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DREAM Module Identification Challenge – Consensus modules

PPI-STRING_Consensus_mod216

Assigned name NA Network PPI-STRING Module ID PPI-STRING_Consensus_mod216 Module size 23 genes

Module genes

This module comprises the following genes:

Gene ID Gene Symbol Gene Name 9478 CABP1 calcium binding protein 1 51475 CABP2 calcium binding protein 2 57010 CABP4 calcium binding protein 4 56344 CABP5 calcium binding protein 5 164633 CABP7 calcium binding protein 7 793 CALB1 calbindin 1 794 CALB2 calbindin 2 91860 CALML4 calmodulin like 4 83698 CALN1 calneuron 1 1068 CETN1 centrin 1 1070 CETN3 centrin 3 90141 EFCAB11 EF-hand calcium binding domain 11 124989 EFCAB13 EF-hand calcium binding domain 13 84288 EFCAB2 EF-hand calcium binding domain 2 146779 EFCAB3 EF-hand calcium binding domain 3 64800 EFCAB6 EF-hand calcium binding domain 6 84455 EFCAB7 EF-hand calcium binding domain 7 285588 EFCAB9 EF-hand calcium binding domain 9 654231 OCM oncomodulin 4951 OCM2 oncomodulin 2 5816 PVALB parvalbumin 10590 SCGN secretagogin, EF-hand calcium binding protein 374955 SPATA21 spermatogenesis associated 21

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 8.85e-02 8.85e-08 GO regulation of long-term synaptic potentiation biological_process 5.32e-02 5.31e-13 GO regulation of cytosolic calcium ion concentration 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 0.00e+00 0.00e+00 calcium ion binding 1.08e-07 3.67e-05 terminal bouton 1.46e-06 6.73e-04 regulation of cytosolic calcium ion concentration 2.22e-06 6.14e-04 axon terminus 3.35e-06 8.92e-04 neuron projection terminus 6.62e-06 2.66e-03 cellular calcium ion homeostasis 8.17e-06 3.23e-03 calcium ion homeostasis 1.59e-05 5.86e-03 cellular metal ion homeostasis 3.15e-05 1.07e-02 cellular cation homeostasis 3.27e-05 1.11e-02 cellular ion homeostasis 3.35e-05 1.13e-02 metal ion homeostasis 4.68e-05 1.51e-02 cellular chemical homeostasis 6.56e-05 2.03e-02 ion homeostasis 9.42e-05 2.78e-02 cellular homeostasis 1.34e-04 2.53e-02 synapse 2.29e-04 4.06e-02 presynapse 3.14e-04 7.64e-02 retina morphogenesis in camera-type eye 5.19e-04 1.15e-01 neural retina development 5.33e-04 8.53e-02 axon 6.49e-04 1.39e-01 camera-type eye morphogenesis

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

²FDR corrected p-value (Benjamini-Hochberg)

Mouse mutant phenotypes

P-value1 FDR2 Term 2.38e-04 3.9e-01 abnormal nervous system electrophysiology 3.75e-03 1.0e+00 abnormal retinal rod cell morphology 3.75e-03 1.0e+00 abnormal retinal cone cell morphology 5.61e-03 1.0e+00 thin retinal outer plexiform layer 5.61e-03 1.0e+00 abnormal retinal rod bipolar cell morphology 7.48e-03 1.0e+00 abnormal retinal rod cell outer segment morphology 7.50e-03 1.0e+00 abnormal retinal neuronal layer morphology 9.35e-03 1.0e+00 abnormal muscle contractility 1.14e-02 1.0e+00 deafness 1.50e-02 1.0e+00 thin retinal outer nuclear layer 1.68e-02 1.0e+00 abnormal mitochondrion morphology 1.87e-02 1.0e+00 abnormal long term potentiation 2.25e-02 1.0e+00 abnormal cone electrophysiology 2.43e-02 1.0e+00 abnormal Purkinje cell morphology 2.84e-02 1.0e+00 ataxia 2.99e-02 1.0e+00 abnormal eye physiology 3.20e-02 1.0e+00 abnormal retina morphology 3.36e-02 1.0e+00 abnormal rod electrophysiology 4.84e-02 1.0e+00 abnormal eye electrophysiology 4.84e-02 1.0e+00 reduced long term potentiation

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

²FDR corrected p-value (Benjamini-Hochberg)