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DREAM Module Identification Challenge – Consensus modules

PPI-STRING_Consensus_mod275

Assigned name NA Network PPI-STRING Module ID PPI-STRING_Consensus_mod275 Module size 31 genes

Module genes

This module comprises the following genes:

Gene ID Gene Symbol Gene Name 15 AANAT aralkylamine N-acetyltransferase 79370 BCL2L14 BCL2 like 14 666 BOK BCL2 family apoptosis regulator BOK 81576 CCDC130 coiled-coil domain containing 130 130940 CCDC148 coiled-coil domain containing 148 1656 DDX6 DEAD-box helicase 6 9988 DMTF1 cyclin D binding myb like transcription factor 1 138311 FAM69B family with sequence similarity 69 member B 64841 GNPNAT1 glucosamine-phosphate N-acetyltransferase 1 3831 KLC1 kinesin light chain 1 147700 KLC2 kinesin light chain 3 147700 KLC3 kinesin light chain 3 89953 KLC4 kinesin light chain 4 4602 MYB MYB proto-oncogene, transcription factor 4605 MYBL2 MYB proto-oncogene like 2 4763 NF1 neurofibromin 1 23207 PLEKHM2 pleckstrin homology and RUN domain containing M2 51426 POLQ DNA polymerase kappa 5478 PPIA peptidylprolyl isomerase A 653505 PPIAL4A peptidylprolyl isomerase A like 4A 653505 PPIAL4B peptidylprolyl isomerase A like 4A 653598 PPIAL4C peptidylprolyl isomerase A like 4C 645142 PPIAL4D peptidylprolyl isomerase A like 4D 644591 PPIAL4G peptidylprolyl isomerase A like 4G 10450 PPIE peptidylprolyl isomerase E 6992 PPP1R11 protein phosphatase 1 regulatory inhibitor subunit 11 23369 PUM2 pumilio RNA binding family member 2 10861 SAT1 solute carrier family 26 member 1 340562 SATL1 spermidine/spermine N1-acetyl transferase like 1 6621 SNAPC4 small nuclear RNA activating complex polypeptide 4 55133 SRBD1 S1 RNA binding domain 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 1.87e-01 1.59e-09 Reactome RHO GTPases activate KTN1 Signal Transduction 1.24e-01 1.10e-12 GO cyclosporin A binding molecular_function 2.24e-02 4.71e-03 Reactome Interconversion of polyamines Metabolism 1.94e-02 1.30e-04 GO N-acetyltransferase activity molecular_function 6.52e-03 8.94e-12 GO peptidyl-prolyl cis-trans isomerase 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 1.34e-09 9.81e-07 protein peptidyl-prolyl isomerization 6.46e-09 3.02e-06 peptidyl-prolyl cis-trans isomerase activity 8.98e-09 4.13e-06 transcription factor activity, RNA polymerase II transcription factor recruiting 1.53e-06 4.70e-04 isomerase activity 1.99e-06 5.54e-04 kinesin complex 4.10e-06 1.72e-03 protein folding 8.97e-06 2.37e-03 diamine N-acetyltransferase activity 1.07e-05 2.78e-03 N-acetyltransferase activity 1.74e-05 4.33e-03 acetyltransferase activity 1.85e-05 4.59e-03 N-acyltransferase activity 2.18e-05 7.75e-03 spermine catabolic process 3.02e-05 1.03e-02 spermidine acetylation 3.54e-05 1.19e-02 cellular biogenic amine metabolic process 3.76e-05 8.76e-03 transcription factor activity, RNA polymerase II transcription factor binding 4.52e-05 1.03e-02 kinesin binding 5.01e-05 1.61e-02 amine metabolic process 5.44e-05 1.73e-02 polyamine catabolic process 1.00e-04 2.07e-02 microtubule motor activity 1.01e-04 2.94e-02 spermidine metabolic process 1.14e-04 2.20e-02 microtubule associated complex

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

²FDR corrected p-value (Benjamini-Hochberg)

Reactome

P-value1 FDR2 Term 1.17e-07 2.26e-05 KINESINS 1.93e-07 4.84e-05 KINESINS 3.86e-07 9.23e-05 FACTORS INVOLVED IN MEGAKARYOCYTE DEVELOPMENT AND PLATELET PRODUCTION 6.18e-07 1.11e-04 FACTORS INVOLVED IN MEGAKARYOCYTE DEVELOPMENT AND PLATELET PRODUCTION 5.15e-06 1.03e-03 MHC CLASS II ANTIGEN PRESENTATION 1.40e-05 2.04e-03 MHC CLASS II ANTIGEN PRESENTATION 1.81e-03 1.71e-01 INTEGRATION OF PROVIRUS 3.43e-03 3.35e-01 BINDING AND ENTRY OF HIV VIRION 3.62e-03 3.12e-01 BINDING AND ENTRY OF HIV VIRION 6.64e-03 5.24e-01 APOBEC3G MEDIATED RESISTANCE TO HIV1 INFECTION 6.86e-03 5.92e-01 INTEGRATION OF PROVIRUS 7.05e-03 6.04e-01 APOBEC3G MEDIATED RESISTANCE TO HIV1 INFECTION 7.23e-03 5.62e-01 EARLY PHASE OF HIV LIFE CYCLE 8.57e-03 7.08e-01 EARLY PHASE OF HIV LIFE CYCLE 1.98e-02 1.00e+00 BASIGIN INTERACTIONS 2.75e-02 1.00e+00 AMINE DERIVED HORMONES 3.15e-02 1.00e+00 BASIGIN INTERACTIONS 3.19e-02 1.00e+00 RNA POL III TRANSCRIPTION INITIATION FROM TYPE 3 PROMOTER 3.29e-02 1.00e+00 AMINE DERIVED HORMONES 3.42e-02 1.00e+00 HOST INTERACTIONS OF HIV FACTORS

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 dilated seminal vesicles 5.63e-03 1e+00 delayed muscle development 7.51e-03 1e+00 increased ear pigmentation 7.51e-03 1e+00 abnormal platelet shape 1.12e-02 1e+00 increased adrenal gland tumor incidence 1.13e-02 1e+00 abnormal neural crest cell morphology 1.31e-02 1e+00 increased circulating interleukin-4 level 1.31e-02 1e+00 tau protein deposits 1.31e-02 1e+00 abnormal common lymphocyte progenitor cell morphology 1.50e-02 1e+00 pleural effusion 1.68e-02 1e+00 abnormal vein morphology 1.68e-02 1e+00 abnormal myeloblast morphology/development 1.87e-02 1e+00 increased tail pigmentation 1.87e-02 1e+00 increased atrioventricular cushion size 2.05e-02 1e+00 small ectoplacental cone 2.05e-02 1e+00 distended urinary bladder 2.05e-02 1e+00 increased mast cell degranulation 2.05e-02 1e+00 blepharitis 2.12e-02 1e+00 decreased thymocyte number 2.19e-02 1e+00 increased tumor incidence

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

²FDR corrected p-value (Benjamini-Hochberg)