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DREAM Module Identification Challenge – Consensus modules

PPI-STRING_Consensus_mod141

Assigned name NA Network PPI-STRING Module ID PPI-STRING_Consensus_mod141 Module size 42 genes

Module genes

This module comprises the following genes:

Gene ID Gene Symbol Gene Name 256076 COL6A5 collagen type VI alpha 5 chain 131873 COL6A6 collagen type VI alpha 6 chain 25304 COMP cartilage oligomeric matrix protein 80864 EGFL8 EGF like domain multiple 8 8515 ITGA10 integrin subunit alpha 10 22801 ITGA11 integrin subunit alpha 11 3673 ITGA2 integrin subunit alpha 2 3674 ITGA2B integrin subunit alpha 2b 3675 ITGA3 integrin subunit alpha 3 3676 ITGA4 integrin subunit alpha 4 3678 ITGA5 integrin subunit alpha 5 3655 ITGA6 integrin subunit alpha 6 3679 ITGA7 integrin subunit alpha 7 8516 ITGA8 integrin subunit alpha 8 3680 ITGA9 integrin subunit alpha 9 3681 ITGAD integrin subunit alpha D 3682 ITGAE integrin subunit alpha E 3683 ITGAL integrin subunit alpha L 3685 ITGAV integrin subunit alpha V 3687 ITGAX integrin subunit alpha X 3691 ITGB4 integrin subunit beta 4 3693 ITGB5 integrin subunit beta 5 3694 ITGB6 integrin subunit beta 6 3695 ITGB7 integrin subunit beta 7 3696 ITGB8 integrin subunit beta 8 9358 ITGBL1 integrin subunit beta like 1 22798 LAMB4 laminin subunit beta 4 59274 MESDC1 talin rod domain containing 1 255743 NPNT nephronectin 5649 RELN reelin 55298 RNF121 ring finger protein 121 285533 RNF175 ring finger protein 175 6696 SPP1 secreted phosphoprotein 1 7057 THBS1 thrombospondin 1 7058 THBS2 thrombospondin 2 7059 THBS3 thrombospondin 3 7060 THBS4 thrombospondin 4 83660 TLN2 talin 2 3371 TNC tenascin C 63923 TNN tenascin N 7143 TNR tenascin R 10077 TSPAN32 tetraspanin 32

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 4.53e-01 4.08e-49 GO integrin complex cellular_component 1.40e-01 7.01e-07 GO growth plate cartilage development biological_process 1.36e-01 2.51e-07 Reactome RUNX3 Regulates Immune Response and Cell Migration Gene expression (Transcription) 9.37e-02 1.32e-49 Reactome Integrin cell surface interactions Extracellular matrix organization 3.04e-02 3.66e-11 Reactome Signaling by PDGF Signal Transduction 2.23e-02 1.95e-14 Reactome Syndecan interactions Extracellular matrix organization 2.13e-02 1.72e-23 Reactome ECM proteoglycans Extracellular matrix organization 1.92e-02 2.30e-43 GO integrin-mediated signaling pathway biological_process 1.69e-02 1.64e-35 GO cell-matrix adhesion biological_process 2.52e-03 2.47e-04 GO behavioral response to pain 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 extracellular structure organization 0.00e+00 0.00e+00 extracellular matrix organization 0.00e+00 0.00e+00 single organismal cell-cell adhesion 0.00e+00 0.00e+00 cell-cell adhesion 0.00e+00 0.00e+00 cell-substrate adhesion 0.00e+00 0.00e+00 integrin-mediated signaling pathway 0.00e+00 0.00e+00 cell adhesion mediated by integrin 0.00e+00 0.00e+00 cell-matrix adhesion 0.00e+00 0.00e+00 integrin complex 0.00e+00 0.00e+00 plasma membrane protein complex 0.00e+00 0.00e+00 protein complex involved in cell adhesion 0.00e+00 0.00e+00 receptor complex 0.00e+00 0.00e+00 cell surface 0.00e+00 0.00e+00 protein complex binding 0.00e+00 0.00e+00 integrin binding 0.00e+00 0.00e+00 extracellular matrix binding 6.23e-12 5.64e-09 heterotypic cell-cell adhesion 8.56e-11 5.26e-08 collagen binding 1.12e-10 6.80e-08 cell adhesion molecule binding 9.06e-10 4.10e-07 proteinaceous extracellular matrix

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 INTEGRIN CELL SURFACE INTERACTIONS 0.00e+00 0.00e+00 INTEGRIN CELL SURFACE INTERACTIONS 8.61e-08 1.69e-05 SIGNAL TRANSDUCTION BY L1 1.01e-06 1.75e-04 L1CAM INTERACTIONS 1.06e-06 1.83e-04 SIGNALING BY PDGF 7.88e-06 1.20e-03 CELL SURFACE INTERACTIONS AT THE VASCULAR WALL 3.55e-04 4.76e-02 CELL SURFACE INTERACTIONS AT THE VASCULAR WALL 3.65e-04 4.09e-02 AXON GUIDANCE 5.39e-04 6.88e-02 SIGNAL TRANSDUCTION BY L1 7.68e-04 9.33e-02 L1CAM INTERACTIONS 3.42e-03 2.97e-01 ANTIGEN PROCESSING CROSS PRESENTATION 3.62e-03 3.12e-01 PECAM1 INTERACTIONS 7.48e-03 6.35e-01 SIGNALING BY PDGF 2.22e-02 1.00e+00 RESPONSE TO ELEVATED PLATELET CYTOSOLIC CA2 2.75e-02 1.00e+00 PLATELET ADHESION TO EXPOSED COLLAGEN 2.86e-02 1.00e+00 GRB2 SOS PROVIDES LINKAGE TO MAPK SIGNALING FOR INTERGRINS 3.22e-02 1.00e+00 P130CAS LINKAGE TO MAPK SIGNALING FOR INTEGRINS 4.97e-02 1.00e+00 INTEGRIN ALPHAIIB BETA3 SIGNALING

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

²FDR corrected p-value (Benjamini-Hochberg)

Mouse mutant phenotypes

P-value1 FDR2 Term 8.43e-05 2.03e-01 abnormal blood vessel morphology 1.31e-04 2.71e-01 abnormal leukocyte migration 1.78e-04 3.25e-01 abnormal cell adhesion 1.09e-03 9.45e-01 vascular smooth muscle cell hyperplasia 1.41e-03 1.00e+00 abnormal leukocyte adhesion 1.73e-03 1.00e+00 abnormal platelet aggregation 2.25e-03 1.00e+00 abnormal lymphocyte physiology 3.19e-03 1.00e+00 abnormal coronary vessel morphology 3.83e-03 1.00e+00 altered susceptibility to infection 3.84e-03 1.00e+00 abnormal immune system physiology 3.98e-03 1.00e+00 centrally nucleated skeletal muscle fibers 4.08e-03 1.00e+00 abnormal tendon morphology 4.77e-03 1.00e+00 abnormal physiological neovascularization 4.98e-03 1.00e+00 small kidney 5.11e-03 1.00e+00 intracerebral hemorrhage 5.25e-03 1.00e+00 blistering 5.85e-03 1.00e+00 abnormal hippocampus CA1 region morphology 7.12e-03 1.00e+00 abnormal response to infection 7.82e-03 1.00e+00 abnormal cellular extravasation 8.21e-03 1.00e+00 abnormal hippocampus pyramidal cell layer

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

²FDR corrected p-value (Benjamini-Hochberg)