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DREAM Module Identification Challenge – Consensus modules

PPI-STRING_Consensus_mod100

Assigned name NA Network PPI-STRING Module ID PPI-STRING_Consensus_mod100 Module size 48 genes

Module genes

This module comprises the following genes:

Gene ID Gene Symbol Gene Name 348980 HCN1 hyperpolarization activated cyclic nucleotide gated potassium channel 1 610 HCN2 hyperpolarization activated cyclic nucleotide gated potassium and sodium channel 2 57657 HCN3 hyperpolarization activated cyclic nucleotide gated potassium channel 3 10021 HCN4 hyperpolarization activated cyclic nucleotide gated potassium channel 4 3736 KCNA1 potassium voltage-gated channel subfamily A member 1 3744 KCNA10 potassium voltage-gated channel subfamily A member 10 3737 KCNA2 potassium voltage-gated channel subfamily A member 2 3738 KCNA3 potassium voltage-gated channel subfamily A member 3 3739 KCNA4 potassium voltage-gated channel subfamily A member 4 3741 KCNA5 potassium voltage-gated channel subfamily A member 5 3742 KCNA6 potassium voltage-gated channel subfamily A member 6 3743 KCNA7 potassium voltage-gated channel subfamily A member 7 7881 KCNAB1 potassium voltage-gated channel subfamily A member regulatory beta subunit 1 8514 KCNAB2 potassium voltage-gated channel subfamily A regulatory beta subunit 2 9196 KCNAB3 potassium voltage-gated channel subfamily A regulatory beta subunit 3 3745 KCNB1 potassium voltage-gated channel subfamily B member 1 9312 KCNB2 potassium voltage-gated channel subfamily B member 2 3746 KCNC1 potassium voltage-gated channel subfamily C member 1 3747 KCNC2 potassium voltage-gated channel subfamily C member 2 3748 KCNC3 potassium voltage-gated channel subfamily C member 3 3749 KCNC4 potassium voltage-gated channel subfamily C member 4 3751 KCND2 potassium voltage-gated channel subfamily D member 2 3752 KCND3 potassium voltage-gated channel subfamily D member 3 9992 KCNE2 potassium voltage-gated channel subfamily E regulatory subunit 2 3754 KCNF1 potassium voltage-gated channel modifier subfamily F member 1 3755 KCNG1 potassium voltage-gated channel modifier subfamily G member 1 26251 KCNG2 potassium voltage-gated channel modifier subfamily G member 2 170850 KCNG3 potassium voltage-gated channel modifier subfamily G member 3 93107 KCNG4 potassium voltage-gated channel modifier subfamily G member 4 3756 KCNH1 potassium voltage-gated channel subfamily H member 1 3757 KCNH2 potassium voltage-gated channel subfamily H member 2 23416 KCNH3 potassium voltage-gated channel subfamily H member 3 23415 KCNH4 potassium voltage-gated channel subfamily H member 4 27133 KCNH5 potassium voltage-gated channel subfamily H member 5 81033 KCNH6 potassium voltage-gated channel subfamily H member 6 90134 KCNH7 potassium voltage-gated channel subfamily H member 7 131096 KCNH8 potassium voltage-gated channel subfamily H member 8 3784 KCNQ1 potassium voltage-gated channel subfamily Q member 1 3785 KCNQ2 potassium voltage-gated channel subfamily Q member 2 3786 KCNQ3 potassium voltage-gated channel subfamily Q member 3 9132 KCNQ4 potassium voltage-gated channel subfamily Q member 4 56479 KCNQ5 potassium voltage-gated channel subfamily Q member 5 3787 KCNS1 potassium voltage-gated channel modifier subfamily S member 1 3788 KCNS2 potassium voltage-gated channel modifier subfamily S member 2 3790 KCNS3 potassium voltage-gated channel modifier subfamily S member 3 27012 KCNV1 potassium voltage-gated channel modifier subfamily V member 1 169522 KCNV2 potassium voltage-gated channel modifier subfamily V member 2 25961 NUDT13 nudix hydrolase 13

