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DREAM Module Identification Challenge – Consensus modules

PPI-STRING_Consensus_mod14

Assigned name NA Network PPI-STRING Module ID PPI-STRING_Consensus_mod14 Module size 63 genes

Module genes

This module comprises the following genes:

Gene ID Gene Symbol Gene Name 11047 ADRM1 adhesion regulating molecule 1 642 BLMH bleomycin hydrolase 51053 GMNN geminin, DNA replication inhibitor 23072 HECW1 HECT, C2 and WW domain containing E3 ubiquitin protein ligase 1 23392 KIAA0368 Ecm29 proteasome adaptor and scaffold 4012 LNPEP leucyl and cystinyl aminopeptidase 84954 MPND MPN domain containing 9520 NPEPPS aminopeptidase puromycin sensitive 4946 OAZ1 ornithine decarboxylase antizyme 1 4947 OAZ2 ornithine decarboxylase antizyme 2 51686 OAZ3 ornithine decarboxylase antizyme 3 4953 ODC1 ornithine decarboxylase 1 80227 PAAF1 proteasomal ATPase associated factor 1 51251 POMP 5'-nucleotidase, cytosolic IIIA 5682 PSMA1 proteasome subunit alpha 1 5683 PSMA2 proteasome subunit alpha 2 5684 PSMA3 proteasome subunit alpha 3 5685 PSMA4 proteasome subunit alpha 4 5686 PSMA5 proteasome subunit alpha 5 5687 PSMA6 proteasome subunit alpha 6 5688 PSMA7 proteasome subunit alpha 7 143471 PSMA8 proteasome subunit alpha 8 5689 PSMB1 proteasome subunit beta 1 5699 PSMB10 proteasome subunit beta 10 122706 PSMB11 proteasome subunit beta 11 5690 PSMB2 proteasome subunit beta 2 5691 PSMB3 proteasome subunit beta 3 5692 PSMB4 proteasome subunit beta 4 5693 PSMB5 proteasome subunit beta 5 5694 PSMB6 proteasome subunit beta 6 5695 PSMB7 proteasome subunit beta 7 5696 PSMB8 proteasome subunit beta 8 5698 PSMB9 proteasome subunit beta 9 5700 PSMC1 proteasome 26S subunit, ATPase 1 5701 PSMC2 proteasome 26S subunit, ATPase 2 5702 PSMC3 proteasome 26S subunit, ATPase 3 5704 PSMC4 proteasome 26S subunit, ATPase 4 5705 PSMC5 proteasome 26S subunit, ATPase 5 5706 PSMC6 proteasome 26S subunit, ATPase 6 5707 PSMD1 proteasome 26S subunit, non-ATPase 1 5716 PSMD10 proteasome 26S subunit, non-ATPase 10 5717 PSMD11 proteasome 26S subunit, non-ATPase 11 5718 PSMD12 proteasome 26S subunit, non-ATPase 12 5719 PSMD13 proteasome 26S subunit, non-ATPase 13 10213 PSMD14 proteasome 26S subunit, non-ATPase 14 5708 PSMD2 proteasome 26S subunit, non-ATPase 2 5709 PSMD3 proteasome 26S subunit, non-ATPase 3 5710 PSMD4 proteasome 26S subunit, non-ATPase 4 5711 PSMD5 proteasome 26S subunit, non-ATPase 5 9861 PSMD6 proteasome 26S subunit, non-ATPase 6 5713 PSMD7 proteasome 26S subunit, non-ATPase 7 5714 PSMD8 proteasome 26S subunit, non-ATPase 8 5715 PSMD9 proteasome 26S subunit, non-ATPase 9 5720 PSME1 proteasome activator subunit 1 5721 PSME2 proteasome activator subunit 2 10197 PSME3 proteasome activator subunit 3 23198 PSME4 proteasome activator subunit 4 9491 PSMF1 proteasome inhibitor subunit 1 9232 PTTG1 pituitary tumor-transforming 1 81847 RNF146 ring finger protein 146 7174 TPP2 tripeptidyl peptidase 2 56061 UBFD1 ubiquitin family domain containing 1 9097 USP14 ubiquitin specific peptidase 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 4.82e-01 9.57e-126 Reactome Regulation of ornithine decarboxylase (ODC) Metabolism 1.27e-01 4.69e-98 GO proteasome complex cellular_component 7.84e-02 1.10e-110 Reactome Cross-presentation of soluble exogenous antigens (endosomes) Immune System 7.50e-02 2.00e-110 Reactome Degradation of AXIN Signal Transduction 5.53e-02 4.82e-109 Reactome Degradation of DVL Signal Transduction 4.78e-02 2.03e-06 GO aminopeptidase activity molecular_function 4.19e-02 9.05e-108 Reactome CDT1 association with the CDC6:ORC:origin complex Cell Cycle#DNA Replication 3.96e-02 1.19e-10 GO proteasome assembly biological_process 1.39e-02 1.83e-103 Reactome APC/C:Cdc20 mediated degradation of Securin Cell Cycle 1.37e-02 7.39e-106 Reactome Metabolism of polyamines Metabolism 1.34e-02 1.85e-51 GO proteasome core complex cellular_component 1.00e-03 1.55e-102 Reactome Regulation of PTEN stability and activity Signal Transduction 8.96e-04 9.33e-10 GO proteasome binding 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 0e+00 0e+00 regulation of protein catabolic process 0e+00 0e+00 regulation of cellular amino acid metabolic process 0e+00 0e+00 regulation of cellular ketone metabolic process 0e+00 0e+00 positive regulation of cellular protein catabolic process 0e+00 0e+00 regulation of DNA-templated transcription in response to stress 0e+00 0e+00 regulation of cell cycle phase transition 0e+00 0e+00 antigen processing and presentation of exogenous peptide antigen via MHC class I, TAP-dependent 0e+00 0e+00 response to hypoxia 0e+00 0e+00 immune response-activating signal transduction 0e+00 0e+00 innate immune response-activating signal transduction 0e+00 0e+00 antigen processing and presentation of peptide antigen 0e+00 0e+00 antigen processing and presentation 0e+00 0e+00 proteasomal protein catabolic process 0e+00 0e+00 protein modification by small protein conjugation 0e+00 0e+00 regulation of mitotic cell cycle phase transition 0e+00 0e+00 negative regulation of mitotic cell cycle phase transition 0e+00 0e+00 negative regulation of mitotic cell cycle 0e+00 0e+00 immune response-regulating signaling pathway 0e+00 0e+00 negative regulation of cell cycle process 0e+00 0e+00 immune response-regulating cell surface receptor signaling pathway

