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DREAM Module Identification Challenge – Consensus modules

PPI-STRING_Consensus_mod253

Assigned name NA Network PPI-STRING Module ID PPI-STRING_Consensus_mod253 Module size 49 genes

Module genes

This module comprises the following genes:

Gene ID Gene Symbol Gene Name 11101 ATE1 arginyltransferase 1 10485 C1orf61 chromosome 1 open reading frame 61 169436 C9orf96 serine/threonine kinase like domain containing 1 8900 CCNA1 cyclin A1 890 CCNA2 cyclin A2 891 CCNB1 cyclin B1 9133 CCNB2 cyclin B2 85417 CCNB3 cyclin B3 894 CCND2 cyclin D2 899 CCNF cyclin F 900 CCNG1 cyclin G1 901 CCNG2 cyclin G2 10983 CCNI cyclin I 645121 CCNI2 cyclin I family member 2 54619 CCNJ cyclin J 79616 CCNJL cyclin J like 10309 CCNO cyclin O 219771 CCNY cyclin Y 166979 CDC20B cell division cycle 20B 5218 CDK14 cyclin dependent kinase 14 5127 CDK16 cyclin dependent kinase 16 5128 CDK17 cyclin dependent kinase 17 1017 CDK2 cyclin dependent kinase 2 1018 CDK3 cyclin dependent kinase 3 1019 CDK4 cyclin dependent kinase 4 1020 CDK5 cyclin dependent kinase 5 8941 CDK5R2 cyclin dependent kinase 5 regulatory subunit 2 1021 CDK6 cyclin dependent kinase 6 1163 CKS1B CDC28 protein kinase regulatory subunit 1B 1164 CKS2 CDC28 protein kinase regulatory subunit 2 79935 CNTD2 cyclin N-terminal domain containing 2 79187 FSD1 fibronectin type III and SPRY domain containing 1 22858 ICK intestinal cell kinase 388324 INCA1 inhibitor of CDK, cyclin A1 interacting protein 1 23189 KANK1 KN motif and ankyrin repeat domains 1 57538 MAK alpha kinase 3 8569 MKNK1 MAP kinase interacting serine/threonine kinase 1 5891 MOK MOK protein kinase 932 MS4A3 membrane spanning 4-domains A3 51537 MTFP1 mitochondrial fission process 1 152110 NEK10 NIMA related kinase 10 6787 NEK4 NIMA related kinase 4 341676 NEK5 NIMA related kinase 5 9088 PKMYT1 protein kinase, membrane associated tyrosine/threonine 1 1263 PLK3 polo like kinase 3 147011 PROCA1 protein interacting with cyclin A1 245711 SPDYA speedy/RINGO cell cycle regulator family member A 7465 WEE1 WEE1 G2 checkpoint kinase 494551 WEE2 WEE1 homolog 2

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 2.63e-01 2.46e-10 Reactome G2/M DNA replication checkpoint Cell Cycle 2.24e-01 1.57e-43 GO cyclin-dependent protein kinase holoenzyme complex cellular_component 1.12e-01 1.91e-07 Reactome G2 Phase Cell Cycle 8.66e-02 1.13e-36 GO cyclin-dependent protein serine/threonine kinase regulator activity molecular_function 8.33e-02 3.33e-32 GO regulation of mitotic nuclear division biological_process 4.54e-02 5.38e-30 GO positive regulation of cell cycle biological_process 3.85e-02 1.48e-20 GO cyclin-dependent protein serine/threonine kinase activity molecular_function 3.17e-02 2.07e-32 GO regulation of cyclin-dependent protein serine/threonine kinase activity biological_process 9.19e-03 3.97e-04 GO layer formation in cerebral cortex biological_process 7.25e-03 1.70e-10 GO cyclin binding molecular_function 6.57e-03 4.56e-26 GO mitotic cell cycle 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 cell division 0.00e+00 0.00e+00 organelle fission 0.00e+00 0.00e+00 mitotic cell cycle process 0.00e+00 0.00e+00 mitotic nuclear division 0.00e+00 0.00e+00 mitotic cell cycle 0.00e+00 0.00e+00 cell cycle phase transition 0.00e+00 0.00e+00 mitotic cell cycle phase transition 0.00e+00 0.00e+00 regulation of cyclin-dependent protein serine/threonine kinase activity 0.00e+00 0.00e+00 cyclin-dependent protein kinase holoenzyme complex 0.00e+00 0.00e+00 serine/threonine protein kinase complex 0.00e+00 0.00e+00 protein kinase complex 0.00e+00 0.00e+00 protein kinase activity 0.00e+00 0.00e+00 cyclin-dependent protein serine/threonine kinase activity 0.00e+00 0.00e+00 protein serine/threonine kinase activity 0.00e+00 0.00e+00 cyclin-dependent protein kinase activity 0.00e+00 0.00e+00 phosphotransferase activity, alcohol group as acceptor 1.01e-11 6.73e-09 cyclin binding 1.22e-10 1.00e-07 cell cycle G1/S phase transition 1.29e-09 9.47e-07 G2/M transition of mitotic cell cycle 1.39e-09 1.01e-06 cell cycle G2/M phase transition

