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DREAM Module Identification Challenge – Consensus modules

PPI-STRING_Consensus_mod166

Assigned name NA Network PPI-STRING Module ID PPI-STRING_Consensus_mod166 Module size 51 genes

Module genes

This module comprises the following genes:

Gene ID Gene Symbol Gene Name 202 AIM1 crystallin beta-gamma domain containing 1 54443 ANLN anillin actin binding protein 55160 ARHGEF10L Rho guanine nucleotide exchange factor 10 like 84904 ARHGEF39 Rho guanine nucleotide exchange factor 39 259266 ASPM abnormal spindle microtubule assembly 9212 AURKB aurora kinase B 90417 C15orf23 kinetochore localized astrin (SPAG5) binding protein 78995 C17orf53 chromosome 17 open reading frame 53 157313 CDCA2 cell division cycle associated 2 83461 CDCA3 cell division cycle associated 3 55165 CEP55 centrosomal protein 55 26586 CKAP2 cytoskeleton associated protein 2 150468 CKAP2L cytoskeleton associated protein 2 like 55635 DEPDC1 DEP domain containing 1 9787 DLGAP5 DLG associated protein 5 157570 ESCO2 establishment of sister chromatid cohesion N-acetyltransferase 2 81610 FAM83D family with sequence similarity 83 member D 55632 G2E3 G2/M-phase specific E3 ubiquitin protein ligase 283431 GAS2L3 growth arrest specific 2 like 3 83903 GSG2 histone H3 associated protein kinase 3161 HMMR hyaluronan mediated motility receptor 9768 KIAA0101 PCNA clamp associated factor 57650 KIAA1524 cell proliferation regulating inhibitor of protein phosphatase 2A 10112 KIF20A kinesin family member 20A 9493 KIF23 kinesin family member 23 24137 KIF4A kinesin family member 4A 4288 MKI67 marker of proliferation Ki-67 9918 NCAPD2 non-SMC condensin I complex subunit D2 23310 NCAPD3 non-SMC condensin II complex subunit D3 64151 NCAPG non-SMC condensin I complex subunit G 54892 NCAPG2 non-SMC condensin II complex subunit G2 23397 NCAPH non-SMC condensin I complex subunit H 29781 NCAPH2 non-SMC condensin II complex subunit H2 51203 NUSAP1 nucleolar and spindle associated protein 1 55010 PARPBP PARP1 binding protein 9055 PRC1 protein regulator of cytokinesis 1 55771 PRR11 proline rich 11 10635 RAD51AP1 RAD51 associated protein 1 79801 SHCBP1 SHC binding and spindle associated 1 81626 SHCBP1L SHC binding and spindle associated 1 like 10615 SPAG5 sperm associated antigen 5 293142 SPC25 signal peptidase complex subunit 2 6491 STIL STIL, centriolar assembly protein 10579 TACC2 transforming acidic coiled-coil containing protein 2 10460 TACC3 transforming acidic coiled-coil containing protein 3 6941 TCF19 transcription factor 19 83659 TEKT1 tektin 1 56155 TEX14 testis expressed 14, intercellular bridge forming factor 311546 TPX2 TPX2, microtubule nucleation factor 10024 TROAP trophinin associated protein 7272 TTK TTK protein kinase

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 4.49e-01 1.26e-12 GO condensin complex cellular_component 9.43e-02 4.98e-08 GO spindle organization biological_process 8.11e-02 1.50e-06 GO mitotic spindle midzone assembly biological_process 3.55e-02 2.58e-10 GO mitotic chromosome condensation biological_process 3.08e-02 6.24e-11 GO intercellular bridge cellular_component 2.50e-02 1.29e-10 GO mitotic cytokinesis biological_process 1.90e-02 1.98e-04 GO regulation of chromosome segregation biological_process 1.40e-02 4.89e-14 GO midbody cellular_component 1.33e-02 4.24e-08 GO mitotic spindle organization biological_process 3.05e-03 1.24e-08 GO mitotic spindle cellular_component 8.14e-06 1.98e-04 GO attachment of spindle microtubules to kinetochore 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 spindle organization 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 nuclear division 0.00e+00 0.00e+00 microtubule cytoskeleton organization 0.00e+00 0.00e+00 mitotic cell cycle 0.00e+00 0.00e+00 microtubule-based process 0.00e+00 0.00e+00 cell division 0.00e+00 0.00e+00 organelle fission 0.00e+00 0.00e+00 mitotic sister chromatid segregation 0.00e+00 0.00e+00 cytokinesis 0.00e+00 0.00e+00 microtubule cytoskeleton organization involved in mitosis 0.00e+00 0.00e+00 chromosome condensation 0.00e+00 0.00e+00 spindle 1.09e-11 9.79e-09 mitotic spindle organization 1.34e-11 1.20e-08 mitotic cytokinesis 9.26e-11 4.80e-08 condensin complex 9.72e-11 5.02e-08 spindle pole 5.78e-10 2.68e-07 midbody

