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DREAM Module Identification Challenge – Consensus modules

PPI-STRING_Consensus_mod142

Assigned name NA Network PPI-STRING Module ID PPI-STRING_Consensus_mod142 Module size 32 genes

Module genes

This module comprises the following genes:

Gene ID Gene Symbol Gene Name 375790 AGRN agrin 126792 B3GALT6 beta-1,3-galactosyltransferase 6 11285 B4GALT7 beta-1,4-galactosyltransferase 7 2131 EXT1 exostosin glycosyltransferase 1 2132 EXT2 exostosin glycosyltransferase 2 26035 GLCE glucuronic acid epimerase 221914 GPC2 glypican 2 2719 GPC3 glypican 3 2239 GPC4 glypican 4 2262 GPC5 glypican 5 10082 GPC6 glypican 6 283464 GXYLT1 glucoside xylosyltransferase 1 10855 HPSE heparanase 60495 HPSE2 heparanase 2 (inactive) 9957 HS3ST1 heparan sulfate-glucosamine 3-sulfotransferase 1 9956 HS3ST2 heparan sulfate-glucosamine 3-sulfotransferase 2 9955 HS3ST3A1 heparan sulfate-glucosamine 3-sulfotransferase 3A1 9953 HS3ST3B1 heparan sulfate-glucosamine 3-sulfotransferase 3B1 9951 HS3ST4 heparan sulfate-glucosamine 3-sulfotransferase 4 64711 HS3ST5 heparan sulfate-glucosamine 3-sulfotransferase 6 64711 HS3ST6 heparan sulfate-glucosamine 3-sulfotransferase 6 9394 HS6ST1 heparan sulfate 6-O-sulfotransferase 1 90161 HS6ST2 heparan sulfate 6-O-sulfotransferase 2 3339 HSPG2 heparan sulfate proteoglycan 2 3425 IDUA iduronidase, alpha-L- 3340 NDST1 N-deacetylase and N-sulfotransferase 1 8509 NDST2 N-deacetylase and N-sulfotransferase 2 6382 SDC1 syndecan 1 6383 SDC2 syndecan 2 9672 SDC3 syndecan 3 6385 SDC4 syndecan 4 11046 SLC35D2 solute carrier family 35 member D2

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 3.96e-01 4.93e-73 Reactome HS-GAG biosynthesis Metabolism 1.81e-01 7.83e-69 GO glycosaminoglycan biosynthetic process biological_process 1.25e-01 1.53e-81 Reactome Heparan sulfate/heparin (HS-GAG) metabolism Metabolism 7.47e-02 2.45e-35 Reactome HS-GAG degradation Metabolism 1.74e-02 9.37e-34 GO glycosaminoglycan catabolic process 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 0e+00 0e+00 glycosaminoglycan biosynthetic process 0e+00 0e+00 glycosaminoglycan metabolic process 0e+00 0e+00 isoprenoid metabolic process 0e+00 0e+00 glycosaminoglycan catabolic process 0e+00 0e+00 retinoid metabolic process 0e+00 0e+00 diterpenoid metabolic process 0e+00 0e+00 sulfur compound metabolic process 0e+00 0e+00 heparan sulfate proteoglycan biosynthetic process 0e+00 0e+00 glycoprotein biosynthetic process 0e+00 0e+00 glycoprotein metabolic process 0e+00 0e+00 proteoglycan metabolic process 0e+00 0e+00 proteoglycan biosynthetic process 0e+00 0e+00 heparan sulfate proteoglycan metabolic process 0e+00 0e+00 Golgi lumen 0e+00 0e+00 lysosomal lumen 0e+00 0e+00 [heparan sulfate]-glucosamine 3-sulfotransferase 1 activity 0e+00 0e+00 sulfotransferase activity 0e+00 0e+00 glycoprotein binding 0e+00 0e+00 proteoglycan binding 0e+00 0e+00 heparan sulfate proteoglycan binding

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 HS GAG BIOSYNTHESIS 0.00e+00 0.00e+00 HEPARAN SULFATE HEPARIN HS GAG METABOLISM 0.00e+00 0.00e+00 GLYCOSAMINOGLYCAN METABOLISM 0.00e+00 0.00e+00 METABOLISM OF CARBOHYDRATES 0.00e+00 0.00e+00 A TETRASACCHARIDE LINKER SEQUENCE IS REQUIRED FOR GAG SYNTHESIS 0.00e+00 0.00e+00 HS GAG DEGRADATION 0.00e+00 0.00e+00 CHONDROITIN SULFATE DERMATAN SULFATE METABOLISM 0.00e+00 0.00e+00 HS GAG BIOSYNTHESIS 0.00e+00 0.00e+00 HEPARAN SULFATE HEPARIN HS GAG METABOLISM 0.00e+00 0.00e+00 GLYCOSAMINOGLYCAN METABOLISM 0.00e+00 0.00e+00 METABOLISM OF CARBOHYDRATES 0.00e+00 0.00e+00 HS GAG DEGRADATION 0.00e+00 0.00e+00 A TETRASACCHARIDE LINKER SEQUENCE IS REQUIRED FOR GAG SYNTHESIS 0.00e+00 0.00e+00 CHONDROITIN SULFATE DERMATAN SULFATE METABOLISM 7.77e-03 6.56e-01 CHYLOMICRON MEDIATED LIPID TRANSPORT 1.21e-02 8.59e-01 CHYLOMICRON MEDIATED LIPID TRANSPORT 2.06e-02 1.00e+00 LIPOPROTEIN METABOLISM 2.29e-02 1.00e+00 LIPOPROTEIN METABOLISM 3.55e-02 1.00e+00 LIPID DIGESTION MOBILIZATION AND TRANSPORT 3.90e-02 1.00e+00 LIPID DIGESTION MOBILIZATION AND TRANSPORT

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

²FDR corrected p-value (Benjamini-Hochberg)

Mouse mutant phenotypes

P-value1 FDR2 Term 3.17e-04 4.66e-01 iris coloboma 7.53e-04 7.64e-01 abnormal eye morphology 1.87e-03 1.00e+00 camptodactyly 1.95e-03 1.00e+00 absent mandible 2.06e-03 1.00e+00 abnormal aortic valve morphology 3.26e-03 1.00e+00 abnormal skeleton development 3.50e-03 1.00e+00 abnormal skeletal muscle fiber type ratio 3.59e-03 1.00e+00 abnormal basicranium morphology 3.74e-03 1.00e+00 increased post-tetanic potentiation 5.60e-03 1.00e+00 failure of primitive streak formation 7.52e-03 1.00e+00 abnormal ascending aorta and coronary artery attachment 8.18e-03 1.00e+00 failure to gastrulate 8.61e-03 1.00e+00 abnormal telencephalon morphology 9.33e-03 1.00e+00 increased urination frequency 9.37e-03 1.00e+00 abnormal node of Ranvier morphology 9.38e-03 1.00e+00 failure of neuromuscular synapse presynaptic differentiation 1.25e-02 1.00e+00 abnormal neuromuscular synapse morphology 1.30e-02 1.00e+00 urinary incontinence 1.31e-02 1.00e+00 absent conotruncal ridges 1.32e-02 1.00e+00 delayed wound healing

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

²FDR corrected p-value (Benjamini-Hochberg)