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DREAM Module Identification Challenge – Consensus modules

PPI-STRING_Consensus_mod123

Assigned name NA Network PPI-STRING Module ID PPI-STRING_Consensus_mod123 Module size 13 genes

Module genes

This module comprises the following genes:

Gene ID Gene Symbol Gene Name 29943 PADI1 peptidyl arginine deiminase 1 11240 PADI2 peptidyl arginine deiminase 2 51702 PADI3 peptidyl arginine deiminase 3 23569 PADI4 peptidyl arginine deiminase 4 6799 SULT1A2 sulfotransferase family 1A member 2 6818 SULT1A3 sulfotransferase family 1A member 3 445329 SULT1A4 sulfotransferase family 1A member 4 27284 SULT1B1 sulfotransferase family 1B member 1 27233 SULT1C2 sulfotransferase family 1C member 4 442038 SULT1C3 sulfotransferase family 1C member 3 27233 SULT1C4 sulfotransferase family 1C member 4 25830 SULT4A1 sulfotransferase family 4A member 1 391365 SULT6B1 sulfotransferase family 6B member 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 5.38e-01 4.39e-28 GO aryl sulfotransferase activity molecular_function 4.95e-01 9.86e-13 GO protein-arginine deiminase activity molecular_function 2.16e-02 2.99e-22 GO 3'-phosphoadenosine 5'-phosphosulfate metabolic 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 3'-phosphoadenosine 5'-phosphosulfate metabolic process 0.00e+00 0.00e+00 sulfotransferase activity 0.00e+00 0.00e+00 aryl sulfotransferase activity 2.18e-11 1.41e-08 protein-arginine deiminase activity 6.18e-11 5.24e-08 sulfation 7.72e-11 6.48e-08 protein citrullination 7.72e-11 6.48e-08 histone citrullination 7.90e-09 5.20e-06 sulfur compound metabolic process 2.49e-08 1.54e-05 purine nucleotide metabolic process 2.92e-08 1.78e-05 ribonucleotide metabolic process 1.43e-07 7.87e-05 phenol-containing compound metabolic process 1.51e-07 8.27e-05 nucleotide metabolic process 2.08e-07 1.11e-04 steroid metabolic process 3.81e-07 1.95e-04 nucleobase-containing small molecule metabolic process 5.90e-06 2.40e-03 catecholamine metabolic process 8.01e-06 2.14e-03 hydrolase activity, acting on carbon-nitrogen (but not peptide) bonds 3.13e-05 1.06e-02 histone modification 3.67e-05 1.23e-02 amine metabolic process 5.71e-05 1.80e-02 flavonoid metabolic process 8.49e-05 2.54e-02 xenobiotic metabolic process

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 CYTOSOLIC SULFONATION OF SMALL MOLECULES 0.00e+00 0.00e+00 BIOLOGICAL OXIDATIONS 0.00e+00 0.00e+00 PHASE II CONJUGATION 0.00e+00 0.00e+00 CYTOSOLIC SULFONATION OF SMALL MOLECULES 1.50e-11 4.36e-09 PHASE II CONJUGATION 6.15e-10 1.54e-07 BIOLOGICAL OXIDATIONS 4.25e-03 4.00e-01 ACTIVATION OF CHAPERONE GENES BY XBP1S 5.51e-03 4.95e-01 UNFOLDED PROTEIN RESPONSE 7.17e-03 5.59e-01 ACTIVATION OF CHAPERONE GENES BY XBP1S 9.73e-03 7.85e-01 DIABETES PATHWAYS 1.12e-02 8.03e-01 UNFOLDED PROTEIN RESPONSE 1.44e-02 9.84e-01 DIABETES PATHWAYS

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

²FDR corrected p-value (Benjamini-Hochberg)

Mouse mutant phenotypes

P-value1 FDR2 Term 1.87e-03 1e+00 impaired neutrophil phagocytosis 1.87e-03 1e+00 decreased susceptibility to weight loss 5.62e-03 1e+00 autoimmune response 9.35e-03 1e+00 decreased susceptibility to viral infection 1.12e-02 1e+00 abnormal mast cell physiology 1.31e-02 1e+00 partial lethality 1.50e-02 1e+00 abnormal neutrophil physiology 3.39e-02 1e+00 partial preweaning lethality

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

²FDR corrected p-value (Benjamini-Hochberg)