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DREAM Module Identification Challenge – Consensus modules

PPI-STRING_Consensus_mod342

Assigned name NA Network PPI-STRING Module ID PPI-STRING_Consensus_mod342 Module size 35 genes

Module genes

This module comprises the following genes:

Gene ID Gene Symbol Gene Name 84267 C9orf64 chromosome 9 open reading frame 64 57018 CCNL1 cyclin L1 81602 CDADC1 cytidine and dCMP deaminase domain containing 1 92806 CENPBD1 CENPB DNA-binding domain containing 1 10036 CHAF1A chromatin assembly factor 1 subunit A 54921 CHTF8 chromosome transmission fidelity factor 8 80174 DBF4B DBF4 zinc finger B 166614 DCLK2 doublecortin like kinase 2 85443 DCLK3 doublecortin like kinase 3 1716 DGUOK deoxyguanosine kinase 79075 DSCC1 DNA replication and sister chromatid cohesion 1 1854 DUT deoxyuridine triphosphatase 114799 ESCO1 establishment of sister chromatid cohesion N-acetyltransferase 1 55218 EXD2 exonuclease 3'-5' domain containing 2 8690 JRKL JRK like 26013 L3MBTL1 L3MBTL1, histone methyl-lysine binding protein 222229 LRWD1 leucine rich repeats and WD repeat domain containing 1 4678 NASP nuclear autoantigenic sperm protein 301430 ORC2 origin recognition complex, subunit 2 90826 PRMT10 protein arginine methyltransferase 9 5982 RFC2 replication factor C subunit 2 10535 RNASEH2A ribonuclease H2 subunit A 79621 RNASEH2B ribonuclease H2 subunit B 84153 RNASEH2C ribonuclease H2 subunit C 6240 RRM1 ribonucleotide reductase catalytic subunit M1 6241 RRM2 ribonucleotide reductase regulatory subunit M2 50484 RRM2B ribonucleotide reductase regulatory TP53 inducible subunit M2B 100533107 RTEL1-TNFRSF6B RTEL1-TNFRSF6B readthrough (NMD candidate) 26470 SEZ6L2 seizure related 6 homolog like 2 200765 TIGD1 tigger transposable element derived 1 220359 TIGD3 tigger transposable element derived 3 201798 TIGD4 tigger transposable element derived 4 7083 TK1 thymidine kinase 1 7084 TK2 thymidine kinase 2, mitochondrial 7298 TYMS thymidylate synthetase

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 1.19e-01 2.89e-07 GO nucleotide biosynthetic process biological_process 5.74e-02 4.13e-07 GO nucleoside kinase activity molecular_function 5.41e-02 9.00e-10 Reactome Interconversion of nucleotide di- and triphosphates Metabolism 4.10e-02 6.62e-05 GO DNA clamp loader activity molecular_function 2.34e-02 8.51e-05 GO nuclear origin of replication recognition complex cellular_component 2.29e-02 1.06e-04 GO DNA replication-dependent nucleosome assembly biological_process 2.22e-02 2.80e-15 GO DNA replication biological_process 1.02e-02 8.79e-06 GO RNA catabolic process biological_process 9.34e-03 2.78e-06 Reactome Activation of E2F1 target genes at G1/S Cell Cycle 6.92e-03 2.78e-06 Reactome G1/S-Specific Transcription Cell Cycle 7.67e-04 2.14e-04 GO negative regulation of protein localization to nucleus 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 DNA metabolic process 0.00e+00 0.00e+00 DNA replication 5.23e-12 4.76e-09 deoxyribonucleoside monophosphate biosynthetic process 2.41e-10 1.92e-07 deoxyribonucleotide biosynthetic process 5.81e-09 3.89e-06 nucleotide biosynthetic process 1.20e-08 5.40e-06 ribonucleoside-diphosphate reductase activity, thioredoxin disulfide as acceptor 5.86e-08 3.43e-05 deoxyribonucleoside triphosphate metabolic process 8.23e-08 2.84e-05 ribonuclease H2 complex 1.58e-07 5.18e-05 chromatin 9.18e-07 4.40e-04 nucleotide metabolic process 1.62e-06 7.40e-04 pyrimidine nucleoside biosynthetic process 1.99e-06 8.93e-04 nucleobase-containing small molecule metabolic process 2.11e-06 9.42e-04 nucleoside monophosphate biosynthetic process 2.17e-06 6.00e-04 Ctf18 RFC-like complex 4.31e-06 1.21e-03 nucleoside kinase activity 4.88e-06 2.03e-03 post-translational protein acetylation 7.98e-06 3.16e-03 regulation of DNA replication 8.14e-06 3.22e-03 nucleoside metabolic process 9.61e-06 3.73e-03 pyrimidine nucleoside metabolic process 1.33e-05 3.38e-03 DNA-dependent ATPase activity

