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DREAM Module Identification Challenge – Consensus modules

PPI-STRING_Consensus_mod229

Assigned name NA Network PPI-STRING Module ID PPI-STRING_Consensus_mod229 Module size 22 genes

Module genes

This module comprises the following genes:

Gene ID Gene Symbol Gene Name 79872 CBLL1 Cbl proto-oncogene like 1 999 CDH1 cadherin 1 1008 CDH10 cadherin 10 1009 CDH11 cadherin 11 1010 CDH12 cadherin 12 1012 CDH13 cadherin 13 1013 CDH15 cadherin 15 1015 CDH17 cadherin 17 1016 CDH18 cadherin 18 1000 CDH2 cadherin 2 64403 CDH24 cadherin 24 1013 CDH3 cadherin 15 1002 CDH4 cadherin 4 1003 CDH5 cadherin 5 1004 CDH6 cadherin 6 28513 CDH7 cadherin 19 1006 CDH8 cadherin 8 1007 CDH9 cadherin 9 1495 CTNNA1 catenin alpha 1 1500 CTNND1 catenin delta 1 342184 FMN1 formin 1 51474 LIMA1 LIM domain and actin binding 1

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 2.82e-01 9.17e-53 Reactome Adherens junctions interactions Cell-Cell communication 2.06e-01 1.03e-47 GO cell-cell adhesion mediated by cadherin biological_process 1.31e-01 3.66e-50 GO catenin complex cellular_component 3.89e-02 2.86e-45 GO cell-cell junction assembly biological_process 6.38e-03 1.66e-41 GO calcium-dependent cell-cell adhesion via plasma membrane cell adhesion molecules 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 single organismal cell-cell adhesion 0.00e+00 0.00e+00 adherens junction organization 0.00e+00 0.00e+00 cell-cell junction organization 0.00e+00 0.00e+00 cell-cell adhesion 0.00e+00 0.00e+00 cell-cell adhesion via plasma-membrane adhesion molecules 0.00e+00 0.00e+00 homophilic cell adhesion via plasma membrane adhesion molecules 0.00e+00 0.00e+00 calcium ion binding 2.73e-07 9.68e-05 gamma-catenin binding 3.23e-07 1.02e-04 adherens junction 8.11e-07 3.92e-04 entry of bacterium into host cell 1.81e-06 5.07e-04 cell-cell adherens junction 2.37e-06 7.00e-04 beta-catenin binding 3.04e-06 8.79e-04 cell adhesion molecule binding 5.92e-06 1.52e-03 catenin complex 7.11e-06 1.79e-03 plasma membrane raft 8.07e-06 2.01e-03 cell-cell junction 8.83e-06 2.33e-03 cadherin binding 1.44e-05 5.36e-03 calcium-dependent cell-cell adhesion via plasma membrane cell adhesion molecules 7.06e-05 2.16e-02 cellular response to indole-3-methanol 8.71e-05 1.74e-02 caveola

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 CELL CELL COMMUNICATION 0.00e+00 0.00e+00 CELL CELL JUNCTION ORGANIZATION 0.00e+00 0.00e+00 ADHERENS JUNCTIONS INTERACTIONS 0.00e+00 0.00e+00 CELL JUNCTION ORGANIZATION 0.00e+00 0.00e+00 CELL CELL JUNCTION ORGANIZATION 0.00e+00 0.00e+00 CELL CELL COMMUNICATION 0.00e+00 0.00e+00 ADHERENS JUNCTIONS INTERACTIONS 0.00e+00 0.00e+00 CELL JUNCTION ORGANIZATION 1.43e-07 2.73e-05 MYOGENESIS 8.39e-07 1.91e-04 MYOGENESIS 4.65e-02 1.00e+00 DEVELOPMENTAL BIOLOGY

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

²FDR corrected p-value (Benjamini-Hochberg)

Mouse mutant phenotypes

P-value1 FDR2 Term 6.03e-04 6.77e-01 failure to form blastocele 9.41e-04 8.71e-01 abnormal skin physiology 3.75e-03 1.00e+00 abnormal vein development 3.87e-03 1.00e+00 distended pericardium 4.20e-03 1.00e+00 abnormal kidney development 5.61e-03 1.00e+00 abnormal placenta physiology 5.62e-03 1.00e+00 mammary gland alveolar hyperplasia 5.63e-03 1.00e+00 abnormal lymphatic vessel endothelium morphology 7.47e-03 1.00e+00 increased trophectoderm apoptosis 7.50e-03 1.00e+00 mammary gland duct hyperplasia 9.33e-03 1.00e+00 absent trophectoderm 9.34e-03 1.00e+00 abnormal retina outer limiting membrane morphology 9.36e-03 1.00e+00 blind ureter 9.37e-03 1.00e+00 decreased germinal center B cell number 1.09e-02 1.00e+00 complete embryonic lethality before implantation 1.10e-02 1.00e+00 abnormal vitelline vasculature morphology 1.14e-02 1.00e+00 abnormal extraembryonic tissue morphology 1.30e-02 1.00e+00 abnormal calcaneum morphology 1.30e-02 1.00e+00 failure of morula compaction 1.30e-02 1.00e+00 retinal spots

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

²FDR corrected p-value (Benjamini-Hochberg)