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DREAM Module Identification Challenge – Consensus modules

PPI-STRING_Consensus_mod372

Assigned name NA Network PPI-STRING Module ID PPI-STRING_Consensus_mod372 Module size 4 genes

Module genes

This module comprises the following genes:

Gene ID Gene Symbol Gene Name 29993 PACSIN1 protein kinase C and casein kinase substrate in neurons 1 11252 PACSIN2 protein kinase C and casein kinase substrate in neurons 2 29763 PACSIN3 protein kinase C and casein kinase substrate in neurons 3 219790 RTKN2 rhotekin 2

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 5.14e-02 2.15e-09 GO plasma membrane tubulation biological_process 2.52e-03 2.68e-06 GO negative regulation of endocytosis biological_process

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 2.19e-08 1.36e-05 plasma membrane tubulation 5.36e-08 3.16e-05 negative regulation of endocytosis 4.25e-06 1.78e-03 regulation of endocytosis 8.92e-06 3.49e-03 plasma membrane organization 2.20e-05 7.81e-03 negative regulation of transport 3.11e-05 7.38e-03 lipid binding 6.84e-05 2.10e-02 regulation of vesicle-mediated transport 1.41e-04 3.91e-02 endomembrane system organization 2.33e-04 5.96e-02 endocytosis 8.82e-04 1.38e-01 phosphatidic acid binding 9.71e-04 1.50e-01 phospholipid binding 1.02e-03 1.56e-01 calcium channel inhibitor activity 1.95e-03 3.34e-01 caveola assembly 1.95e-03 3.34e-01 plasma membrane raft assembly 1.95e-03 3.34e-01 caveolin-mediated endocytosis 2.92e-03 3.91e-01 ion channel inhibitor activity 2.92e-03 3.91e-01 channel inhibitor activity 3.72e-03 4.37e-01 ruffle membrane 3.89e-03 5.71e-01 membrane raft assembly 3.89e-03 5.71e-01 positive regulation of membrane protein ectodomain proteolysis

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

²FDR corrected p-value (Benjamini-Hochberg)

Mouse mutant phenotypes

P-value1 FDR2 Term 1.87e-03 1e+00 decreased circulating interferon-alpha level 1.87e-03 1e+00 abnormal plasmacytoid dendritic cell physiology 1.87e-03 1e+00 decreased excitatory postsynaptic current amplitude 1.91e-03 1e+00 increased hematocrit 3.74e-03 1e+00 decreased synaptic depression 3.75e-03 1e+00 decreased interferon-alpha secretion 3.78e-03 1e+00 abnormal vesicle-mediated transport 5.61e-03 1e+00 abnormal synaptic vesicle morphology 5.61e-03 1e+00 abnormal retinal outer plexiform layer morphology 7.48e-03 1e+00 abnormal synapse morphology 9.36e-03 1e+00 tonic-clonic seizures 1.12e-02 1e+00 abnormal miniature inhibitory postsynaptic currents 1.30e-02 1e+00 abnormal synaptic vesicle recycling 1.31e-02 1e+00 decreased rib number 1.49e-02 1e+00 abnormal synaptic vesicle number 1.87e-02 1e+00 abnormal miniature excitatory postsynaptic currents 2.06e-02 1e+00 abnormal nervous system electrophysiology 2.07e-02 1e+00 reduced fertility 2.24e-02 1e+00 abnormal inhibitory postsynaptic currents

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

²FDR corrected p-value (Benjamini-Hochberg)