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 METABOLISM OF NUCLEOTIDES 0.00e+00 0.00e+00 METABOLISM OF NUCLEOTIDES 1.72e-07 4.33e-05 PYRIMIDINE METABOLISM 3.17e-07 5.86e-05 PYRIMIDINE METABOLISM 2.04e-06 4.35e-04 E2F MEDIATED REGULATION OF DNA REPLICATION 2.25e-06 3.70e-04 E2F MEDIATED REGULATION OF DNA REPLICATION 2.26e-06 4.79e-04 SYNTHESIS AND INTERCONVERSION OF NUCLEOTIDE DI AND TRIPHOSPHATES 1.30e-05 2.43e-03 G1 S SPECIFIC TRANSCRIPTION 1.70e-05 2.45e-03 G1 S SPECIFIC TRANSCRIPTION 2.49e-05 3.50e-03 SYNTHESIS AND INTERCONVERSION OF NUCLEOTIDE DI AND TRIPHOSPHATES 2.36e-04 2.75e-02 G1 S TRANSITION 2.50e-04 3.50e-02 G1 S TRANSITION 4.49e-04 5.85e-02 MITOTIC G1 G1 S PHASES 4.63e-04 6.02e-02 CELL CYCLE MITOTIC 5.53e-04 5.94e-02 MITOTIC G1 G1 S PHASES 1.22e-03 1.39e-01 CELL CYCLE 4.21e-03 3.55e-01 ACTIVATION OF ATR IN RESPONSE TO REPLICATION STRESS 4.62e-03 4.28e-01 ACTIVATION OF ATR IN RESPONSE TO REPLICATION STRESS 5.15e-03 4.21e-01 G2 M CHECKPOINTS 6.05e-03 5.35e-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 1.88e-03 1e+00 abnormal glomerular endothelium fenestra morphology 1.93e-03 1e+00 glomerulosclerosis 2.23e-03 1e+00 increased sacral vertebrae number 2.72e-03 1e+00 vertebral transformation 2.97e-03 1e+00 decreased lumbar vertebrae number 5.10e-03 1e+00 chromosomal instability 5.62e-03 1e+00 abnormal sublingual gland morphology 5.64e-03 1e+00 abnormal glomerular capsule parietal layer morphology 5.64e-03 1e+00 podocyte hypertrophy 7.49e-03 1e+00 thyroid inflammation 7.49e-03 1e+00 arteriosclerosis 7.52e-03 1e+00 increased renal tubule apoptosis 1.12e-02 1e+00 renal glomerulus fibrosis 1.12e-02 1e+00 abnormal renal glomerular capsule morphology 1.13e-02 1e+00 proximal convoluted tubule brush border loss 1.30e-02 1e+00 pancreatic acinar cell zymogen granule accumulation 1.31e-02 1e+00 abnormal adaptive thermogenesis 1.31e-02 1e+00 arteritis 1.31e-02 1e+00 skeletal muscle atrophy 1.31e-02 1e+00 abnormal submandibular gland morphology

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

²FDR corrected p-value (Benjamini-Hochberg)