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DREAM Module Identification Challenge – Consensus modules

PPI-STRING_Consensus_mod116

Assigned name NA Network PPI-STRING Module ID PPI-STRING_Consensus_mod116 Module size 21 genes

Module genes

This module comprises the following genes:

Gene ID Gene Symbol Gene Name 11174 ADAMTS6 ADAM metallopeptidase with thrombospondin type 1 motif 6 1134 CHRNA1 cholinergic receptor nicotinic alpha 1 subunit 9815 GIT2 GIT ArfGAP 2 3672 ITGA1 integrin subunit alpha 1 284217 LAMA1 laminin subunit alpha 1 3908 LAMA2 laminin subunit alpha 2 3910 LAMA3 laminin subunit alpha 4 3911 LAMA5 laminin subunit alpha 5 3912 LAMB1 laminin subunit beta 1 3915 LAMB2 laminin subunit gamma 1 3914 LAMB3 laminin subunit beta 3 3915 LAMC1 laminin subunit gamma 1 3918 LAMC2 laminin subunit gamma 2 10319 LAMC3 laminin subunit gamma 3 91355 LRP5L LDL receptor related protein 5 like 1955 MEGF9 multiple EGF like domains 9 5913 RAPSN receptor associated protein of the synapse 9900 SV2A synaptic vesicle glycoprotein 2A 9899 SV2B synaptic vesicle glycoprotein 2B 22987 SV2C synaptic vesicle glycoprotein 2C 79875 THSD4 thrombospondin type 1 domain containing 4

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 3.05e-01 4.94e-28 Reactome Laminin interactions Extracellular matrix organization 1.25e-01 3.14e-08 Reactome Toxicity of botulinum toxin type D (BoNT/D) Disease 1.25e-01 3.14e-08 Reactome Toxicity of botulinum toxin type F (BoNT/F) Disease 8.01e-02 5.50e-08 Reactome Anchoring fibril formation Extracellular matrix organization 6.38e-02 8.53e-06 Reactome Toxicity of botulinum toxin type E (BoNT/E) Disease 4.22e-02 1.32e-07 Reactome Toxicity of botulinum toxin type A (BoNT/A) Disease 2.49e-02 8.29e-22 Reactome Non-integrin membrane-ECM interactions Extracellular matrix organization 2.45e-03 5.00e-09 GO regulation of embryonic development 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 basement membrane 0.00e+00 0.00e+00 basal lamina 0.00e+00 0.00e+00 extracellular matrix 0.00e+00 0.00e+00 proteinaceous extracellular matrix 2.30e-09 1.64e-06 hemidesmosome assembly 3.25e-09 2.26e-06 cell-substrate junction assembly 6.46e-08 2.29e-05 laminin-5 complex 8.69e-08 2.98e-05 laminin-1 complex 1.27e-07 4.25e-05 laminin-11 complex 1.27e-07 4.25e-05 laminin-10 complex 3.36e-07 1.17e-04 structural molecule activity 7.60e-07 3.70e-04 cell junction assembly 1.41e-06 6.52e-04 extracellular matrix disassembly 1.54e-06 7.07e-04 endoderm development 2.38e-06 1.05e-03 extracellular matrix assembly 6.74e-06 2.71e-03 regulation of embryonic development 9.00e-06 3.52e-03 cell morphogenesis 2.05e-05 7.33e-03 substrate adhesion-dependent cell spreading

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

²FDR corrected p-value (Benjamini-Hochberg)

Reactome

P-value1 FDR2 Term 3.29e-11 9.41e-09 INTEGRIN CELL SURFACE INTERACTIONS 6.59e-08 1.74e-05 INTEGRIN CELL SURFACE INTERACTIONS 2.80e-06 4.53e-04 L1CAM INTERACTIONS 3.37e-05 4.64e-03 CELL JUNCTION ORGANIZATION 1.29e-04 1.95e-02 L1CAM INTERACTIONS 1.86e-04 2.22e-02 CELL CELL COMMUNICATION 3.56e-04 3.99e-02 AXON GUIDANCE 1.54e-03 1.71e-01 CELL JUNCTION ORGANIZATION 4.90e-03 4.50e-01 CELL CELL COMMUNICATION 8.57e-03 7.08e-01 PRESYNAPTIC NICOTINIC ACETYLCHOLINE RECEPTORS 8.57e-03 7.08e-01 HIGHLY CALCIUM PERMEABLE POSTSYNAPTIC NICOTINIC ACETYLCHOLINE RECEPTORS 8.58e-03 7.09e-01 ACETYLCHOLINE BINDING AND DOWNSTREAM EVENTS 8.61e-03 7.11e-01 AXON GUIDANCE 1.49e-02 1.00e+00 OTHER SEMAPHORIN INTERACTIONS 2.15e-02 1.00e+00 PRESYNAPTIC NICOTINIC ACETYLCHOLINE RECEPTORS 2.15e-02 1.00e+00 HIGHLY CALCIUM PERMEABLE POSTSYNAPTIC NICOTINIC ACETYLCHOLINE RECEPTORS 2.68e-02 1.00e+00 ACETYLCHOLINE BINDING AND DOWNSTREAM EVENTS 3.12e-02 1.00e+00 OTHER SEMAPHORIN INTERACTIONS 3.49e-02 1.00e+00 DEVELOPMENTAL BIOLOGY 4.23e-02 1.00e+00 SMOOTH MUSCLE CONTRACTION

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

²FDR corrected p-value (Benjamini-Hochberg)

Mouse mutant phenotypes

P-value1 FDR2 Term 1.18e-05 5.28e-02 blistering 8.47e-05 2.03e-01 failure of neuromuscular synapse postsynaptic differentiation 1.24e-04 2.59e-01 abnormal basal lamina morphology 2.07e-04 3.56e-01 abnormal retina inner limiting membrane morphology 2.55e-04 4.04e-01 abnormal amacrine cell morphology 2.75e-04 4.28e-01 dermal-epidermal separation 3.28e-04 4.72e-01 abnormal parietal endoderm morphology 5.98e-04 6.73e-01 abnormal neuromuscular synapse morphology 6.64e-04 7.18e-01 abnormal Muller cell morphology 1.98e-03 1.00e+00 abnormal basement membrane morphology 2.09e-03 1.00e+00 abnormal miniature endplate potential 2.94e-03 1.00e+00 abnormal renal glomerulus basement membrane morphology 7.00e-03 1.00e+00 muscle weakness 7.47e-03 1.00e+00 carpoptosis 9.77e-03 1.00e+00 atrioventricular septal defect 1.02e-02 1.00e+00 kidney failure 1.06e-02 1.00e+00 abnormal retina morphology 1.09e-02 1.00e+00 absent kidney 1.12e-02 1.00e+00 decreased amacrine cell number 1.12e-02 1.00e+00 failure of neuromuscular synapse presynaptic differentiation

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

²FDR corrected p-value (Benjamini-Hochberg)