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DREAM Module Identification Challenge – Consensus modules

PPI-STRING_Consensus_mod84

Assigned name NA Network PPI-STRING Module ID PPI-STRING_Consensus_mod84 Module size 47 genes

Module genes

This module comprises the following genes:

Gene ID Gene Symbol Gene Name 472 ATM ATM serine/threonine kinase 84168 ATR ANTXR cell adhesion molecule 1 84126 ATRIP ATR interacting protein 360254 BRCA2 BRCA2, DNA repair associated 80233 C17orf70 FA core complex associated protein 100 91442 C19orf40 FA core complex associated protein 24 199990 C1orf86 FA core complex associated protein 20 2175 FANCA FA complementation group A 2187 FANCB FA complementation group B 2176 FANCC FA complementation group C 2177 FANCD2 FA complementation group D2 2178 FANCE FA complementation group E 499155 FANCF FA complementation group F 2189 FANCG FA complementation group G 55215 FANCI FA complementation group I 55120 FANCL FA complementation group L 92292 GLYATL1 glycine-N-acyltransferase like 1 219970 GLYATL2 glycine-N-acyltransferase like 2 389396 GLYATL3 glycine-N-acyltransferase like 3 3364 HUS1 HUS1 checkpoint clamp component 135458 HUS1B HUS1 checkpoint clamp component B 84057 MND1 meiotic nuclear divisions 1 9048 NBN artemin 79728 PALB2 partner and localizer of BRCA2 29893 PSMC3IP PSMC3 interacting protein 5810 RAD1 RAD1 checkpoint DNA exonuclease 5884 RAD17 RAD17 checkpoint clamp loader component 5883 RAD9A RAD9 checkpoint clamp component A 144715 RAD9B RAD9 checkpoint clamp component B 5983 RFC3 replication factor C subunit 3 5984 RFC4 replication factor C subunit 4 5985 RFC5 replication factor C subunit 5 80010 RMI1 RecQ mediated genome instability 1 116028 RMI2 RecQ mediated genome instability 2 6117 RPA1 replication protein A1 6118 RPA2 replication protein A2 50485 SMARCAL1 SWI/SNF related, matrix associated, actin dependent regulator of chromatin, subfamily a like 1 8553 STRA13 basic helix-loop-helix family member e40 10732 TCFL5 transcription factor like 5 56154 TEX15 testis expressed 15, meiosis and synapsis associated 90381 TICRR TOPBP1 interacting checkpoint and replication regulator 7156 TOP3A DNA topoisomerase III alpha 11073 TOPBP1 DNA topoisomerase II binding protein 1 11277 TREX1 three prime repair exonuclease 1 11219 TREX2 three prime repair exonuclease 2 29089 UBE2T ubiquitin conjugating enzyme E2 T 7398 USP1 ubiquitin specific peptidase 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 4.34e-01 2.56e-03 Reactome Regulation by TREX1 Immune System 2.34e-01 3.12e-07 Reactome Conjugation of benzoate with glycine Metabolism 2.14e-01 3.29e-33 Reactome Fanconi Anemia Pathway DNA Repair 1.81e-01 1.49e-15 GO Fanconi anaemia nuclear complex cellular_component 1.80e-01 4.33e-43 Reactome Homologous DNA Pairing and Strand Exchange DNA Repair 1.66e-01 3.98e-11 GO mitotic DNA replication checkpoint biological_process 8.54e-02 6.76e-39 Reactome HDR through Single Strand Annealing (SSA) DNA Repair 8.47e-02 3.99e-41 Reactome Presynaptic phase of homologous DNA pairing and strand exchange DNA Repair 4.83e-02 2.60e-09 GO DNA clamp loader activity molecular_function 4.02e-02 8.71e-07 Reactome Conjugation of salicylate with glycine Metabolism 3.75e-02 2.73e-23 Reactome Activation of ATR in response to replication stress Cell Cycle 1.01e-02 2.65e-07 GO DNA metabolic process biological_process 1.26e-03 7.14e-15 GO DNA damage checkpoint 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 0e+00 0e+00 DNA repair 0e+00 0e+00 DNA replication 0e+00 0e+00 regulation of signal transduction by p53 class mediator 0e+00 0e+00 DNA recombination 0e+00 0e+00 strand displacement 0e+00 0e+00 cellular response to DNA damage stimulus 0e+00 0e+00 DNA synthesis involved in DNA repair 0e+00 0e+00 DNA metabolic process 0e+00 0e+00 meiotic cell cycle 0e+00 0e+00 DNA biosynthetic process 0e+00 0e+00 mitotic cell cycle checkpoint 0e+00 0e+00 DNA damage checkpoint 0e+00 0e+00 cell cycle checkpoint 0e+00 0e+00 negative regulation of cell cycle 0e+00 0e+00 mitotic G2/M transition checkpoint 0e+00 0e+00 mitotic DNA integrity checkpoint 0e+00 0e+00 DNA replication checkpoint 0e+00 0e+00 interstrand cross-link repair 0e+00 0e+00 nuclear chromosome 0e+00 0e+00 Fanconi anaemia nuclear complex