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

²FDR corrected p-value (Benjamini-Hochberg)

Reactome

P-value1 FDR2 Term 0e+00 0e+00 METABOLISM OF AMINO ACIDS AND DERIVATIVES 0e+00 0e+00 REGULATION OF ORNITHINE DECARBOXYLASE ODC 0e+00 0e+00 CELL CYCLE 0e+00 0e+00 SCFSKP2 MEDIATED DEGRADATION OF P27 P21 0e+00 0e+00 HIV INFECTION 0e+00 0e+00 ORC1 REMOVAL FROM CHROMATIN 0e+00 0e+00 VIF MEDIATED DEGRADATION OF APOBEC3G 0e+00 0e+00 AUTODEGRADATION OF CDH1 BY CDH1 APC C 0e+00 0e+00 APC C CDH1 MEDIATED DEGRADATION OF CDC20 AND OTHER APC C CDH1 TARGETED PROTEINS IN LATE MITOSIS EARLY G1 0e+00 0e+00 CDK MEDIATED PHOSPHORYLATION AND REMOVAL OF CDC6 0e+00 0e+00 SCF BETA TRCP MEDIATED DEGRADATION OF EMI1 0e+00 0e+00 ANTIGEN PROCESSING CROSS PRESENTATION 0e+00 0e+00 ACTIVATION OF NF KAPPAB IN B CELLS 0e+00 0e+00 SIGNALING BY WNT 0e+00 0e+00 APC C CDC20 MEDIATED DEGRADATION OF MITOTIC PROTEINS 0e+00 0e+00 CLASS I MHC MEDIATED ANTIGEN PROCESSING PRESENTATION 0e+00 0e+00 MITOTIC G1 G1 S PHASES 0e+00 0e+00 MITOTIC M M G1 PHASES 0e+00 0e+00 METABOLISM OF MRNA 0e+00 0e+00 M G1 TRANSITION

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

²FDR corrected p-value (Benjamini-Hochberg)

Mouse mutant phenotypes

P-value1 FDR2 Term 1.04e-04 2.32e-01 decreased CD8-positive, alpha-beta T cell number 4.17e-04 5.45e-01 abnormal CD8-positive, alpha-beta cytotoxic T cell morphology 2.13e-03 1.00e+00 thymus hyperplasia 2.35e-03 1.00e+00 failure of embryo implantation 3.77e-03 1.00e+00 abnormal limbic system morphology 5.18e-03 1.00e+00 abnormal cytotoxic T cell physiology 5.62e-03 1.00e+00 decreased hippocampal commissure size 5.62e-03 1.00e+00 ovarian follicular cyst 5.62e-03 1.00e+00 abnormal single-positive T cell number 5.72e-03 1.00e+00 complete embryonic lethality between implantation and somite formation 6.17e-03 1.00e+00 abnormal immune system organ morphology 6.97e-03 1.00e+00 abnormal cell cycle checkpoint function 8.63e-03 1.00e+00 decreased cell proliferation 9.35e-03 1.00e+00 abnormal self tolerance 9.35e-03 1.00e+00 increased leiomyosarcoma incidence 9.39e-03 1.00e+00 short lumbar vertebrae 1.01e-02 1.00e+00 complete embryonic lethality before implantation 1.03e-02 1.00e+00 increased T cell number 1.26e-02 1.00e+00 decreased double-positive T cell number 1.30e-02 1.00e+00 defective assembly of class I molecules

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

²FDR corrected p-value (Benjamini-Hochberg)