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DREAM Module Identification Challenge – Consensus modules

PPI-STRING_Consensus_mod265

Assigned name NA Network PPI-STRING Module ID PPI-STRING_Consensus_mod265 Module size 65 genes

Module genes

This module comprises the following genes:

Gene ID Gene Symbol Gene Name 25909 AHCTF1 AT-hook containing transcription factor 1 378708 APITD1 centromere protein S 80776 B9D2 B9 domain containing 2 332 BIRC5 baculoviral IAP repeat containing 5 57082 CASC5 kinetochore scaffold 1 113130 CDCA5 cell division cycle associated 5 55143 CDCA8 cell division cycle associated 8 1060 CENPC1 centromere protein C 1062 CENPE centromere protein E 1063 CENPF centromere protein F 64946 CENPH centromere protein H 2491 CENPI centromere protein I 64105 CENPK centromere protein K 91687 CENPL centromere protein L 79019 CENPM centromere protein M 55839 CENPN centromere protein N 79172 CENPO centromere protein O 401541 CENPP centromere protein P 55166 CENPQ centromere protein Q 80152 CENPT centromere protein T 387103 CENPW centromere protein W 23122 CLASP2 cytoplasmic linker associated protein 2 6249 CLIP1 CAP-Gly domain containing linker protein 1 79980 DSN1 DSN1 homolog, MIS12 kinetochore complex component 54821 ERCC6L ERCC excision repair 6 like, spindle assembly checkpoint helicase 9700 ESPL1 extra spindle pole bodies like 1, separase 401145 FAM190A coiled-coil serine rich protein 1 55355 HJURP Holliday junction recognition protein 3619 INCENP inner centromere protein 23421 ITGB3BP integrin subunit beta 3 binding protein 81930 KIF18A kinesin family member 18A 3796 KIF2A kinesin family member 2A 84643 KIF2B kinesin family member 2B 11004 KIF2C kinesin family member 2C 9735 KNTC1 kinetochore associated 1 8379 MAD1L1 mitotic arrest deficient 1 like 1 79003 MIS12 MIS12, kinetochore complex component 54069 MIS18A MIS18 kinetochore protein A 55320 MIS18BP1 MIS18 binding protein 1 79682 MLF1IP centromere protein U 10403 NDC80 NDC80, kinetochore complex component 81565 NDEL1 nudE neurodevelopment protein 1 like 1 11270 NRM nurim 284058 NSL1 KAT8 regulatory NSL complex subunit 1 10726 NUDC nuclear distribution C, dynein complex regulator 83540 NUF2 NDC80 kinetochore complex component NUF2 11339 OIP5 Opa interacting protein 5 23244 PDS5A PDS5 cohesin associated factor A 23047 PDS5B PDS5 cohesin associated factor B 100527963 PMF1 PMF1-BGLAP readthrough 55920 RCC2 regulator of chromosome condensation 2 51773 RSF1 remodeling and spacing factor 1 151648 SGOL1 shugoshin 1 151246 SGOL2 shugoshin 2 348235 SKA2 spindle and kinetochore associated complex subunit 2 147841 SPC24 SPC24, NDC80 kinetochore complex component 54908 SPDL1 spindle apparatus coiled-coil protein 1 56937 STAG1 prostate transmembrane protein, androgen induced 1 10735 STAG2 stromal antigen 2 57551 TAOK1 TAO kinase 1 23063 WAPAL WAPL cohesin release factor 149708 WFDC5 WAP four-disulfide core domain 5 9183 ZW10 zw10 kinetochore protein 55055 ZWILCH zwilch kinetochore protein 11130 ZWINT ZW10 interacting kinetochore protein

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 1.99e-01 1.85e-35 GO CENP-A containing nucleosome assembly biological_process 1.78e-01 1.78e-104 Reactome Resolution of Sister Chromatid Cohesion Cell Cycle 9.51e-02 6.00e-40 GO chromosome, centromeric region cellular_component 8.85e-02 1.03e-12 GO metaphase plate congression biological_process 7.47e-02 1.70e-92 Reactome Amplification of signal from unattached kinetochores via a MAD2 inhibitory signal Cell Cycle 7.43e-02 1.70e-92 Reactome Amplification of signal from the kinetochores Cell Cycle 5.77e-02 2.43e-18 GO mitotic sister chromatid segregation biological_process 4.60e-02 1.67e-10 Reactome Establishment of Sister Chromatid Cohesion Cell Cycle 4.22e-02 2.36e-13 GO attachment of mitotic spindle microtubules to kinetochore biological_process 2.12e-02 1.25e-52 GO condensed chromosome kinetochore cellular_component 1.88e-02 1.54e-32 Reactome Nucleosome assembly Cell Cycle 1.87e-02 1.54e-32 Reactome Deposition of new CENPA-containing nucleosomes at the centromere Cell Cycle 1.63e-02 5.36e-95 Reactome Separation of Sister Chromatids Cell Cycle 1.43e-02 3.81e-28 GO chromosome segregation biological_process 4.15e-04 2.06e-93 Reactome Mitotic Anaphase Cell Cycle