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 DNA REPAIR 0.00e+00 0.00e+00 ACTIVATION OF ATR IN RESPONSE TO REPLICATION STRESS 0.00e+00 0.00e+00 G2 M CHECKPOINTS 0.00e+00 0.00e+00 FANCONI ANEMIA PATHWAY 0.00e+00 0.00e+00 DNA REPAIR 0.00e+00 0.00e+00 ACTIVATION OF ATR IN RESPONSE TO REPLICATION STRESS 0.00e+00 0.00e+00 G2 M CHECKPOINTS 0.00e+00 0.00e+00 FANCONI ANEMIA PATHWAY 2.28e-11 6.59e-09 CELL CYCLE CHECKPOINTS 1.09e-10 3.95e-08 CELL CYCLE CHECKPOINTS 4.83e-10 1.64e-07 MEIOSIS 8.29e-10 2.76e-07 MEIOTIC RECOMBINATION 3.56e-08 7.34e-06 HOMOLOGOUS RECOMBINATION REPAIR OF REPLICATION INDEPENDENT DOUBLE STRAND BREAKS 4.13e-08 1.12e-05 HOMOLOGOUS RECOMBINATION REPAIR OF REPLICATION INDEPENDENT DOUBLE STRAND BREAKS 5.64e-08 1.14e-05 MEIOSIS 6.93e-08 1.38e-05 REGULATION OF THE FANCONI ANEMIA PATHWAY 1.32e-07 3.36e-05 DOUBLE STRAND BREAK REPAIR 1.94e-07 3.67e-05 REPAIR SYNTHESIS FOR GAP FILLING BY DNA POL IN TC NER 2.16e-07 4.07e-05 DOUBLE STRAND BREAK REPAIR 2.20e-07 5.46e-05 REGULATION OF THE FANCONI ANEMIA PATHWAY

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

²FDR corrected p-value (Benjamini-Hochberg)

Mouse mutant phenotypes

P-value1 FDR2 Term 1.20e-09 4.17e-05 induced chromosome breakage 1.54e-09 5.08e-05 chromosome breakage 9.02e-09 2.41e-04 absent ovarian follicles 8.15e-08 1.19e-03 spontaneous chromosome breakage 2.46e-06 1.72e-02 small testis 2.74e-06 1.90e-02 ovary degeneration 3.25e-06 2.11e-02 small ovary 1.91e-05 7.35e-02 seminiferous tubule degeneration 2.47e-05 9.00e-02 abnormal chromosome morphology 5.01e-05 1.43e-01 abnormal cell cycle checkpoint function 5.51e-05 1.53e-01 ovary hypoplasia 5.55e-05 1.53e-01 increased sensitivity to induced cell death 6.33e-05 1.66e-01 chromosomal instability 7.87e-05 1.94e-01 abnormal male meiosis 1.11e-04 2.42e-01 absent oocytes 2.38e-04 3.90e-01 abnormal seminiferous tubule morphology 3.80e-04 5.19e-01 increased mortality induced by gamma-irradiation 4.48e-04 5.68e-01 decreased fibroblast proliferation 4.49e-04 5.68e-01 abnormal double-strand DNA break repair 4.82e-04 5.95e-01 increased cellular sensitivity to methylmethanesulfonate

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

²FDR corrected p-value (Benjamini-Hochberg)