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DREAM Module Identification Challenge – Consensus modules

PPI-STRING_Consensus_mod190

Assigned name NA Network PPI-STRING Module ID PPI-STRING_Consensus_mod190 Module size 18 genes

Module genes

This module comprises the following genes:

Gene ID Gene Symbol Gene Name 859 CAV3 caveolin 3 114489 DAG1 dystroglycan 1 79147 FKRP fukutin related protein 3766 KCNJ10 potassium voltage-gated channel subfamily J member 10 3880 KRT19 keratin 19 51438 MAGEE1 MAGE family member C2 6442 SGCA sarcoglycan alpha 6443 SGCB sarcoglycan beta 6444 SGCD sarcoglycan delta 8910 SGCE sarcoglycan epsilon 6445 SGCG sarcoglycan gamma 137868 SGCZ sarcoglycan zeta 6640 SNTA1 syntrophin alpha 1 6641 SNTB1 syntrophin beta 1 6645 SNTB2 syntrophin beta 2 54212 SNTG1 syntrophin gamma 1 54221 SNTG2 syntrophin gamma 2 8082 SSPN sarcospan

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 5.41e-01 2.46e-35 GO dystrophin-associated glycoprotein complex cellular_component 4.57e-02 2.11e-07 GO heart contraction biological_process 2.84e-02 3.14e-03 Reactome Potassium transport channels Neuronal System 1.07e-02 3.24e-29 GO sarcolemma cellular_component

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 plasma membrane protein complex 0.00e+00 0.00e+00 sarcolemma 0.00e+00 0.00e+00 dystrophin-associated glycoprotein complex 0.00e+00 0.00e+00 dystroglycan complex 0.00e+00 0.00e+00 sarcoglycan complex 3.52e-10 2.02e-07 structural molecule activity 3.98e-08 2.39e-05 muscle organ development 4.31e-08 2.58e-05 heart contraction 4.71e-08 2.80e-05 muscle cell development 4.97e-08 2.95e-05 muscle structure development 1.93e-07 6.27e-05 syntrophin complex 5.26e-07 1.76e-04 actin binding 8.53e-07 4.11e-04 muscle system process 1.57e-06 7.20e-04 muscle cell differentiation 5.39e-06 2.21e-03 muscle contraction 8.09e-06 3.20e-03 cardiac muscle tissue development 4.65e-05 1.06e-02 nitric-oxide synthase binding 5.22e-05 1.67e-02 striated muscle tissue development 6.83e-05 2.10e-02 blood circulation 6.88e-05 2.11e-02 muscle tissue development

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

²FDR corrected p-value (Benjamini-Hochberg)

Reactome

P-value1 FDR2 Term 1.54e-02 1e+00 INHIBITION OF VOLTAGE GATED CA2 CHANNELS VIA GBETA GAMMA SUBUNITS 1.71e-02 1e+00 GABA B RECEPTOR ACTIVATION 2.23e-02 1e+00 INWARDLY RECTIFYING K CHANNELS 2.39e-02 1e+00 GABA RECEPTOR ACTIVATION

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 dystrophic muscle 1.26e-09 4.24e-05 increased circulating creatine kinase level 3.32e-07 3.78e-03 cardiac fibrosis 1.16e-06 9.79e-03 cardiomyopathy 4.64e-06 2.77e-02 skeletal muscle fiber necrosis 5.02e-06 2.94e-02 abnormal sarcolemma morphology 5.61e-06 3.17e-02 centrally nucleated skeletal muscle fibers 1.37e-05 5.77e-02 myocardial necrosis 3.64e-05 1.15e-01 muscle degeneration 1.14e-04 2.46e-01 calcified muscle 1.71e-04 3.19e-01 abnormal tibialis anterior morphology 2.87e-04 4.38e-01 abnormal skeletal muscle fiber morphology 3.21e-04 4.69e-01 skeletal muscle necrosis 3.27e-04 4.72e-01 skeletal muscle fiber degeneration 6.07e-04 6.78e-01 abnormal muscle contractility 2.52e-03 1.00e+00 increased variability of skeletal muscle fiber size 3.76e-03 1.00e+00 abnormal cochlear endolymph ionic homeostasis 3.84e-03 1.00e+00 thick ventricular wall 5.61e-03 1.00e+00 ectopic manchette 5.62e-03 1.00e+00 decreased QRS amplitude

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

²FDR corrected p-value (Benjamini-Hochberg)