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

²FDR corrected p-value (Benjamini-Hochberg)

Reactome

P-value1 FDR2 Term 3.11e-06 6.44e-04 KINESINS 1.75e-05 3.20e-03 MITOTIC M M G1 PHASES 2.00e-05 3.61e-03 DNA REPLICATION 2.31e-05 3.26e-03 MITOTIC M M G1 PHASES 3.38e-05 4.65e-03 DNA REPLICATION 3.50e-05 4.81e-03 KINESINS 1.06e-04 1.34e-02 MHC CLASS II ANTIGEN PRESENTATION 1.36e-04 1.68e-02 FACTORS INVOLVED IN MEGAKARYOCYTE DEVELOPMENT AND PLATELET PRODUCTION 1.86e-04 2.69e-02 MHC CLASS II ANTIGEN PRESENTATION 2.87e-04 3.94e-02 CELL CYCLE MITOTIC 6.27e-04 7.84e-02 CELL CYCLE 7.48e-04 9.11e-02 FACTORS INVOLVED IN MEGAKARYOCYTE DEVELOPMENT AND PLATELET PRODUCTION 7.42e-03 6.30e-01 HYALURONAN UPTAKE AND DEGRADATION 8.14e-03 6.21e-01 APC C CDH1 MEDIATED DEGRADATION OF CDC20 AND OTHER APC C CDH1 TARGETED PROTEINS IN LATE MITOSIS EARLY G1 8.16e-03 6.22e-01 REGULATION OF MITOTIC CELL CYCLE 8.63e-03 7.11e-01 APC C CDH1 MEDIATED DEGRADATION OF CDC20 AND OTHER APC C CDH1 TARGETED PROTEINS IN LATE MITOSIS EARLY G1 9.13e-03 7.44e-01 HYALURONAN METABOLISM 9.60e-03 7.76e-01 MITOTIC PROMETAPHASE 1.19e-02 9.15e-01 REGULATION OF MITOTIC CELL CYCLE 1.31e-02 9.12e-01 MITOTIC PROMETAPHASE

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

²FDR corrected p-value (Benjamini-Hochberg)

Mouse mutant phenotypes

P-value1 FDR2 Term 1.21e-05 5.38e-02 abnormal mitotic spindle morphology 1.76e-05 6.95e-02 abnormal mitosis 4.40e-05 1.31e-01 embryonic lethality 8.12e-04 7.98e-01 polyploidy 1.71e-03 1.00e+00 decreased hematopoietic stem cell number 1.87e-03 1.00e+00 absent caudal vertebrae 2.69e-03 1.00e+00 abnormal inner cell mass apoptosis 3.74e-03 1.00e+00 decreased secondary ovarian follicle number 3.75e-03 1.00e+00 abnormal granulosa cell morphology 4.28e-03 1.00e+00 abnormal inner cell mass morphology 5.61e-03 1.00e+00 pituitary intermediate lobe hyperplasia 5.61e-03 1.00e+00 iris hypoplasia 5.61e-03 1.00e+00 abnormal barrel cortex morphology 6.17e-03 1.00e+00 decreased thymocyte number 6.80e-03 1.00e+00 oligozoospermia 6.97e-03 1.00e+00 abnormal Sertoli cell morphology 7.47e-03 1.00e+00 abnormal splenocyte morphology 7.48e-03 1.00e+00 abnormal thymus corticomedullary boundary morphology 8.67e-03 1.00e+00 thymus hypoplasia 9.33e-03 1.00e+00 increased cell nucleus count

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

²FDR corrected p-value (Benjamini-Hochberg)