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DREAM Module Identification Challenge – Consensus modules

PPI-STRING_Consensus_mod144

Assigned name NA Network PPI-STRING Module ID PPI-STRING_Consensus_mod144 Module size 33 genes

Module genes

This module comprises the following genes:

Gene ID Gene Symbol Gene Name 27087 B3GAT1 beta-1,3-glucuronyltransferase 1 26229 B3GAT3 beta-1,3-glucuronyltransferase 3 283358 B4GALNT3 beta-1,4-N-acetyl-galactosaminyltransferase 3 338707 B4GALNT4 beta-1,4-N-acetyl-galactosaminyltransferase 4 63827 BCAN brevican 79586 CHPF chondroitin polymerizing factor 54480 CHPF2 chondroitin polymerizing factor 2 50515 CHST11 carbohydrate sulfotransferase 11 55501 CHST12 carbohydrate sulfotransferase 12 166012 CHST13 carbohydrate sulfotransferase 13 113189 CHST14 carbohydrate sulfotransferase 14 51363 CHST15 carbohydrate sulfotransferase 15 9469 CHST3 carbohydrate sulfotransferase 3 56548 CHST7 carbohydrate sulfotransferase 7 22856 CHSY1 chondroitin sulfate synthase 1 337876 CHSY3 chondroitin sulfate synthase 3 55790 CSGALNACT1 chondroitin sulfate N-acetylgalactosaminyltransferase 1 55454 CSGALNACT2 chondroitin sulfate N-acetylgalactosaminyltransferase 2 1464 CSPG4 chondroitin sulfate proteoglycan 4 10675 CSPG5 chondroitin sulfate proteoglycan 5 29940 DSE dermatan sulfate epimerase 222611 GPR111 adhesion G protein-coupled receptor F2 347088 GPR144 adhesion G protein-coupled receptor D2 222487 GPR97 adhesion G protein-coupled receptor G3 1463 NCAN neurocan 1527 TEX28 testis expressed 28 1527 TEX28P1 testis expressed 28 1527 TEX28P2 testis expressed 28 57458 TMCC3 transmembrane and coiled-coil domain family 3 10090 UST uronyl 2-sulfotransferase 1462 VCAN versican 64131 XYLT1 xylosyltransferase 1 64132 XYLT2 xylosyltransferase 2

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 3.06e-01 6.02e-57 GO chondroitin sulfate biosynthetic process biological_process 2.41e-01 1.29e-48 Reactome Chondroitin sulfate biosynthesis Metabolism 2.02e-01 5.41e-16 GO chondroitin sulfate proteoglycan biosynthetic process biological_process 9.97e-02 5.71e-62 Reactome Chondroitin sulfate/dermatan sulfate metabolism Metabolism 9.90e-02 1.92e-24 GO dermatan sulfate biosynthetic process biological_process 1.12e-02 1.06e-10 GO acetylgalactosaminyltransferase activity molecular_function

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 chondroitin sulfate biosynthetic process 0e+00 0e+00 chondroitin sulfate proteoglycan biosynthetic process 0e+00 0e+00 sulfur compound metabolic process 0e+00 0e+00 glycoprotein biosynthetic process 0e+00 0e+00 glycoprotein metabolic process 0e+00 0e+00 glycosaminoglycan biosynthetic process 0e+00 0e+00 proteoglycan biosynthetic process 0e+00 0e+00 proteoglycan metabolic process 0e+00 0e+00 chondroitin sulfate metabolic process 0e+00 0e+00 glycosaminoglycan metabolic process 0e+00 0e+00 dermatan sulfate biosynthetic process 0e+00 0e+00 dermatan sulfate proteoglycan biosynthetic process 0e+00 0e+00 dermatan sulfate proteoglycan metabolic process 0e+00 0e+00 Golgi membrane 0e+00 0e+00 UDP-glycosyltransferase activity 0e+00 0e+00 transferase activity, transferring glycosyl groups 0e+00 0e+00 transferase activity, transferring hexosyl groups 0e+00 0e+00 glucuronosyltransferase activity 0e+00 0e+00 glucuronosyl-N-acetylgalactosaminyl-proteoglycan 4-beta-N-acetylgalactosaminyltransferase activity 0e+00 0e+00 acetylgalactosaminyltransferase activity

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 CHONDROITIN SULFATE BIOSYNTHESIS 0.00e+00 0.00e+00 GLYCOSAMINOGLYCAN METABOLISM 0.00e+00 0.00e+00 METABOLISM OF CARBOHYDRATES 0.00e+00 0.00e+00 CHONDROITIN SULFATE DERMATAN SULFATE METABOLISM 0.00e+00 0.00e+00 CHONDROITIN SULFATE BIOSYNTHESIS 0.00e+00 0.00e+00 GLYCOSAMINOGLYCAN METABOLISM 0.00e+00 0.00e+00 METABOLISM OF CARBOHYDRATES 0.00e+00 0.00e+00 CHONDROITIN SULFATE DERMATAN SULFATE METABOLISM 2.54e-10 8.88e-08 A TETRASACCHARIDE LINKER SEQUENCE IS REQUIRED FOR GAG SYNTHESIS 6.01e-10 1.51e-07 A TETRASACCHARIDE LINKER SEQUENCE IS REQUIRED FOR GAG SYNTHESIS 3.48e-08 9.51e-06 CS DS DEGRADATION 6.83e-08 1.36e-05 CS DS DEGRADATION 7.99e-07 1.83e-04 HEPARAN SULFATE HEPARIN HS GAG METABOLISM 8.97e-06 1.35e-03 HEPARAN SULFATE HEPARIN HS GAG METABOLISM

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

²FDR corrected p-value (Benjamini-Hochberg)

Mouse mutant phenotypes

P-value1 FDR2 Term 2.93e-06 1.99e-02 short limbs 3.03e-04 4.49e-01 small thoracic cage 4.68e-04 5.84e-01 short mandible 5.55e-04 6.46e-01 decreased skin tensile strength 6.39e-04 6.98e-01 abnormal cartilage morphology 7.05e-04 7.38e-01 abnormal phalanx morphology 7.64e-04 7.68e-01 decreased width of hypertrophic chondrocyte zone 7.73e-04 7.75e-01 short humerus 1.05e-03 9.25e-01 short ribs 1.62e-03 1.00e+00 abnormal long bone hypertrophic chondrocyte zone 1.67e-03 1.00e+00 abnormal long term potentiation 1.68e-03 1.00e+00 decreased bone trabecula number 1.87e-03 1.00e+00 abnormal hindlimb stylopod morphology 2.27e-03 1.00e+00 disproportionate dwarf 3.74e-03 1.00e+00 increased Schwann cell proliferation 3.75e-03 1.00e+00 kinked tail 3.75e-03 1.00e+00 liver cysts 3.75e-03 1.00e+00 liver hyperplasia 4.08e-03 1.00e+00 short femur 5.61e-03 1.00e+00 brachypodia

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

²FDR corrected p-value (Benjamini-Hochberg)