Back to main page

DREAM Module Identification Challenge – Consensus modules

PPI-STRING_Consensus_mod101

Assigned name NA Network PPI-STRING Module ID PPI-STRING_Consensus_mod101 Module size 60 genes

Module genes

This module comprises the following genes:

Gene ID Gene Symbol Gene Name 64137 ABCG4 ATP binding cassette subfamily G member 4 64682 ANAPC1 anaphase promoting complex subunit 1 10393 ANAPC10 anaphase promoting complex subunit 10 51529 ANAPC11 anaphase promoting complex subunit 11 25847 ANAPC13 anaphase promoting complex subunit 13 25906 ANAPC15 anaphase promoting complex subunit 15 119504 ANAPC16 anaphase promoting complex subunit 16 29882 ANAPC2 anaphase promoting complex subunit 2 29945 ANAPC4 anaphase promoting complex subunit 4 51433 ANAPC5 anaphase promoting complex subunit 5 51434 ANAPC7 anaphase promoting complex subunit 7 171023 ASXL1 ASXL transcriptional regulator 1 29086 BABAM1 BRISC and BRCA1 A complex member 1 8314 BAP1 BRCA1 associated protein 1 580 BARD1 BRCA1 associated RING domain 1 54880 BCOR BCL6 corepressor 63035 BCORL1 BCL6 corepressor like 1 648 BMI1 BMI1 proto-oncogene, polycomb ring finger 362704 BRE BRISC and BRCA1 A complex member 2 388115 C15orf52 coiled-coil domain containing 9B 84733 CBX2 chromobox 2 8535 CBX4 chromobox 4 23492 CBX7 chromobox 7 57332 CBX8 chromobox 8 8881 CDC16 cell division cycle 16 8697 CDC23 cell division cycle 23 246184 CDC26 cell division cycle 26 293144 CDC27 DNA polymerase delta 3, accessory subunit 9820 CUL7 cullin 7 23172 FAM175B abraxas 2, BRISC complex subunit 125228 FAM210A family with sequence similarity 210 member A 64319 FBRS fibrosin 57666 FBRSL1 fibrosin like 1 56287 GKN1 gastrokine 1 360203 GLT6D1 glycosyltransferase 6 domain containing 1 57608 KIAA1462 junctional cadherin 5 associated 56890 MDM1 Mdm1 nuclear protein 84759 PCGF1 polycomb group ring finger 1 7703 PCGF2 polycomb group ring finger 2 10336 PCGF3 polycomb group ring finger 3 84333 PCGF5 polycomb group ring finger 5 84108 PCGF6 polycomb group ring finger 6 1911 PHC1 polyhomeotic homolog 1 1912 PHC2 polyhomeotic homolog 2 80012 PHC3 polyhomeotic homolog 3 10744 PTTG2 pituitary tumor-transforming 2 6015 RING1 ring finger protein 1 6045 RNF2 ring finger protein 2 643904 RNF222 ring finger protein 222 23429 RYBP RING1 and YY1 binding protein 10389 SCML2 Scm polycomb group protein like 2 51460 SFMBT1 Scm like with four mbt domains 1 23512 SUZ12 SUZ12, polycomb repressive complex 2 subunit 168451 THAP5 THAP domain containing 5 79613 TMCO7 transport and golgi organization 6 homolog 27338 UBE2S ubiquitin conjugating enzyme E2 S 7425 VGF VGF nerve growth factor inducible 653067 XAGE1D X antigen family member 1B 10138 YAF2 YY1 associated factor 2 151126 ZNF385B zinc finger protein 385B

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 5.37e-01 3.93e-38 GO PRC1 complex cellular_component 4.71e-01 1.10e-37 GO anaphase-promoting complex cellular_component 2.29e-01 3.17e-40 GO PcG protein complex cellular_component 1.95e-01 1.24e-29 Reactome Phosphorylation of the APC/C Cell Cycle 6.28e-02 1.94e-04 GO BRCA1-A complex cellular_component 3.39e-02 3.94e-18 Reactome Transcriptional Regulation by E2F6 Gene expression (Transcription) 2.35e-02 5.37e-26 GO protein K11-linked ubiquitination biological_process 2.15e-02 2.39e-06 Reactome Metalloprotease DUBs Metabolism of proteins 2.05e-03 2.51e-22 Reactome SUMOylation of DNA methylation proteins Metabolism of proteins

