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DREAM Module Identification Challenge – Consensus modules

PPI-STRING_Consensus_mod138

Assigned name NA Network PPI-STRING Module ID PPI-STRING_Consensus_mod138 Module size 22 genes

Module genes

This module comprises the following genes:

Gene ID Gene Symbol Gene Name 410 ARSA arylsulfatase A 411 ARSB arylsulfatase B 414 ARSD arylsulfatase D 415 ARSE arylsulfatase E 416 ARSF arylsulfatase F 22901 ARSG arylsulfatase G 347527 ARSH arylsulfatase family member H 340075 ARSI arylsulfatase family member I 79642 ARSJ arylsulfatase family member J 153642 ARSK arylsulfatase family member K 2588 GALNS galactosamine (N-acetyl)-6-sulfatase 2799 GNS glucosamine (N-acetyl)-6-sulfatase 138050 HGSNAT heparan-alpha-glucosaminide N-acetyltransferase 23553 HYAL4 hyaluronidase 4 3423 IDS iduronate 2-sulfatase 6448 SGSH N-sulfoglucosamine sulfohydrolase 6677 SPAM1 sperm adhesion molecule 1 412 STS steroid sulfatase 23213 SULF1 sulfatase 1 55959 SULF2 sulfatase 2 285362 SUMF1 sulfatase modifying factor 1 25870 SUMF2 sulfatase modifying factor 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 5.00e-01 2.75e-40 Reactome The activation of arylsulfatases Metabolism of proteins 4.30e-01 1.28e-03 Reactome Interaction With Cumulus Cells Reproduction 3.89e-01 4.72e-37 GO arylsulfatase activity molecular_function 8.57e-02 1.11e-10 GO glycosaminoglycan catabolic process biological_process 1.30e-03 1.03e-04 GO keratan sulfate 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 0.00e+00 0.00e+00 membrane lipid metabolic process 0.00e+00 0.00e+00 glycosphingolipid metabolic process 0.00e+00 0.00e+00 post-translational protein modification 0.00e+00 0.00e+00 glycolipid metabolic process 0.00e+00 0.00e+00 sphingolipid metabolic process 0.00e+00 0.00e+00 glycosaminoglycan catabolic process 0.00e+00 0.00e+00 endoplasmic reticulum lumen 0.00e+00 0.00e+00 hydrolase activity, acting on ester bonds 0.00e+00 0.00e+00 sulfuric ester hydrolase activity 0.00e+00 0.00e+00 arylsulfatase activity 3.98e-10 3.10e-07 glycosaminoglycan metabolic process 1.40e-09 1.02e-06 proteoglycan metabolic process 2.01e-09 1.44e-06 sulfur compound metabolic process 2.82e-09 1.20e-06 lysosome 8.14e-09 3.27e-06 lysosomal lumen 1.43e-08 5.56e-06 vacuole 3.90e-08 1.60e-05 N-acetylglucosamine-6-sulfatase activity 5.35e-08 3.16e-05 chondroitin sulfate catabolic process 3.18e-06 1.37e-03 glycoprotein metabolic process 1.30e-05 3.12e-03 azurophil granule lumen

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 GLYCOSPHINGOLIPID METABOLISM 0.00e+00 0.00e+00 THE ACTIVATION OF ARYLSULFATASES 0.00e+00 0.00e+00 PTM GAMMA CARBOXYLATION HYPUSINE FORMATION AND ARYLSULFATASE ACTIVATION 0.00e+00 0.00e+00 POST TRANSLATIONAL PROTEIN MODIFICATION 0.00e+00 0.00e+00 PHOSPHOLIPID METABOLISM 0.00e+00 0.00e+00 SPHINGOLIPID METABOLISM 0.00e+00 0.00e+00 GLYCOSPHINGOLIPID METABOLISM 0.00e+00 0.00e+00 THE ACTIVATION OF ARYLSULFATASES 0.00e+00 0.00e+00 PTM GAMMA CARBOXYLATION HYPUSINE FORMATION AND ARYLSULFATASE ACTIVATION 0.00e+00 0.00e+00 POST TRANSLATIONAL PROTEIN MODIFICATION 0.00e+00 0.00e+00 SPHINGOLIPID METABOLISM 0.00e+00 0.00e+00 PHOSPHOLIPID METABOLISM 3.23e-04 4.38e-02 CS DS DEGRADATION 8.23e-04 9.93e-02 GLYCOSAMINOGLYCAN METABOLISM 1.73e-03 1.64e-01 CS DS DEGRADATION 2.63e-03 2.37e-01 GLYCOSAMINOGLYCAN METABOLISM 4.52e-03 4.20e-01 METABOLISM OF CARBOHYDRATES 4.96e-03 4.54e-01 HS GAG DEGRADATION 5.47e-03 4.41e-01 HS GAG DEGRADATION 9.10e-03 7.43e-01 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 1.56e-06 1.20e-02 lysosomal protein accumulation 1.12e-05 5.09e-02 increased urine glycosaminoglycan level 1.45e-05 6.05e-02 abnormal cell morphology 1.80e-05 7.03e-02 abnormal microglial cell morphology 1.16e-04 2.49e-01 sternebra fusion 2.10e-04 3.59e-01 abnormal lysosome physiology 3.09e-04 4.57e-01 abnormal neuron morphology 5.42e-04 6.38e-01 abnormal cartilage morphology 5.87e-04 6.67e-01 abnormal macrophage morphology 5.88e-04 6.67e-01 decreased cranium height 6.46e-04 7.03e-01 abnormal heart valve morphology 1.07e-03 9.34e-01 increased fibroblast proliferation 1.87e-03 1.00e+00 mitral valve regurgitation 1.87e-03 1.00e+00 split vertebrae 1.90e-03 1.00e+00 decreased Purkinje cell number 2.37e-03 1.00e+00 abnormal digit morphology 2.46e-03 1.00e+00 short stride length 3.40e-03 1.00e+00 decreased length of long bones 3.74e-03 1.00e+00 enlarged esophagus 3.74e-03 1.00e+00 exostosis

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

²FDR corrected p-value (Benjamini-Hochberg)