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DREAM Module Identification Challenge – Consensus modules

PPI-STRING_Consensus_mod5

Assigned name NA Network PPI-STRING Module ID PPI-STRING_Consensus_mod5 Module size 63 genes

Module genes

This module comprises the following genes:

Gene ID Gene Symbol Gene Name 54829 ASPN asporin 633 BGN biglycan 150356 CHADL chondroadherin like 1842 ECM2 extracellular matrix protein 2 1833 EPYC epiphycan 84435 GPR123 adhesion G protein-coupled receptor A1 25960 GPR124 adhesion G protein-coupled receptor A2 3671 ISLR immunoglobulin superfamily containing leucine rich repeat 57611 ISLR2 immunoglobulin superfamily containing leucine rich repeat 2 84894 LINGO1 leucine rich repeat and Ig domain containing 1 158038 LINGO2 leucine rich repeat and Ig domain containing 2 645191 LINGO3 leucine rich repeat and Ig domain containing 3 339398 LINGO4 leucine rich repeat and Ig domain containing 4 23143 LRCH1 leucine rich repeats and calponin homology domain containing 1 57622 LRFN1 leucine rich repeat and fibronectin type III domain containing 1 57497 LRFN2 leucine rich repeat and fibronectin type III domain containing 2 79414 LRFN3 leucine rich repeat and fibronectin type III domain containing 3 78999 LRFN4 leucine rich repeat and fibronectin type III domain containing 4 145581 LRFN5 leucine rich repeat and fibronectin type III domain containing 5 340745 LRIT2 leucine rich repeat, Ig-like and transmembrane domains 2 131578 LRRC15 leucine rich repeat containing 15 10234 LRRC17 leucine rich repeat containing 17 64922 LRRC19 leucine rich repeat containing 19 441381 LRRC24 leucine rich repeat containing 24 389816 LRRC26 leucine rich repeat containing 26 2615 LRRC32 leucine rich repeat containing 32 375387 LRRC33 negative regulator of reactive oxygen species 126755 LRRC38 leucine rich repeat containing 38 64101 LRRC4 leucine rich repeat containing 4 94030 LRRC4B leucine rich repeat containing 4B 57689 LRRC4C leucine rich repeat containing 4C 440699 LRRC52 leucine rich repeat containing 52 105378803 LRRC53 leucine rich repeat containing 53 219527 LRRC55 leucine rich repeat containing 55 220416 LRRC63 leucine rich repeat containing 63 339977 LRRC66 leucine rich repeat containing 66 100130733 LRRC70 leucine rich repeat containing 70 56262 LRRC8A leucine rich repeat containing 8 VRAC subunit A 23507 LRRC8B leucine rich repeat containing 8 VRAC subunit B 84230 LRRC8C leucine rich repeat containing 8 VRAC subunit C 55144 LRRC8D leucine rich repeat containing 8 VRAC subunit D 80131 LRRC8E leucine rich repeat containing 8 VRAC subunit E 57633 LRRN1 leucine rich repeat neuronal 1 26045 LRRN2 leucine rich repeat transmembrane neuronal 2 164312 LRRN4 leucine rich repeat neuronal 4 347730 LRRTM1 leucine rich repeat transmembrane neuronal 1 26045 LRRTM2 leucine rich repeat transmembrane neuronal 2 347731 LRRTM3 leucine rich repeat transmembrane neuronal 3 57408 LRTM1 leucine rich repeats and transmembrane domains 1 654429 LRTM2 leucine rich repeats and transmembrane domains 2 9258 MFHAS1 malignant fibrous histiocytoma amplified sequence 1 25878 MXRA5 matrix remodeling associated 5 4974 OMG oligodendrocyte myelin glycoprotein 26254 OPTC opticin 127435 PODN podocan 79883 PODNL1 podocan like 1 65078 RTN4R reticulon 4 receptor 146760 RTN4RL1 reticulon 4 receptor like 1 349667 RTN4RL2 reticulon 4 receptor like 2 202500 TCTE1 t-complex-associated-testis-expressed 1 25987 TSKU tsukushi, small leucine rich proteoglycan 114990 VASN vasorin 143570 XRRA1 X-ray radiation resistance associated 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 3.07e-01 8.52e-12 GO volume-sensitive anion channel activity molecular_function 1.34e-01 5.73e-08 GO extracellular matrix structural constituent conferring compression resistance molecular_function 9.69e-02 7.29e-09 GO aspartate transmembrane transport biological_process 6.79e-02 1.21e-13 GO positive regulation of synapse assembly biological_process 6.15e-02 3.38e-07 Reactome Synaptic adhesion-like molecules Neuronal System 5.92e-02 2.21e-04 Reactome Axonal growth inhibition (RHOA activation) Signal Transduction 5.50e-02 1.91e-11 GO ion channel complex cellular_component 2.46e-02 3.54e-04 GO negative regulation of axon regeneration biological_process 7.63e-03 6.25e-09 Reactome Miscellaneous transport and binding events Transport of small molecules 4.20e-03 1.30e-10 Reactome Protein-protein interactions at synapses Neuronal System