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

²FDR corrected p-value (Benjamini-Hochberg)

Reactome

P-value1 FDR2 Term 6.20e-11 1.73e-08 CYCLIN A B1 ASSOCIATED EVENTS DURING G2 M TRANSITION 1.66e-10 4.44e-08 MITOTIC G1 G1 S PHASES 6.52e-10 1.62e-07 MITOTIC G2 G2 M PHASES 1.84e-09 5.87e-07 CYCLIN A B1 ASSOCIATED EVENTS DURING G2 M TRANSITION 2.92e-08 8.10e-06 MITOTIC G2 G2 M PHASES 3.90e-08 1.06e-05 MITOTIC G1 G1 S PHASES 4.62e-07 1.09e-04 CELL CYCLE MITOTIC 1.20e-06 2.06e-04 CYCLIN E ASSOCIATED EVENTS DURING G1 S TRANSITION 1.45e-06 2.46e-04 G1 S TRANSITION 4.72e-06 9.50e-04 CELL CYCLE 1.98e-05 3.58e-03 CYCLIN E ASSOCIATED EVENTS DURING G1 S TRANSITION 2.90e-05 4.03e-03 S PHASE 3.23e-05 5.64e-03 G1 S TRANSITION 3.81e-05 5.21e-03 G1 PHASE 5.57e-05 7.43e-03 G2 M CHECKPOINTS 1.74e-04 2.09e-02 G0 AND EARLY G1 2.03e-04 2.91e-02 G1 PHASE 3.31e-04 3.75e-02 SCFSKP2 MEDIATED DEGRADATION OF P27 P21 3.38e-04 4.56e-02 S PHASE 3.62e-04 4.84e-02 G2 M CHECKPOINTS

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

²FDR corrected p-value (Benjamini-Hochberg)

Mouse mutant phenotypes

P-value1 FDR2 Term 1.47e-04 2.92e-01 abnormal cell cycle 2.37e-03 1.00e+00 female infertility 2.88e-03 1.00e+00 abnormal cerebellar foliation 2.90e-03 1.00e+00 abnormal male reproductive system morphology 3.02e-03 1.00e+00 abnormal female reproductive system morphology 3.03e-03 1.00e+00 testicular atrophy 3.75e-03 1.00e+00 delayed estrous cycle 3.75e-03 1.00e+00 thymus cortex atrophy 4.53e-03 1.00e+00 abnormal seminiferous tubule morphology 5.00e-03 1.00e+00 increased cellular sensitivity to gamma-irradiation 7.48e-03 1.00e+00 uterus atrophy 7.48e-03 1.00e+00 impaired luteinization 7.48e-03 1.00e+00 increased DN1 thymic pro-T cell number 8.14e-03 1.00e+00 azoospermia 8.78e-03 1.00e+00 increased double-negative T cell number 9.34e-03 1.00e+00 decreased DN4 thymocyte number 9.34e-03 1.00e+00 abnormal sperm annulus morphology 9.48e-03 1.00e+00 abnormal fertility/fecundity 1.04e-02 1.00e+00 oligozoospermia 1.09e-02 1.00e+00 abnormal cell cycle checkpoint function

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

²FDR corrected p-value (Benjamini-Hochberg)