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DREAM Module Identification Challenge – Consensus modules

PPI-STRING_Consensus_mod230

Assigned name NA Network PPI-STRING Module ID PPI-STRING_Consensus_mod230 Module size 44 genes

Module genes

This module comprises the following genes:

Gene ID Gene Symbol Gene Name 84250 ANKRD32 SMC5-SMC6 complex localization factor 1 121551 BTBD11 BTB domain containing 11 280636 C11orf31 selenoprotein H 287961 CDC45 cell division cycle 45 990 CDC6 cell division cycle 6 8317 CDC7 cell division cycle 7 83879 CDCA7 cell division cycle associated 7 63922 CHTF18 chromosome transmission fidelity factor 18 63967 CLSPN claspin 10926 DBF4 DBF4 zinc finger 1663 DDX11 DEAD/H-box helicase 11 29980 DONSON downstream neighbor of SON 9837 GINS1 GINS complex subunit 1 51659 GINS2 GINS complex subunit 2 64785 GINS3 GINS complex subunit 3 84296 GINS4 GINS complex subunit 4 3978 LIG1 DNA ligase 1 55388 MCM10 minichromosome maintenance 10 replication initiation factor 4176 MCM2 minichromosome maintenance complex component 7 4172 MCM3 minichromosome maintenance complex component 3 4173 MCM4 minichromosome maintenance complex component 4 4174 MCM5 minichromosome maintenance complex component 5 4175 MCM6 minichromosome maintenance complex component 6 4176 MCM7 minichromosome maintenance complex component 7 84515 MCM8 minichromosome maintenance 8 homologous recombination repair factor 254394 MCM9 minichromosome maintenance 9 homologous recombination repair factor 79892 MCMBP minichromosome maintenance complex binding protein 157777 MCMDC2 minichromosome maintenance domain containing 2 253714 MMS22L MMS22 like, DNA repair protein 4998 ORC1 origin recognition complex subunit 1 23595 ORC3 origin recognition complex subunit 3 5000 ORC4 origin recognition complex subunit 4 5001 ORC5 origin recognition complex subunit 5 291927 ORC6 origin recognition complex, subunit 6 5422 POLA1 DNA polymerase alpha 1, catalytic subunit 23649 POLA2 DNA polymerase alpha 2, accessory subunit 5427 POLE2 DNA polymerase epsilon 2, accessory subunit 5557 PRIM1 DNA primase subunit 1 55183 RIF1 replication timing regulatory factor 1 6119 RPA3 replication protein A3 29935 RPA4 replication protein A4 83508 TIMELESS timeless circadian regulator 54962 TIPIN TIMELESS interacting protein 11169 WDHD1 WD repeat and HMG-box DNA binding protein 1

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 3.28e-01 8.07e-33 Reactome Unwinding of DNA Cell Cycle#DNA Replication 2.53e-01 3.81e-52 GO DNA replication initiation biological_process 2.51e-01 4.24e-56 Reactome Activation of the pre-replicative complex Cell Cycle#DNA Replication 1.39e-01 1.13e-06 GO replication fork protection biological_process 1.10e-01 4.95e-29 GO DNA replication origin binding molecular_function 7.67e-02 5.13e-38 Reactome DNA strand elongation Cell Cycle#DNA Replication 7.53e-02 5.65e-21 GO MCM complex cellular_component 2.95e-02 2.47e-18 Reactome CDC6 association with the ORC:origin complex Cell Cycle#DNA Replication 2.86e-02 1.07e-09 GO 3'-5' DNA helicase activity molecular_function 2.37e-02 2.15e-09 GO DNA replication checkpoint biological_process 4.77e-03 3.26e-42 Reactome Activation of ATR in response to replication stress 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 nuclear DNA replication 0e+00 0e+00 DNA geometric change 0e+00 0e+00 mitotic cell cycle process 0e+00 0e+00 DNA replication 0e+00 0e+00 DNA-dependent DNA replication 0e+00 0e+00 DNA metabolic process 0e+00 0e+00 mitotic cell cycle 0e+00 0e+00 DNA duplex unwinding 0e+00 0e+00 DNA repair 0e+00 0e+00 DNA replication initiation 0e+00 0e+00 double-strand break repair via homologous recombination 0e+00 0e+00 DNA recombination 0e+00 0e+00 cellular response to DNA damage stimulus 0e+00 0e+00 double-strand break repair 0e+00 0e+00 mitotic cell cycle phase transition 0e+00 0e+00 G1/S transition of mitotic cell cycle 0e+00 0e+00 cell cycle G1/S phase transition 0e+00 0e+00 cell cycle phase transition 0e+00 0e+00 protein-DNA complex 0e+00 0e+00 nuclear chromosome

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

²FDR corrected p-value (Benjamini-Hochberg)

Reactome

P-value1 FDR2 Term 0e+00 0e+00 S PHASE 0e+00 0e+00 CELL CYCLE 0e+00 0e+00 SYNTHESIS OF DNA 0e+00 0e+00 DNA STRAND ELONGATION 0e+00 0e+00 UNWINDING OF DNA 0e+00 0e+00 CELL CYCLE MITOTIC 0e+00 0e+00 DNA REPLICATION 0e+00 0e+00 ACTIVATION OF ATR IN RESPONSE TO REPLICATION STRESS 0e+00 0e+00 G1 S TRANSITION 0e+00 0e+00 CELL CYCLE CHECKPOINTS 0e+00 0e+00 MITOTIC G1 G1 S PHASES 0e+00 0e+00 MITOTIC M M G1 PHASES 0e+00 0e+00 G2 M CHECKPOINTS 0e+00 0e+00 ACTIVATION OF THE PRE REPLICATIVE COMPLEX 0e+00 0e+00 M G1 TRANSITION 0e+00 0e+00 SYNTHESIS OF DNA 0e+00 0e+00 S PHASE 0e+00 0e+00 DNA STRAND ELONGATION 0e+00 0e+00 UNWINDING OF DNA 0e+00 0e+00 DNA REPLICATION

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

²FDR corrected p-value (Benjamini-Hochberg)

Mouse mutant phenotypes

P-value1 FDR2 Term 9.36e-08 1.35e-03 chromosomal instability 8.19e-07 7.43e-03 abnormal erythrocyte morphology 3.15e-06 2.07e-02 abnormal cell nucleus morphology 5.62e-06 3.17e-02 spontaneous chromosome breakage 1.03e-05 4.78e-02 abnormal DNA replication 1.37e-05 5.77e-02 decreased fibroblast proliferation 3.72e-05 1.17e-01 absent inner cell mass proliferation 3.89e-05 1.21e-01 abnormal cell cycle 9.00e-05 2.12e-01 complete embryonic lethality between implantation and somite formation 2.99e-04 4.47e-01 complete prenatal lethality 6.25e-04 6.89e-01 polyploidy 6.33e-04 6.94e-01 decreased inner cell mass proliferation 1.04e-03 9.21e-01 increased ovary tumor incidence 1.28e-03 1.00e+00 increased tumor incidence 1.53e-03 1.00e+00 abnormal double-strand DNA break repair 1.96e-03 1.00e+00 increased T cell derived lymphoma incidence 2.20e-03 1.00e+00 abnormal male germ cell apoptosis 3.00e-03 1.00e+00 increased cellular sensitivity to gamma-irradiation 3.75e-03 1.00e+00 intestine polyps 4.51e-03 1.00e+00 decreased cell proliferation

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

²FDR corrected p-value (Benjamini-Hochberg)