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DREAM Module Identification Challenge – Consensus modules

PPI-STRING_Consensus_mod78

Assigned name NA Network PPI-STRING Module ID PPI-STRING_Consensus_mod78 Module size 22 genes

Module genes

This module comprises the following genes:

Gene ID Gene Symbol Gene Name 9076 CLDN1 claudin 1 9071 CLDN10 claudin 10 5010 CLDN11 claudin 11 9069 CLDN12 claudin 12 23562 CLDN14 claudin 14 24146 CLDN15 claudin 15 10686 CLDN16 claudin 16 26285 CLDN17 claudin 17 51208 CLDN18 claudin 18 149461 CLDN19 claudin 19 9075 CLDN2 claudin 2 49861 CLDN20 claudin 20 53842 CLDN22 claudin 22 137075 CLDN23 claudin 23 100132463 CLDN24 claudin 24 644672 CLDN25 claudin 25 7122 CLDN5 claudin 5 9074 CLDN6 claudin 6 9073 CLDN8 claudin 8 9080 CLDN9 claudin 9 90952 ESAM endothelial cell adhesion molecule 27134 TJP3 tight junction protein 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 5.98e-01 3.71e-54 GO calcium-independent cell-cell adhesion via plasma membrane cell-adhesion molecules biological_process 6.63e-02 2.41e-49 Reactome Tight junction interactions Cell-Cell communication 1.20e-02 8.86e-49 GO bicellular tight junction 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 calcium-independent cell-cell adhesion via plasma membrane cell-adhesion molecules 0.00e+00 0.00e+00 cell-cell adhesion via plasma-membrane adhesion molecules 0.00e+00 0.00e+00 cell-cell adhesion 0.00e+00 0.00e+00 bicellular tight junction 0.00e+00 0.00e+00 cell-cell junction 0.00e+00 0.00e+00 apical junction complex 0.00e+00 0.00e+00 structural molecule activity 8.48e-08 4.85e-05 cell-cell junction organization 1.46e-06 4.17e-04 apicolateral plasma membrane 1.20e-05 4.56e-03 cell-cell junction assembly 2.21e-05 5.06e-03 lateral plasma membrane 8.94e-05 2.65e-02 cell junction assembly 2.93e-04 7.21e-02 apical junction assembly 1.38e-03 2.57e-01 cellular response to transforming growth factor beta stimulus 1.48e-03 2.72e-01 response to transforming growth factor beta 1.95e-03 3.34e-01 establishment of blood-nerve barrier 1.95e-03 3.34e-01 cellular response to lead ion 1.95e-03 3.34e-01 response to interleukin-18 2.63e-03 4.25e-01 response to ethanol 3.89e-03 5.71e-01 negative regulation of osteoclast development

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

²FDR corrected p-value (Benjamini-Hochberg)

Reactome

P-value1 FDR2 Term 0e+00 0e+00 CELL CELL JUNCTION ORGANIZATION 0e+00 0e+00 CELL CELL COMMUNICATION 0e+00 0e+00 TIGHT JUNCTION INTERACTIONS 0e+00 0e+00 CELL JUNCTION ORGANIZATION 0e+00 0e+00 CELL CELL JUNCTION ORGANIZATION 0e+00 0e+00 CELL CELL COMMUNICATION 0e+00 0e+00 TIGHT JUNCTION INTERACTIONS 0e+00 0e+00 CELL JUNCTION ORGANIZATION

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

²FDR corrected p-value (Benjamini-Hochberg)

Mouse mutant phenotypes

P-value1 FDR2 Term 4.22e-05 1.28e-01 deafness 4.83e-05 1.39e-01 cochlear outer hair cell degeneration 1.46e-04 2.92e-01 abnormal renal reabsorbtion 3.81e-04 5.19e-01 increased urine calcium level 5.03e-04 6.07e-01 increased or absent threshold for auditory brainstem response 1.87e-03 1.00e+00 abnormal renal calcium reabsorbtion 1.88e-03 1.00e+00 increased circulating parathyroid hormone level 3.75e-03 1.00e+00 abnormal grip strength 3.75e-03 1.00e+00 abnormal stria vascularis morphology 5.61e-03 1.00e+00 decreased trabecular bone connectivity density 5.61e-03 1.00e+00 decreased endocochlear potential 5.62e-03 1.00e+00 decreased vascular permeability 7.48e-03 1.00e+00 decreased urine pH 9.05e-03 1.00e+00 abnormal blood-brain barrier function 9.33e-03 1.00e+00 abnormal renal sodium reabsorbtion 1.12e-02 1.00e+00 wrinkled skin 1.12e-02 1.00e+00 abnormal digestive system morphology 1.12e-02 1.00e+00 polycystic kidney 1.30e-02 1.00e+00 abnormal jejunum morphology 1.31e-02 1.00e+00 decreased trabecular bone thickness

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

²FDR corrected p-value (Benjamini-Hochberg)