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DREAM Module Identification Challenge – Consensus modules

PPI-STRING_Consensus_mod195

Assigned name NA Network PPI-STRING Module ID PPI-STRING_Consensus_mod195 Module size 29 genes

Module genes

This module comprises the following genes:

Gene ID Gene Symbol Gene Name 3276 PRMT1 protein arginine methyltransferase 1 3275 PRMT2 protein arginine methyltransferase 2 23034 SAMD4A sterile alpha motif domain containing 4A 55095 SAMD4B sterile alpha motif domain containing 4B 122402 TDRD9 tudor domain containing 9 392188 USP17L10 ubiquitin specific peptidase 17-like family member 8 100287178 USP17L11 ubiquitin specific peptidase 17-like family member 11 100287205 USP17L12 ubiquitin specific peptidase 17-like family member 12 100287238 USP17L13 ubiquitin specific peptidase 17-like family member 13 100288520 USP17L15 ubiquitin specific peptidase 17-like family member 15 100287327 USP17L17 ubiquitin specific peptidase 17-like family member 17 100287364 USP17L18 ubiquitin specific peptidase 17-like family member 18 100287404 USP17L19 ubiquitin specific peptidase 17-like family member 19 377630 USP17L2 ubiquitin specific peptidase 17-like family member 2 100287441 USP17L20 ubiquitin specific peptidase 17-like family member 20 100287478 USP17L21 ubiquitin specific peptidase 17-like family member 21 100287513 USP17L22 ubiquitin specific peptidase 17-like family member 22 101241878 USP17L23 ubiquitin specific peptidase 17-like family member 23 728369 USP17L24 ubiquitin specific peptidase 17-like family member 24 728373 USP17L25 ubiquitin specific peptidase 17-like family member 25 728379 USP17L26 ubiquitin specific peptidase 17-like family member 26 728393 USP17L27 ubiquitin specific peptidase 17-like family member 27 728400 USP17L28 ubiquitin specific peptidase 17-like family member 28 728405 USP17L29 ubiquitin specific peptidase 17-like family member 29 728419 USP17L30 ubiquitin specific peptidase 17-like family member 30 728386 USP17L5 ubiquitin specific peptidase 17-like family member 5 57602 USP36 ubiquitin specific peptidase 36 84132 USP42 ubiquitin specific peptidase 42 23174 ZCCHC14 zinc finger CCHC-type containing 14

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 9.70e-02 7.13e-30 GO thiol-dependent ubiquitinyl hydrolase activity molecular_function 3.21e-02 4.78e-05 GO peptidyl-arginine methylation, to asymmetrical-dimethyl arginine biological_process 2.89e-02 4.78e-05 GO protein-arginine omega-N asymmetric methyltransferase activity molecular_function 1.40e-02 1.12e-04 GO translation repressor activity molecular_function 7.96e-03 3.81e-24 Reactome Ub-specific processing proteases Metabolism of proteins 1.57e-03 9.36e-05 GO histone methyltransferase 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 0.00e+00 0.00e+00 protein deubiquitination 0.00e+00 0.00e+00 protein catabolic process 0.00e+00 0.00e+00 cellular protein catabolic process 0.00e+00 0.00e+00 modification-dependent protein catabolic process 0.00e+00 0.00e+00 proteolysis involved in cellular protein catabolic process 0.00e+00 0.00e+00 ubiquitin-dependent protein catabolic process 0.00e+00 0.00e+00 protein modification by small protein removal 0.00e+00 0.00e+00 ubiquitinyl hydrolase activity 0.00e+00 0.00e+00 cysteine-type peptidase activity 0.00e+00 0.00e+00 peptidase activity 0.00e+00 0.00e+00 thiol-dependent ubiquitinyl hydrolase activity 2.54e-05 6.13e-03 histone-arginine N-methyltransferase activity 4.80e-05 1.09e-02 protein-arginine N-methyltransferase activity 5.85e-05 1.84e-02 histone arginine methylation 6.03e-05 1.33e-02 thiol-dependent ubiquitin-specific protease activity 1.19e-04 2.28e-02 cytoplasmic ribonucleoprotein granule 1.32e-04 3.70e-02 peptidyl-arginine N-methylation 1.35e-04 3.77e-02 peptidyl-arginine methylation 1.48e-04 2.77e-02 ribonucleoprotein granule 1.10e-03 1.67e-01 histone methyltransferase activity

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 abnormal body composition 1.87e-03 1e+00 decreased skeletal muscle glycogen level 3.74e-03 1e+00 absent amniotic folds 3.74e-03 1e+00 abnormal white fat cell morphology 5.61e-03 1e+00 increased subcutaneous adipose tissue amount 5.64e-03 1e+00 empty decidua capsularis 7.46e-03 1e+00 abnormal DNA methylation during gametogenesis 7.47e-03 1e+00 muscle hypoplasia 9.32e-03 1e+00 absent ectoplacental cavity 9.33e-03 1e+00 absent proamniotic cavity 1.12e-02 1e+00 distorted hair follicle pattern 1.12e-02 1e+00 decreased body mass index 1.30e-02 1e+00 abnormal synaptonemal complex 1.31e-02 1e+00 abnormal spermatogonia morphology 1.31e-02 1e+00 abnormal muscle fiber morphology 1.67e-02 1e+00 decreased inguinal fat pad weight 1.68e-02 1e+00 decreased white fat cell size 1.86e-02 1e+00 myopathy 1.87e-02 1e+00 increased circulating LDL cholesterol level 2.23e-02 1e+00 abnormal egg cylinder morphology

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

²FDR corrected p-value (Benjamini-Hochberg)