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DREAM Module Identification Challenge – Consensus modules

PPI-STRING_Consensus_mod341

Assigned name NA Network PPI-STRING Module ID PPI-STRING_Consensus_mod341 Module size 97 genes

Module genes

This module comprises the following genes:

Gene ID Gene Symbol Gene Name 25841 ABTB2 ankyrin repeat and BTB domain containing 2 55122 AKIRIN2 akirin 2 121642 ALKBH2 alkB homolog 2, alpha-ketoglutarate dependent dioxygenase 25842 ASF1A anti-silencing function 1A histone chaperone 55723 ASF1B anti-silencing function 1B histone chaperone 151516 ASPRV1 aspartic peptidase retroviral like 1 571 BACH1 BTB domain and CNC homolog 1 54841 BIVM basic, immunoglobulin-like variable motif containing 10950 BTG3 BTG anti-proliferation factor 3 56652 C10orf2 twinkle mtDNA helicase 28970 C11orf54 chromosome 11 open reading frame 54 55732 C1orf112 chromosome 1 open reading frame 112 92667 C20orf72 mitochondrial genome maintenance exonuclease 1 79680 C22orf29 retrotransposon Gag like 10 205327 C2orf69 chromosome 2 open reading frame 69 132321 C4orf33 chromosome 4 open reading frame 33 116328 C8orf34 chromosome 8 open reading frame 34 284992 CCDC150 coiled-coil domain containing 150 1111 CHEK1 checkpoint kinase 1 11200 CHEK2 checkpoint kinase 2 27098 CLUL1 clusterin like 1 55086 CXorf57 chromosome X open reading frame 57 51523 CXXC5 CXXC finger protein 5 9937 DCLRE1A DNA cross-link repair 1A 64858 DCLRE1B DNA cross-link repair 1B 79077 DCTPP1 dCTP pyrophosphatase 1 84925 DIRC2 disrupted in renal carcinoma 2 10673 DTL TNF superfamily member 13b 55096 EBLN2 endogenous Bornavirus like nucleoprotein 2 255520 ELMOD2 ELMO domain containing 2 1161 ERCC8 ERCC excision repair 8, CSA ubiquitin ligase complex subunit 79033 ERI3 ERI1 exoribonuclease family member 3 64789 EXO5 exonuclease 5 2175 FAH FA complementation group A 81889 FAHD1 fumarylacetoacetate hydrolase domain containing 1 134145 FAM173B family with sequence similarity 173 member B 84142 FAM175A abraxas 1, BRCA1 A complex subunit 113115 FAM54A mitochondrial fission regulator 2 51115 FAM82B regulator of microtubule dynamics 1 26271 FBXO5 F-box protein 5 55640 FLVCR2 feline leukemia virus subgroup C cellular receptor family member 2 115362 GBP5 guanylate binding protein 5 388323 GLTPD2 glycolipid transfer protein domain containing 2 3014 H2AFX H2A histone family member X 84072 HORMAD1 HORMA domain containing 1 150280 HORMAD2 HORMA domain containing 2 3508 IGHMBP2 immunoglobulin mu DNA binding protein 2 29439 JTB jumping translocation breakpoint 22944 KIN Kin17 DNA and RNA binding protein 3963 LGALS7 galectin 7 10459 MAD2L2 mitotic arrest deficient 2 like 2 84944 MAEL maelstrom spermatogenic transposon silencer 79648 MCPH1 microcephalin 1 9656 MDC1 mediator of DNA damage checkpoint 1 64863 METTL4 methyltransferase like 4 4255 MGMT O-6-methylguanine-DNA methyltransferase 9650 MTFR1 mitochondrial fission regulator 1 4595 MUTYH mutY DNA glycosylase 154215 NKAIN2 sodium/potassium transporting ATPase interacting 2 4913 NTHL1 nth like DNA glycosylase 1 220213 OTUD1 OTU deubiquitinase 1 57092 PCNP PEST proteolytic signal containing nuclear protein 80003 PCNXL2 pecanex 2 201626 PDE12 phosphodiesterase 12 11232 POLB DNA polymerase gamma 2, accessory subunit 54107 POLE3 DNA polymerase epsilon 3, accessory subunit 5591 PRKDC protein kinase, DNA-activated, catalytic subunit 133619 PRRC1 proline rich coiled-coil 1 9317 PTER phosphotriesterase related 5887 RAD23B RAD23 homolog B, nucleotide excision repair protein 5932 RBBP8 RB binding protein 8, endonuclease 