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DREAM Module Identification Challenge – Consensus modules

PPI-STRING_Consensus_mod72

Assigned name NA Network PPI-STRING Module ID PPI-STRING_Consensus_mod72 Module size 47 genes

Module genes

This module comprises the following genes:

Gene ID Gene Symbol Gene Name 6868 ADAM18 ADAM metallopeptidase domain 17 699 BUB1 BUB1 mitotic checkpoint serine/threonine kinase 701 BUB1B BUB1 mitotic checkpoint serine/threonine kinase B 9184 BUB3 BUB3, mitotic checkpoint protein 388135 C15orf59 inhibitory synaptic factor 1 148223 C19orf25 chromosome 19 open reading frame 25 991 CDC20 cell division cycle 20 1058 CENPA centromere protein A 1059 CENPB centromere protein B 9793 CKAP5 cytoskeleton associated protein 5 220965 FAM13C family with sequence similarity 13 member C 165186 FAM179A TOG array regulator of axonemal microtubules 2 54462 FAM190B coiled-coil serine rich protein 2 4085 MAD2L1 mitotic arrest deficient 2 like 1 9587 MAD2L1BP MAD2L1 binding protein 23383 MAU2 MAU2 sister chromatid cohesion factor 9902 MRC2 mannose receptor C type 2 51594 NBAS neuroblastoma amplified sequence 54820 NDE1 nudE neurodevelopment protein 1 252969 NEIL2 nei like DNA glycosylase 2 25836 NIPBL NIPBL, cohesin loading factor 4869 NPM1 nucleophosmin 1 57122 NUP107 nucleoporin 107 55746 NUP133 nucleoporin 133 23279 NUP160 nucleoporin 160 79023 NUP37 nucleoporin 37 348995 NUP43 nucleoporin 43 79902 NUP85 nucleoporin 85 5048 PAFAH1B1 platelet activating factor acetylhydrolase 1b regulatory subunit 1 5284 PIGR polymeric immunoglobulin receptor 389072 PLEKHM3 pleckstrin homology domain containing M3 5501 PPP1CC protein phosphatase 1 catalytic subunit gamma 5885 RAD21 RAD21 cohesin complex component 5903 RANBP2 RAN binding protein 2 5905 RANGAP1 Ran GTPase activating protein 1 6396 SEC13 SEC13 homolog, nuclear pore and COPII coat complex component 89866 SEC16B SEC16 homolog B, endoplasmic reticulum export factor 81929 SEH1L SEH1 like nucleoporin 220134 SKA1 spindle and kinetochore associated complex subunit 1 221150 SKA3 spindle and kinetochore associated complex subunit 3 9126 SMC3 structural maintenance of chromosomes 3 442578 STAG3L3 stromal antigen 3-like 3 (pseudogene) 85363 TRIM5 tripartite motif containing 5 150737 TTC30B tetratricopeptide repeat domain 30B 11334 TUSC2 tumor suppressor 2, mitochondrial calcium regulator 7514 XPO1 exportin 1 22891 ZNF365 zinc finger protein 365

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 4.24e-01 2.28e-20 GO nuclear pore outer ring cellular_component 2.03e-01 5.81e-09 Reactome Cohesin Loading onto Chromatin Cell Cycle 1.05e-01 3.49e-09 GO condensed chromosome outer kinetochore cellular_component 5.23e-02 4.45e-19 Reactome Interactions of Rev with host cellular proteins Disease 4.18e-02 2.77e-40 Reactome Amplification of signal from the kinetochores Cell Cycle 4.15e-02 2.77e-40 Reactome Amplification of signal from unattached kinetochores via a MAD2 inhibitory signal Cell Cycle 3.82e-02 1.19e-09 GO mitotic spindle assembly checkpoint biological_process 3.16e-02 1.29e-29 GO kinetochore cellular_component 2.30e-02 1.32e-07 Reactome Inactivation of APC/C via direct inhibition of the APC/C complex Cell Cycle 1.91e-02 1.32e-07 Reactome Inhibition of the proteolytic activity of APC/C required for the onset of anaphase by mitotic spindle checkpoint components Cell Cycle 1.46e-02 1.02e-43 Reactome Resolution of Sister Chromatid Cohesion Cell Cycle 2.12e-04 2.47e-04 GO ribosomal large subunit export from nucleus 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 sister chromatid segregation 0.00e+00 0.00e+00 mitotic cell cycle process 0.00e+00 0.00e+00 chromosome segregation 0.00e+00 0.00e+00 mitotic cell cycle 0.00e+00 0.00e+00 cell division 0.00e+00 0.00e+00 organelle fission 0.00e+00 0.00e+00 sister chromatid cohesion 0.00e+00 0.00e+00 mitotic nuclear division 0.00e+00 0.00e+00 nuclear envelope disassembly 0.00e+00 0.00e+00 condensed chromosome 0.00e+00 0.00e+00 condensed chromosome, centromeric region 0.00e+00 0.00e+00 condensed chromosome kinetochore 0.00e+00 0.00e+00 kinetochore 0.00e+00 0.00e+00 chromosome, centromeric region 0.00e+00 0.00e+00 nuclear pore outer ring 0.00e+00 0.00e+00 nuclear pore 5.82e-12 5.28e-09 tRNA export from nucleus 1.07e-11 9.61e-09 intracellular transport of virus 1.70e-11 1.52e-08 multi-organism intracellular transport 6.22e-11 5.28e-08 protein sumoylation

