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DREAM Module Identification Challenge – Consensus modules

PPI-STRING_Consensus_mod95

Assigned name NA Network PPI-STRING Module ID PPI-STRING_Consensus_mod95 Module size 20 genes

Module genes

This module comprises the following genes:

Gene ID Gene Symbol Gene Name 163882 CNST consortin, connexin sorting protein 84694 GJA10 gap junction protein alpha 10 2700 GJA3 gap junction protein alpha 3 2701 GJA4 gap junction protein alpha 4 2702 GJA5 gap junction protein alpha 5 81025 GJA9 gap junction protein alpha 9 2705 GJB1 gap junction protein beta 1 2706 GJB2 gap junction protein beta 2 2707 GJB3 gap junction protein beta 3 127534 GJB4 gap junction protein beta 4 2709 GJB5 gap junction protein beta 5 10804 GJB6 gap junction protein beta 6 375519 GJB7 gap junction protein beta 7 125111 GJC1 gap junction protein delta 3 57165 GJC2 gap junction protein gamma 2 349149 GJC3 gap junction protein gamma 3 57369 GJD2 gap junction protein delta 2 125111 GJD3 gap junction protein delta 3 219770 GJD4 gap junction protein delta 4 349149 GJE1 gap junction protein gamma 3

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 4.45e-01 1.30e-59 GO connexin complex cellular_component 2.93e-01 7.09e-53 Reactome Gap junction assembly Vesicle-mediated transport 1.31e-02 8.89e-48 Reactome Gap junction trafficking Vesicle-mediated transport

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 gap junction assembly 0.00e+00 0.00e+00 gap junction 0.00e+00 0.00e+00 cell-cell junction 0.00e+00 0.00e+00 connexin complex 0.00e+00 0.00e+00 plasma membrane protein complex 0.00e+00 0.00e+00 wide pore channel activity 0.00e+00 0.00e+00 channel activity 0.00e+00 0.00e+00 passive transmembrane transporter activity 0.00e+00 0.00e+00 gap junction channel activity 3.36e-11 2.14e-08 gap junction channel activity involved in cell communication by electrical coupling 3.36e-11 2.14e-08 gap junction channel activity involved in cardiac conduction electrical coupling 5.95e-11 5.06e-08 cell-cell junction assembly 3.89e-09 2.67e-06 cell junction assembly 6.38e-09 4.25e-06 AV node cell to bundle of His cell communication by electrical coupling 1.13e-08 7.30e-06 cell-cell junction organization 1.47e-08 6.56e-06 gap junction channel activity involved in AV node cell-bundle of His cell electrical coupling 7.24e-08 4.19e-05 cell communication involved in cardiac conduction 1.70e-07 9.23e-05 AV node cell to bundle of His cell communication 8.76e-07 4.21e-04 cell communication by electrical coupling involved in cardiac conduction 1.54e-06 7.07e-04 cell communication by electrical coupling

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

²FDR corrected p-value (Benjamini-Hochberg)

Reactome

P-value1 FDR2 Term 0.00e+00 0e+00 GAP JUNCTION TRAFFICKING 0.00e+00 0e+00 GAP JUNCTION ASSEMBLY 0.00e+00 0e+00 MEMBRANE TRAFFICKING 0.00e+00 0e+00 GAP JUNCTION TRAFFICKING 0.00e+00 0e+00 GAP JUNCTION ASSEMBLY 0.00e+00 0e+00 MEMBRANE TRAFFICKING 3.41e-02 1e+00 NEURONAL SYSTEM 4.12e-02 1e+00 NEURONAL SYSTEM

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

²FDR corrected p-value (Benjamini-Hochberg)

Mouse mutant phenotypes

P-value1 FDR2 Term 4.89e-04 5.99e-01 abnormal heart electrocardiography waveform feature 5.53e-04 6.45e-01 abnormal impulse conducting system conduction 1.09e-03 9.45e-01 decreased placental labyrinth size 1.41e-03 1.00e+00 abnormal placenta development 3.74e-03 1.00e+00 disorganized retinal outer plexiform layer 3.74e-03 1.00e+00 bundle branch block 3.74e-03 1.00e+00 prolonged PQ interval 3.74e-03 1.00e+00 increased sebocyte number 3.74e-03 1.00e+00 abnormal cochlear endolymph ionic homeostasis 3.75e-03 1.00e+00 ostium primum atrial septal defect 3.75e-03 1.00e+00 common atrioventricular valve 3.79e-03 1.00e+00 small placenta 5.46e-03 1.00e+00 demyelination 6.04e-03 1.00e+00 abnormal myelination 7.47e-03 1.00e+00 abnormal cerebellum white matter morphology 7.47e-03 1.00e+00 abnormal aortic arch and aortic arch branch attachment 7.47e-03 1.00e+00 heart block 7.48e-03 1.00e+00 abnormal stria vascularis vasculature morphology 9.33e-03 1.00e+00 abnormal placenta intervillous maternal lacunae morphology 9.34e-03 1.00e+00 pulmonary artery hypoplasia

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

²FDR corrected p-value (Benjamini-Hochberg)