389075 RESP18 regulated endocrine specific protein 18 246243 RNASEH1 ribonuclease H1 9025 RNF8 ring finger protein 8 51750 RTEL1 regulator of telomere elongation helicase 1 25939 SAMHD1 SAM and HD domain containing deoxynucleoside triphosphate triphosphohydrolase 1 7857 SCG2 secretogranin II 84464 SLX4 SLX4 structure-specific endonuclease subunit 23583 SMUG1 single-strand-selective monofunctional uracil-DNA glycosylase 1 9344 TAOK2 TAO kinase 2 51347 TAOK3 TAO kinase 3 6949 TCOF1 treacle ribosome biogenesis factor 1 166815 TIGD2 tigger transposable element derived 2 91151 TIGD7 tigger transposable element derived 7 25976 TIPARP TCDD inducible poly(ADP-ribose) polymerase 261726 TIPRL TOR signaling pathway regulator 9874 TLK1 tousled like kinase 1 11011 TLK2 tousled like kinase 2 23505 TMEM131 transmembrane protein 131 100288797 TMEM239 transmembrane protein 239 9319 TRIP13 thyroid hormone receptor interactor 13 25809 TTLL1 tubulin tyrosine ligase like 1 7336 UBE2V2 ubiquitin conjugating enzyme E2 V2 115426 UHRF2 ubiquitin like with PHD and ring finger domains 2 51720 UIMC1 ubiquitin interaction motif containing 1 7542 ZFPL1 zinc finger protein like 1 57169 ZNFX1 zinc finger NFX1-type containing 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 4.13e-01 4.19e-03 Reactome ALKBH2 mediated reversal of alkylation damage DNA Repair 4.13e-01 4.19e-03 Reactome MGMT-mediated DNA damage reversal DNA Repair 9.26e-02 8.37e-03 Reactome Mitotic Metaphase/Anaphase Transition Cell Cycle 8.80e-02 5.83e-06 Reactome Displacement of DNA glycosylase by APEX1 DNA Repair 5.97e-02 1.14e-05 GO signal transduction involved in G2 DNA damage checkpoint biological_process 4.49e-02 8.37e-03 Reactome Abasic sugar-phosphate removal via the single-nucleotide replacement pathway DNA Repair 4.18e-02 3.59e-04 GO protection from non-homologous end joining at telomere biological_process 3.65e-02 4.83e-27 Reactome DNA Repair DNA Repair 3.46e-02 1.69e-09 GO chromosome, telomeric region cellular_component 2.48e-02 4.87e-11 GO double-strand break repair via nonhomologous end joining biological_process 2.41e-02 7.63e-04 GO DNA replication-dependent nucleosome assembly biological_process 1.93e-02 1.14e-05 GO DNA N-glycosylase activity molecular_function 1.73e-02 5.38e-06 GO cellular response to gamma radiation biological_process 1.23e-02 1.11e-03 GO hydrolase activity, acting on ester bonds molecular_function 7.29e-03 8.30e-06 Reactome Base-Excision Repair, AP Site Formation DNA Repair 5.02e-03 6.91e-09 GO double-strand break repair biological_process 2.89e-03 3.45e-11 Reactome G2/M DNA damage checkpoint 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 0.00e+00 0.00e+00 DNA repair 0.00e+00 0.00e+00 cellular response to DNA damage stimulus 0.00e+00 0.00e+00 DNA metabolic process 0.00e+00 0.00e+00 DNA damage checkpoint 4.71e-14 4.41e-11 cell cycle checkpoint 6.37e-14 5.96e-11 double-strand break repair 1.88e-12 1.73e-09 double-strand break repair via nonhomologous end joining 2.26e-11 1.99e-08 negative regulation of cell cycle 4.42e-10 2.49e-07 deoxyribonuclease activity 6.97e-10 5.28e-07 G2 DNA damage checkpoint 2.12e-09 9.17e-07 chromosome, telomeric region 2.64e-09 1.86e-06 response to ionizing radiation 2.70e-09 1.34e-06 nuclease activity 6.06e-09 4.05e-06 DNA recombination 2.62e-08 1.62e-05 regulation of DNA repair 1.26e-07 7.00e-05 regulation of response to DNA damage stimulus 1.30e-07 4.35e-05 nuclear chromosome 1.50e-07 4.94e-05 nucleotide-excision repair complex 1.89e-07 1.02e-04 positive regulation of DNA repair 3.08e-07 1.61e-04 DNA replication