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 covalent chromatin modification 0e+00 0e+00 chromatin organization 0e+00 0e+00 histone ubiquitination 0e+00 0e+00 protein ubiquitination 0e+00 0e+00 protein modification by small protein conjugation 0e+00 0e+00 mitotic cell cycle process 0e+00 0e+00 mitotic nuclear division 0e+00 0e+00 mitotic cell cycle 0e+00 0e+00 cell division 0e+00 0e+00 organelle fission 0e+00 0e+00 regulation of protein catabolic process 0e+00 0e+00 protein polyubiquitination 0e+00 0e+00 positive regulation of protein catabolic process 0e+00 0e+00 positive regulation of protein ubiquitination involved in ubiquitin-dependent protein catabolic process 0e+00 0e+00 positive regulation of cellular protein catabolic process 0e+00 0e+00 positive regulation of proteolysis 0e+00 0e+00 cellular protein catabolic process 0e+00 0e+00 negative regulation of ubiquitin-protein transferase activity 0e+00 0e+00 positive regulation of ubiquitin-protein transferase activity 0e+00 0e+00 regulation of protein ubiquitination involved in ubiquitin-dependent protein catabolic 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 APC CDC20 MEDIATED DEGRADATION OF NEK2A 0.00e+00 0.00e+00 CONVERSION FROM APC C CDC20 TO APC C CDH1 IN LATE ANAPHASE 0.00e+00 0.00e+00 ANTIGEN PROCESSING UBIQUITINATION PROTEASOME DEGRADATION 0.00e+00 0.00e+00 AUTODEGRADATION OF CDH1 BY CDH1 APC C 0.00e+00 0.00e+00 APC C CDH1 MEDIATED DEGRADATION OF CDC20 AND OTHER APC C CDH1 TARGETED PROTEINS IN LATE MITOSIS EARLY G1 0.00e+00 0.00e+00 REGULATION OF MITOTIC CELL CYCLE 0.00e+00 0.00e+00 CELL CYCLE CHECKPOINTS 0.00e+00 0.00e+00 APC C CDC20 MEDIATED DEGRADATION OF CYCLIN B 0.00e+00 0.00e+00 PHOSPHORYLATION OF THE APC C 0.00e+00 0.00e+00 APC C CDC20 MEDIATED DEGRADATION OF MITOTIC PROTEINS 0.00e+00 0.00e+00 CLASS I MHC MEDIATED ANTIGEN PROCESSING PRESENTATION 0.00e+00 0.00e+00 INHIBITION OF THE PROTEOLYTIC ACTIVITY OF APC C REQUIRED FOR THE ONSET OF ANAPHASE BY MITOTIC SPINDLE CHECKPOINT COMPONENTS 0.00e+00 0.00e+00 APC C CDC20 MEDIATED DEGRADATION OF CYCLIN B 0.00e+00 0.00e+00 APC CDC20 MEDIATED DEGRADATION OF NEK2A 0.00e+00 0.00e+00 ANTIGEN PROCESSING UBIQUITINATION PROTEASOME DEGRADATION 0.00e+00 0.00e+00 PHOSPHORYLATION OF THE APC C 0.00e+00 0.00e+00 CONVERSION FROM APC C CDC20 TO APC C CDH1 IN LATE ANAPHASE 0.00e+00 0.00e+00 CLASS I MHC MEDIATED ANTIGEN PROCESSING PRESENTATION 0.00e+00 0.00e+00 INHIBITION OF THE PROTEOLYTIC ACTIVITY OF APC C REQUIRED FOR THE ONSET OF ANAPHASE BY MITOTIC SPINDLE CHECKPOINT COMPONENTS 5.49e-11 1.54e-08 AUTODEGRADATION OF CDH1 BY CDH1 APC C

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

²FDR corrected p-value (Benjamini-Hochberg)

Mouse mutant phenotypes

P-value1 FDR2 Term 1.80e-08 3.81e-04 vertebral transformation 6.76e-08 1.03e-03 cervical vertebral transformation 3.65e-06 2.30e-02 lumbar vertebral transformation 1.01e-05 4.74e-02 thoracic vertebral transformation 1.28e-03 1.00e+00 abnormal developmental patterning 1.30e-03 1.00e+00 abnormal occipital bone morphology 3.53e-03 1.00e+00 abnormal cervical atlas morphology 4.45e-03 1.00e+00 cervical vertebral fusion 4.64e-03 1.00e+00 abnormal sternum ossification 4.99e-03 1.00e+00 abnormal heart looping 6.98e-03 1.00e+00 impaired hematopoiesis 7.50e-03 1.00e+00 abnormal epigenetic regulation of gene expression 7.63e-03 1.00e+00 abnormal gastrulation 7.69e-03 1.00e+00 decreased spleen weight 9.05e-03 1.00e+00 early cellular replicative senescence 9.38e-03 1.00e+00 opacity of vitreous body 1.12e-02 1.00e+00 decreased sternebra number 1.12e-02 1.00e+00 split cervical atlas 1.12e-02 1.00e+00 split cervical axis 1.16e-02 1.00e+00 abnormal sternum morphology

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

²FDR corrected p-value (Benjamini-Hochberg)