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DREAM Module Identification Challenge – Consensus modules

PPI-STRING_Consensus_mod96

Assigned name NA Network PPI-STRING Module ID PPI-STRING_Consensus_mod96 Module size 21 genes

Module genes

This module comprises the following genes:

Gene ID Gene Symbol Gene Name 6336 SCN10A sodium voltage-gated channel alpha subunit 10 11280 SCN11A sodium voltage-gated channel alpha subunit 11 6324 SCN1B sodium voltage-gated channel beta subunit 1 6326 SCN2A sodium voltage-gated channel alpha subunit 2 6327 SCN2B sodium voltage-gated channel beta subunit 2 6328 SCN3A sodium voltage-gated channel alpha subunit 3 55800 SCN3B sodium voltage-gated channel beta subunit 3 6329 SCN4A sodium voltage-gated channel alpha subunit 4 6330 SCN4B sodium voltage-gated channel beta subunit 4 6331 SCN5A sodium voltage-gated channel alpha subunit 5 6332 SCN7A sodium voltage-gated channel alpha subunit 7 6334 SCN8A sodium voltage-gated channel alpha subunit 8 6335 SCN9A sodium voltage-gated channel alpha subunit 9 6337 SCNN1A sodium channel epithelial 1 alpha subunit 6338 SCNN1B sodium channel epithelial 1 beta subunit 6339 SCNN1D sodium channel epithelial 1 delta subunit 6340 SCNN1G sodium channel epithelial 1 gamma subunit 1831 TSC22D3 TSC22 domain family member 3 65125 WNK1 WNK lysine deficient protein kinase 1 65268 WNK2 WNK lysine deficient protein kinase 2 65266 WNK4 WNK lysine deficient protein kinase 4

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 6.42e-01 1.57e-39 GO voltage-gated sodium channel complex cellular_component 1.71e-01 8.79e-08 GO ion homeostasis biological_process 1.21e-01 1.17e-09 GO sensory perception of taste biological_process 8.21e-02 1.88e-07 GO sodium ion homeostasis biological_process 4.48e-02 3.97e-33 GO voltage-gated sodium channel activity molecular_function 2.38e-02 1.70e-38 GO sodium ion transmembrane transport biological_process 8.84e-03 7.58e-33 Reactome Interaction between L1 and Ankyrins Developmental Biology

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 monovalent inorganic cation transport 0e+00 0e+00 regulation of ion transport 0e+00 0e+00 cation transmembrane transport 0e+00 0e+00 action potential 0e+00 0e+00 regulation of postsynaptic membrane potential 0e+00 0e+00 regulation of membrane potential 0e+00 0e+00 membrane depolarization 0e+00 0e+00 membrane depolarization during action potential 0e+00 0e+00 sodium ion transport 0e+00 0e+00 regulation of ion transmembrane transport 0e+00 0e+00 metal ion transport 0e+00 0e+00 regulation of sodium ion transport 0e+00 0e+00 sodium ion transmembrane transport 0e+00 0e+00 transmission of nerve impulse 0e+00 0e+00 neuronal action potential 0e+00 0e+00 sodium channel complex 0e+00 0e+00 transmembrane transporter complex 0e+00 0e+00 voltage-gated sodium channel complex 0e+00 0e+00 cation channel complex 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 0.00e+00 0.00e+00 L1CAM INTERACTIONS 0.00e+00 0.00e+00 INTERACTION BETWEEN L1 AND ANKYRINS 0.00e+00 0.00e+00 L1CAM INTERACTIONS 0.00e+00 0.00e+00 INTERACTION BETWEEN L1 AND ANKYRINS 1.88e-11 7.16e-09 AXON GUIDANCE 5.01e-11 1.41e-08 AXON GUIDANCE 3.04e-09 9.37e-07 DEVELOPMENTAL BIOLOGY

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

²FDR corrected p-value (Benjamini-Hochberg)

Mouse mutant phenotypes

P-value1 FDR2 Term 2.81e-08 5.33e-04 abnormal nervous system electrophysiology 1.54e-06 1.19e-02 increased circulating potassium level 2.58e-05 9.31e-02 abnormal action potential 4.76e-05 1.38e-01 alkalosis 7.18e-05 1.81e-01 hypokalemia 2.81e-04 4.34e-01 sinus bradycardia 2.95e-04 4.44e-01 decreased circulating aldosterone level 6.65e-04 7.18e-01 decreased urine potassium level 6.73e-04 7.20e-01 abnormal heart electrocardiography waveform feature 8.81e-04 8.37e-01 abnormal mechanical nociception 8.91e-04 8.42e-01 increased urine sodium level 1.01e-03 9.05e-01 respiratory distress 1.72e-03 1.00e+00 abnormal urine homeostasis 1.74e-03 1.00e+00 oliguria 1.87e-03 1.00e+00 abnormal single cell response 2.58e-03 1.00e+00 abnormal pain threshold 3.34e-03 1.00e+00 decreased circulating sodium level 4.94e-03 1.00e+00 myopathy 4.95e-03 1.00e+00 seizures 5.63e-03 1.00e+00 hypervolemia

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

²FDR corrected p-value (Benjamini-Hochberg)