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 DNA REPAIR 2.11e-07 5.27e-05 BASE FREE SUGAR PHOSPHATE REMOVAL VIA THE SINGLE NUCLEOTIDE REPLACEMENT PATHWAY 2.86e-07 6.97e-05 RESOLUTION OF AP SITES VIA THE MULTIPLE NUCLEOTIDE PATCH REPLACEMENT PATHWAY 4.66e-07 1.10e-04 RESOLUTION OF AP SITES VIA THE SINGLE NUCLEOTIDE REPLACEMENT PATHWAY 5.81e-07 1.36e-04 BASE EXCISION REPAIR 9.52e-07 1.65e-04 BASE FREE SUGAR PHOSPHATE REMOVAL VIA THE SINGLE NUCLEOTIDE REPLACEMENT PATHWAY 1.25e-06 2.14e-04 RESOLUTION OF AP SITES VIA THE SINGLE NUCLEOTIDE REPLACEMENT PATHWAY 2.16e-06 3.57e-04 RESOLUTION OF AP SITES VIA THE MULTIPLE NUCLEOTIDE PATCH REPLACEMENT PATHWAY 2.56e-06 4.17e-04 BASE EXCISION REPAIR 9.52e-05 1.48e-02 DOUBLE STRAND BREAK REPAIR 1.38e-04 1.70e-02 DOUBLE STRAND BREAK REPAIR 1.40e-04 2.10e-02 P53 INDEPENDENT G1 S DNA DAMAGE CHECKPOINT 5.48e-04 6.98e-02 G2 M DNA DAMAGE CHECKPOINT 5.60e-04 5.99e-02 G2 M DNA DAMAGE CHECKPOINT 1.64e-03 1.80e-01 HOMOLOGOUS RECOMBINATION REPAIR OF REPLICATION INDEPENDENT DOUBLE STRAND BREAKS 1.79e-03 1.69e-01 HOMOLOGOUS RECOMBINATION REPAIR OF REPLICATION INDEPENDENT DOUBLE STRAND BREAKS 2.02e-03 2.15e-01 NUCLEOTIDE EXCISION REPAIR 2.59e-03 2.65e-01 G2 M CHECKPOINTS 4.16e-03 3.51e-01 G2 M CHECKPOINTS

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

²FDR corrected p-value (Benjamini-Hochberg)

Mouse mutant phenotypes

P-value1 FDR2 Term 1.60e-10 8.34e-06 abnormal DNA repair 4.79e-08 7.99e-04 small testis 9.81e-07 8.67e-03 increased mortality induced by gamma-irradiation 7.06e-06 3.67e-02 abnormal chiasmata formation 3.23e-05 1.07e-01 increased T cell derived lymphoma incidence 5.16e-05 1.46e-01 abnormal double-strand DNA break repair 2.42e-04 3.94e-01 abnormal male meiosis 2.49e-04 3.98e-01 increased cellular sensitivity to gamma-irradiation 4.25e-04 5.52e-01 abnormal male germ cell apoptosis 4.42e-04 5.65e-01 chromosomal instability 5.65e-04 6.54e-01 induced chromosome breakage 6.22e-04 6.87e-01 abnormal telomere morphology 8.39e-04 8.16e-01 decreased cell proliferation 1.04e-03 9.21e-01 abnormal class switch recombination 1.34e-03 1.00e+00 absent ovarian follicles 1.56e-03 1.00e+00 arrest of male meiosis 1.98e-03 1.00e+00 arrest of spermatogenesis 2.06e-03 1.00e+00 abnormal base-excision repair 2.19e-03 1.00e+00 abnormal chromosome pairing during meiosis 2.21e-03 1.00e+00 abnormal immunoglobulin heavy chain V(D)J recombination

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

²FDR corrected p-value (Benjamini-Hochberg)