulation of membrane potential 0e+00 0e+00 synaptic transmission, cholinergic 0e+00 0e+00 neuromuscular synaptic transmission 0e+00 0e+00 chemical synaptic transmission, postsynaptic 0e+00 0e+00 behavioral response to nicotine 0e+00 0e+00 response to nicotine 0e+00 0e+00 response to organonitrogen compound 0e+00 0e+00 cation transmembrane transport 0e+00 0e+00 transmembrane transporter complex 0e+00 0e+00 receptor complex 0e+00 0e+00 acetylcholine-gated channel complex 0e+00 0e+00 synaptic membrane 0e+00 0e+00 synapse 0e+00 0e+00 postsynapse 0e+00 0e+00 postsynaptic membrane 0e+00 0e+00 ion channel complex

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

²FDR corrected p-value (Benjamini-Hochberg)

Reactome

P-value1 FDR2 Term 0e+00 0e+00 PRESYNAPTIC NICOTINIC ACETYLCHOLINE RECEPTORS 0e+00 0e+00 NEUROTRANSMITTER RECEPTOR BINDING AND DOWNSTREAM TRANSMISSION IN THE POSTSYNAPTIC CELL 0e+00 0e+00 ACETYLCHOLINE BINDING AND DOWNSTREAM EVENTS 0e+00 0e+00 HIGHLY CALCIUM PERMEABLE POSTSYNAPTIC NICOTINIC ACETYLCHOLINE RECEPTORS 0e+00 0e+00 NEURONAL SYSTEM 0e+00 0e+00 TRANSMISSION ACROSS CHEMICAL SYNAPSES 0e+00 0e+00 PRESYNAPTIC NICOTINIC ACETYLCHOLINE RECEPTORS 0e+00 0e+00 NEUROTRANSMITTER RECEPTOR BINDING AND DOWNSTREAM TRANSMISSION IN THE POSTSYNAPTIC CELL 0e+00 0e+00 ACETYLCHOLINE BINDING AND DOWNSTREAM EVENTS 0e+00 0e+00 HIGHLY CALCIUM PERMEABLE POSTSYNAPTIC NICOTINIC ACETYLCHOLINE RECEPTORS 0e+00 0e+00 NEURONAL SYSTEM 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 6.73e-08 1.03e-03 abnormal nicotine-mediated receptor currents 8.06e-06 4.02e-02 abnormal miniature endplate potential 8.67e-05 2.07e-01 abnormal brain morphology 1.11e-04 2.42e-01 decreased immunoglobulin level 2.34e-04 3.85e-01 decreased erythroblast number 2.80e-04 4.33e-01 abnormal inhibitory postsynaptic currents 2.92e-04 4.42e-01 abnormal neuromuscular synapse morphology 2.94e-04 4.43e-01 abnormal urinary bladder physiology 3.45e-04 4.86e-01 decreased chemically-elicited antinociception 7.99e-04 7.91e-01 decreased susceptibility to pharmacologically induced seizures 1.22e-03 1.00e+00 abnormal response to new environment 1.85e-03 1.00e+00 abnormal long term potentiation 1.87e-03 1.00e+00 abnormal GABAergic neuron physiology 3.13e-03 1.00e+00 increased IgG level 3.74e-03 1.00e+00 abnormal cochlear nerve compound action potential 5.61e-03 1.00e+00 abnormal pulmonary ventilation 6.19e-03 1.00e+00 abnormal skeletal muscle fiber morphology 6.72e-03 1.00e+00 abnormal excitatory postsynaptic currents 7.47e-03 1.00e+00 enhanced spatial learning 7.47e-03 1.00e+00 decreased susceptibility to noise-induced hearing loss

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

²FDR corrected p-value (Benjamini-Hochberg)