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 sister chromatid segregation 0e+00 0e+00 sister chromatid cohesion 0e+00 0e+00 chromosome segregation 0e+00 0e+00 cell division 0e+00 0e+00 protein-DNA complex assembly 0e+00 0e+00 histone exchange 0e+00 0e+00 DNA replication-independent nucleosome assembly 0e+00 0e+00 CENP-A containing nucleosome assembly 0e+00 0e+00 centromere complex assembly 0e+00 0e+00 ATP-dependent chromatin remodeling 0e+00 0e+00 DNA replication-independent nucleosome organization 0e+00 0e+00 establishment of organelle localization 0e+00 0e+00 mitotic cell cycle 0e+00 0e+00 mitotic cell cycle process 0e+00 0e+00 organelle fission 0e+00 0e+00 mitotic nuclear division 0e+00 0e+00 regulation of chromosome segregation 0e+00 0e+00 establishment of chromosome localization 0e+00 0e+00 metaphase plate congression 0e+00 0e+00 mitotic sister chromatid segregation

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 CHROMOSOME MAINTENANCE 0.00e+00 0.00e+00 DEPOSITION OF NEW CENPA CONTAINING NUCLEOSOMES AT THE CENTROMERE 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 0.00e+00 0.00e+00 CHROMOSOME MAINTENANCE 0.00e+00 0.00e+00 DEPOSITION OF NEW CENPA CONTAINING NUCLEOSOMES AT THE CENTROMERE 5.16e-05 8.59e-03 KINESINS 1.85e-03 1.74e-01 KINESINS 3.95e-03 3.36e-01 MHC CLASS II ANTIGEN PRESENTATION 4.50e-03 4.19e-01 FACTORS INVOLVED IN MEGAKARYOCYTE DEVELOPMENT AND PLATELET PRODUCTION 5.45e-03 4.40e-01 NRIF SIGNALS CELL DEATH FROM THE NUCLEUS 6.95e-03 5.97e-01 MHC CLASS II ANTIGEN PRESENTATION 1.18e-02 8.41e-01 FACTORS INVOLVED IN MEGAKARYOCYTE DEVELOPMENT AND PLATELET PRODUCTION 2.39e-02 1.00e+00 NRIF SIGNALS CELL DEATH FROM THE NUCLEUS

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

²FDR corrected p-value (Benjamini-Hochberg)

Mouse mutant phenotypes

P-value1 FDR2 Term 1.70e-10 8.65e-06 abnormal mitosis 5.38e-06 3.11e-02 abnormal cell nucleus morphology 1.29e-05 5.64e-02 aneuploidy 3.50e-05 1.12e-01 complete embryonic lethality between implantation and somite formation 1.09e-04 2.40e-01 abnormal inner cell mass proliferation 1.24e-04 2.59e-01 decreased brown adipose tissue amount 1.33e-04 2.74e-01 inner cell mass degeneration 1.53e-04 2.98e-01 abnormal enteric nervous system morphology 8.22e-04 8.04e-01 decreased germ cell number 1.48e-03 1.00e+00 chromosomal instability 2.22e-03 1.00e+00 failure to form blastocele 2.50e-03 1.00e+00 decreased hair follicle number 2.88e-03 1.00e+00 palatal shelves fail to meet at midline 3.55e-03 1.00e+00 increased carcinoma incidence 3.74e-03 1.00e+00 increased cell nucleus count 3.77e-03 1.00e+00 abnormal sympathetic postganglionic fiber morphology 3.89e-03 1.00e+00 perimembraneous ventricular septal defect 4.33e-03 1.00e+00 preweaning lethality 4.43e-03 1.00e+00 failure of blastocyst to hatch from the zona pellucida 7.47e-03 1.00e+00 abnormal tegmentum morphology

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

²FDR corrected p-value (Benjamini-Hochberg)