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DREAM Module Identification Challenge – Consensus modules

PPI-STRING_Consensus_mod45

Assigned name NA Network PPI-STRING Module ID PPI-STRING_Consensus_mod45 Module size 28 genes

Module genes

This module comprises the following genes:

Gene ID Gene Symbol Gene Name 100362547 CHAD adaptor related protein complex 1 subunit gamma 2 221184 CPN2 copine 2 2331 FMOD fibromodulin 2814 GP5 glycoprotein V platelet 11081 KERA keratocan 116844 LRG1 leucine rich alpha-2-glycoprotein 1 55227 LRRC1 leucine rich repeat containing 1 376132 LRRC10 leucine rich repeat containing 10 390205 LRRC10B leucine rich repeat containing 10B 474354 LRRC18 leucine rich repeat containing 18 79442 LRRC2 leucine rich repeat containing 2 55222 LRRC20 leucine rich repeat containing 20 10233 LRRC23 leucine rich repeat containing 23 123355 LRRC28 leucine rich repeat containing 28 339291 LRRC30 leucine rich repeat containing 30 127495 LRRC39 leucine rich repeat containing 39 55631 LRRC40 leucine rich repeat containing 40 255252 LRRC57 leucine rich repeat containing 57 116064 LRRC58 leucine rich repeat containing 58 55379 LRRC59 leucine rich repeat containing 59 100130742 LRRC69 leucine rich repeat containing 69 401387 LRRD1 leucine rich repeats and death domain containing 1 344657 LRRIQ4 leucine rich repeats and IQ motif containing 4 4060 LUM lumican 4969 OGN osteoglycin 4958 OMD osteomodulin 5549 PRELP proline and arginine rich end leucine rich repeat protein 6251 RSU1 Ras suppressor protein 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 2.12e-01 3.64e-18 Reactome Defective CHST6 causes MCDC1 Disease 2.12e-01 3.64e-18 Reactome Defective ST3GAL3 causes MCT12 and EIEE15 Disease 2.09e-01 3.64e-18 Reactome Defective B4GALT1 causes B4GALT1-CDG (CDG-2d) Disease

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 keratan sulfate catabolic process 1.82e-11 1.62e-08 keratan sulfate biosynthetic process 2.73e-11 2.39e-08 glycosaminoglycan catabolic process 3.07e-11 2.68e-08 keratan sulfate metabolic process 1.39e-09 1.01e-06 axonogenesis 1.58e-09 1.15e-06 glycosaminoglycan biosynthetic process 1.75e-09 1.26e-06 axon development 1.87e-09 1.34e-06 cell morphogenesis involved in neuron differentiation 3.28e-09 1.38e-06 lysosomal lumen 5.09e-09 3.44e-06 neuron projection morphogenesis 5.59e-09 3.75e-06 cell projection morphogenesis 6.00e-09 4.01e-06 cell morphogenesis involved in differentiation 7.03e-09 4.66e-06 cell part morphogenesis 1.08e-08 7.00e-06 glycosaminoglycan metabolic process 1.46e-08 5.67e-06 Golgi lumen 1.60e-08 6.15e-06 proteinaceous extracellular matrix 2.56e-08 1.58e-05 cell morphogenesis 3.44e-08 2.08e-05 neuron projection development 8.51e-08 2.93e-05 extracellular matrix 1.66e-07 9.03e-05 neuron development

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 KERATAN SULFATE DEGRADATION 6.90e-12 2.03e-09 KERATAN SULFATE DEGRADATION 2.93e-11 1.11e-08 KERATAN SULFATE BIOSYNTHESIS 3.21e-11 1.21e-08 KERATAN SULFATE KERATIN METABOLISM 3.80e-10 9.75e-08 KERATAN SULFATE BIOSYNTHESIS 4.18e-10 1.07e-07 KERATAN SULFATE KERATIN METABOLISM 2.97e-08 8.23e-06 GLYCOSAMINOGLYCAN METABOLISM 3.20e-08 6.67e-06 GLYCOSAMINOGLYCAN METABOLISM 5.54e-07 1.30e-04 METABOLISM OF CARBOHYDRATES 6.00e-07 1.08e-04 METABOLISM OF CARBOHYDRATES 1.34e-02 1.00e+00 CELL EXTRACELLULAR MATRIX INTERACTIONS 2.08e-02 1.00e+00 CELL EXTRACELLULAR MATRIX INTERACTIONS 2.21e-02 1.00e+00 PLATELET ADHESION TO EXPOSED COLLAGEN 3.89e-02 1.00e+00 PLATELET AGGREGATION PLUG FORMATION 4.20e-02 1.00e+00 INTRINSIC PATHWAY 4.94e-02 1.00e+00 PLATELET ADHESION TO EXPOSED COLLAGEN

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

²FDR corrected p-value (Benjamini-Hochberg)

Mouse mutant phenotypes

P-value1 FDR2 Term 3.48e-05 1.12e-01 decreased cornea thickness 3.69e-05 1.17e-01 abnormal corneal stroma morphology 1.30e-04 2.69e-01 abnormal tendon morphology 2.37e-04 3.89e-01 corneal opacity 3.64e-04 5.02e-01 abnormal inflammatory response 6.01e-04 6.75e-01 abnormal cornea morphology 1.47e-03 1.00e+00 decreased neutrophil cell number 1.87e-03 1.00e+00 bruising 1.87e-03 1.00e+00 abnormal cornea posterior stroma morphology 3.74e-03 1.00e+00 abnormal sclera morphology 3.74e-03 1.00e+00 abnormal articular cartilage morphology 3.75e-03 1.00e+00 increased long bone epiphyseal plate size 5.61e-03 1.00e+00 abnormal adrenocorticotropin level 5.61e-03 1.00e+00 osteoarthritis 5.61e-03 1.00e+00 decreased corneal stroma thickness 5.62e-03 1.00e+00 decreased bone strength 5.63e-03 1.00e+00 abnormal compact bone morphology 5.64e-03 1.00e+00 delayed wound healing 7.47e-03 1.00e+00 abnormal skin tensile strength 7.48e-03 1.00e+00 abnormal iridocorneal angle

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

²FDR corrected p-value (Benjamini-Hochberg)