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 CELL CYCLE 0.00e+00 0.00e+00 MITOTIC PROMETAPHASE 0.00e+00 0.00e+00 CELL CYCLE MITOTIC 0.00e+00 0.00e+00 MITOTIC M M G1 PHASES 0.00e+00 0.00e+00 DNA REPLICATION 0.00e+00 0.00e+00 MITOTIC PROMETAPHASE 0.00e+00 0.00e+00 MITOTIC M M G1 PHASES 0.00e+00 0.00e+00 DNA REPLICATION 1.62e-09 5.22e-07 NEP NS2 INTERACTS WITH THE CELLULAR EXPORT MACHINERY 1.97e-09 4.64e-07 NEP NS2 INTERACTS WITH THE CELLULAR EXPORT MACHINERY 4.49e-08 1.21e-05 REGULATION OF GLUCOKINASE BY GLUCOKINASE REGULATORY PROTEIN 5.34e-08 1.42e-05 TRANSPORT OF RIBONUCLEOPROTEINS INTO THE HOST NUCLEUS 5.35e-08 1.08e-05 REGULATION OF GLUCOKINASE BY GLUCOKINASE REGULATORY PROTEIN 6.92e-08 1.37e-05 TRANSPORT OF RIBONUCLEOPROTEINS INTO THE HOST NUCLEUS 9.23e-08 2.38e-05 INTERACTIONS OF VPR WITH HOST CELLULAR PROTEINS 1.53e-07 3.88e-05 TRANSPORT OF MATURE MRNA DERIVED FROM AN INTRONLESS TRANSCRIPT 1.55e-07 2.96e-05 GLUCOSE TRANSPORT 1.62e-07 3.08e-05 INTERACTIONS OF VPR WITH HOST CELLULAR PROTEINS 2.14e-07 5.33e-05 GLUCOSE TRANSPORT 2.21e-07 4.15e-05 TRANSPORT OF MATURE MRNA DERIVED FROM AN INTRONLESS TRANSCRIPT

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

²FDR corrected p-value (Benjamini-Hochberg)

Mouse mutant phenotypes

P-value1 FDR2 Term 1.29e-08 3.08e-04 aneuploidy 4.83e-08 7.99e-04 abnormal mitosis 7.98e-07 7.36e-03 abnormal mitotic spindle assembly checkpoint 1.26e-05 5.58e-02 complete embryonic lethality between implantation and somite formation 9.29e-05 2.15e-01 increased incidence of induced tumors 1.00e-04 2.26e-01 chromosome breakage 1.19e-04 2.53e-01 increased embryonic tissue cell apoptosis 1.52e-04 2.97e-01 inner cell mass degeneration 1.86e-04 3.33e-01 abnormal chromosome morphology 2.47e-04 3.97e-01 upturned snout 3.64e-04 5.02e-01 increased lymphoma incidence 4.41e-04 5.64e-01 complete embryonic lethality 4.45e-04 5.67e-01 abnormal cell cycle checkpoint function 4.45e-03 1.00e+00 increased hemangiosarcoma incidence 6.21e-03 1.00e+00 increased leukemia incidence 8.76e-03 1.00e+00 abnormal cell nucleus morphology 1.14e-02 1.00e+00 early cellular replicative senescence 1.31e-02 1.00e+00 abnormal cellular replicative senescence 1.31e-02 1.00e+00 absent liver 1.37e-02 1.00e+00 increased leukocyte cell number

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

²FDR corrected p-value (Benjamini-Hochberg)