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 0e+00 0e+00 axon development 0e+00 0e+00 regulation of kinase activity 0e+00 0e+00 response to cytokine 0e+00 0e+00 negative regulation of intracellular signal transduction 0e+00 0e+00 negative regulation of protein kinase activity 0e+00 0e+00 cytokine-mediated signaling pathway 0e+00 0e+00 negative regulation of kinase activity 0e+00 0e+00 regulation of protein kinase activity 0e+00 0e+00 regulation of JAK-STAT cascade 0e+00 0e+00 negative regulation of JAK-STAT cascade 0e+00 0e+00 negative regulation of phosphorylation 0e+00 0e+00 negative regulation of protein phosphorylation 0e+00 0e+00 cellular response to cytokine stimulus 0e+00 0e+00 regulation of synapse organization 0e+00 0e+00 regulation of synapse structure or activity 0e+00 0e+00 positive regulation of synapse assembly 0e+00 0e+00 regulation of synapse assembly 0e+00 0e+00 extracellular matrix 0e+00 0e+00 proteinaceous extracellular matrix 0e+00 0e+00 enzyme inhibitor activity

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

²FDR corrected p-value (Benjamini-Hochberg)

Reactome

P-value1 FDR2 Term 4.35e-04 4.78e-02 P75 NTR RECEPTOR MEDIATED SIGNALLING 5.40e-04 6.89e-02 P75 NTR RECEPTOR MEDIATED SIGNALLING 9.58e-04 9.70e-02 SIGNALLING BY NGF 1.11e-03 1.29e-01 SIGNALLING BY NGF 6.87e-03 5.92e-01 CHONDROITIN SULFATE BIOSYNTHESIS 8.57e-03 7.08e-01 CS DS DEGRADATION 8.58e-03 7.09e-01 A TETRASACCHARIDE LINKER SEQUENCE IS REQUIRED FOR GAG SYNTHESIS 8.61e-03 7.11e-01 HEPARAN SULFATE HEPARIN HS GAG METABOLISM 9.02e-03 6.75e-01 CHONDROITIN SULFATE BIOSYNTHESIS 1.03e-02 8.15e-01 CHONDROITIN SULFATE DERMATAN SULFATE METABOLISM 1.08e-02 7.78e-01 CS DS DEGRADATION 2.70e-02 1.00e+00 GLYCOSAMINOGLYCAN METABOLISM 2.85e-02 1.00e+00 A TETRASACCHARIDE LINKER SEQUENCE IS REQUIRED FOR GAG SYNTHESIS 3.04e-02 1.00e+00 HEPARAN SULFATE HEPARIN HS GAG METABOLISM 3.04e-02 1.00e+00 CHONDROITIN SULFATE DERMATAN SULFATE METABOLISM

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

²FDR corrected p-value (Benjamini-Hochberg)

Mouse mutant phenotypes

P-value1 FDR2 Term 2.36e-05 8.71e-02 decreased exploration in new environment 1.88e-03 1.00e+00 abnormal thymus medulla morphology 3.75e-03 1.00e+00 abnormal long bone diaphysis morphology 5.61e-03 1.00e+00 abnormal tendon collagen fibril morphology 5.61e-03 1.00e+00 absent brain internal capsule 5.62e-03 1.00e+00 abnormal bile duct morphology 5.63e-03 1.00e+00 abnormal long bone metaphysis morphology 9.40e-03 1.00e+00 altered response to CNS ischemic injury 1.12e-02 1.00e+00 abnormal nervous system regeneration 1.31e-02 1.00e+00 small hippocampus 1.31e-02 1.00e+00 abnormal long bone epiphysis morphology 1.31e-02 1.00e+00 thin dermal layer 1.31e-02 1.00e+00 osteoarthritis 1.49e-02 1.00e+00 abnormal central nervous system regeneration 1.49e-02 1.00e+00 abnormal bone collagen fibril morphology 1.50e-02 1.00e+00 abnormal lymph node morphology 1.50e-02 1.00e+00 enhanced cued conditioning behavior 1.50e-02 1.00e+00 perinatal lethality 1.51e-02 1.00e+00 abnormal spatial learning 1.68e-02 1.00e+00 abnormal anterior commissure morphology

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

²FDR corrected p-value (Benjamini-Hochberg)