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 6.37e-01 1.06e-118 Reactome Voltage gated Potassium channels Neuronal System 5.78e-01 5.37e-11 Reactome HCN channels Neuronal System 1.51e-01 3.99e-75 GO delayed rectifier potassium channel activity molecular_function 9.87e-02 1.27e-118 GO voltage-gated potassium channel activity molecular_function 1.85e-02 4.06e-106 Reactome Potassium Channels Neuronal System

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 potassium ion transport 0e+00 0e+00 potassium ion transmembrane transport 0e+00 0e+00 monovalent inorganic cation transport 0e+00 0e+00 cation transmembrane transport 0e+00 0e+00 protein homooligomerization 0e+00 0e+00 regulation of ion transmembrane transport 0e+00 0e+00 metal ion transport 0e+00 0e+00 regulation of ion transport 0e+00 0e+00 protein oligomerization 0e+00 0e+00 regulation of potassium ion transport 0e+00 0e+00 regulation of potassium ion transmembrane transport 0e+00 0e+00 action potential 0e+00 0e+00 phosphorelay signal transduction system 0e+00 0e+00 potassium channel complex 0e+00 0e+00 transmembrane transporter complex 0e+00 0e+00 voltage-gated potassium channel complex 0e+00 0e+00 cation channel complex 0e+00 0e+00 ion channel complex 0e+00 0e+00 channel activity 0e+00 0e+00 potassium ion transmembrane transporter 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 POTASSIUM CHANNELS 0.00e+00 0.00e+00 NEURONAL SYSTEM 0.00e+00 0.00e+00 VOLTAGE GATED POTASSIUM CHANNELS 0.00e+00 0.00e+00 POTASSIUM CHANNELS 0.00e+00 0.00e+00 NEURONAL SYSTEM 0.00e+00 0.00e+00 VOLTAGE GATED POTASSIUM CHANNELS 6.43e-08 1.70e-05 REGULATION OF INSULIN SECRETION BY GLUCAGON LIKE PEPTIDE1 5.64e-07 1.02e-04 REGULATION OF INSULIN SECRETION BY GLUCAGON LIKE PEPTIDE1 7.06e-07 1.63e-04 REGULATION OF INSULIN SECRETION 2.18e-05 3.91e-03 INTEGRATION OF ENERGY METABOLISM 5.80e-05 7.71e-03 REGULATION OF INSULIN SECRETION 2.10e-04 2.48e-02 INTEGRATION OF ENERGY METABOLISM 4.58e-04 5.96e-02 INTERACTION BETWEEN L1 AND ANKYRINS 3.80e-03 3.64e-01 L1CAM INTERACTIONS

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 afterhyperpolarization 0.00e+00 0.00e+00 abnormal nervous system electrophysiology 1.10e-09 3.95e-05 abnormal action potential 7.69e-07 7.26e-03 increased susceptibility to pharmacologically induced seizures 1.26e-06 1.04e-02 seizures 1.29e-05 5.64e-02 tonic-clonic seizures 1.96e-05 7.47e-02 tremors 9.03e-05 2.12e-01 abnormal T wave 1.02e-04 2.29e-01 decreased channel response intensity 1.44e-04 2.89e-01 abnormal depression-related behavior 2.12e-04 3.61e-01 increased circulating gastrin level 2.45e-04 3.97e-01 abnormal sleep pattern 3.01e-04 4.47e-01 hypochlorhydria 3.84e-04 5.20e-01 abnormal brain wave pattern 4.97e-04 6.04e-01 enlarged stomach 8.04e-04 7.93e-01 increased stomach pH 8.22e-04 8.04e-01 prolonged QT interval 8.40e-04 8.16e-01 impaired swimming 1.38e-03 1.00e+00 abnormal seizure response to electrical stimulation 1.56e-03 1.00e+00 abnormal sinoatrial node conduction

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

²FDR corrected p-value (Benjamini-Hochberg)