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DREAM Module Identification Challenge – Consensus modules

PPI-STRING_Consensus_mod339

Assigned name NA Network PPI-STRING Module ID PPI-STRING_Consensus_mod339 Module size 26 genes

Module genes

This module comprises the following genes:

Gene ID Gene Symbol Gene Name 23357 ANGEL1 angel homolog 1 90806 ANGEL2 angel homolog 2 55571 C2orf29 CCR4-NOT transcription complex subunit 11 25819 CCRN4L nocturnin 23019 CNOT1 CCR4-NOT transcription complex subunit 1 25904 CNOT10 CCR4-NOT transcription complex subunit 10 4848 CNOT2 CCR4-NOT transcription complex subunit 2 4849 CNOT3 CCR4-NOT transcription complex subunit 3 4850 CNOT4 CCR4-NOT transcription complex subunit 4 57472 CNOT6 CCR4-NOT transcription complex subunit 6 246175 CNOT6L CCR4-NOT transcription complex subunit 6 like 29883 CNOT7 CCR4-NOT transcription complex subunit 7 9337 CNOT8 CCR4-NOT transcription complex subunit 8 22849 CPEB3 cytoplasmic polyadenylation element binding protein 3 1981 EIF4G1 eukaryotic translation initiation factor 4 gamma 1 1982 EIF4G2 eukaryotic translation initiation factor 4 gamma 2 10605 PAIP1 poly(A) binding protein interacting protein 1 9924 PAN2 poly(A) specific ribonuclease subunit PAN2 171389 PAN3 NLR family pyrin domain containing 6 54039 PCBP3 poly(rC) binding protein 3 57060 PCBP4 poly(rC) binding protein 4 79596 RNF219 ring finger protein 219 9125 RQCD1 CCR4-NOT transcription complex subunit 9 85456 TNKS1BP1 tankyrase 1 binding protein 1 10140 TOB1 transducer of ERBB2, 1 10766 TOB2 transducer of ERBB2, 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 3.31e-01 3.58e-33 GO CCR4-NOT complex cellular_component 2.59e-01 1.67e-39 Reactome Deadenylation of mRNA Metabolism of RNA 1.03e-01 5.03e-21 GO poly(A)-specific ribonuclease activity molecular_function 5.32e-02 9.12e-28 Reactome TP53 regulates transcription of additional cell cycle genes whose exact role in the p53 pathway remain uncertain Gene expression (Transcription) 7.83e-03 8.36e-05 GO eukaryotic initiation factor 4E binding molecular_function

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 aromatic compound catabolic process 0e+00 0e+00 mitotic cell cycle checkpoint 0e+00 0e+00 signal transduction in response to DNA damage 0e+00 0e+00 mRNA catabolic process 0e+00 0e+00 regulation of cell cycle phase transition 0e+00 0e+00 RNA catabolic process 0e+00 0e+00 signal transduction involved in DNA damage checkpoint 0e+00 0e+00 negative regulation of translation 0e+00 0e+00 RNA phosphodiester bond hydrolysis, exonucleolytic 0e+00 0e+00 regulation of mitotic cell cycle phase transition 0e+00 0e+00 positive regulation of cell cycle process 0e+00 0e+00 negative regulation of mitotic cell cycle phase transition 0e+00 0e+00 negative regulation of mitotic cell cycle 0e+00 0e+00 regulation of mitotic cell cycle 0e+00 0e+00 DNA damage checkpoint 0e+00 0e+00 negative regulation of cell cycle process 0e+00 0e+00 cell cycle checkpoint 0e+00 0e+00 signal transduction by p53 class mediator 0e+00 0e+00 DNA damage response, signal transduction by p53 class mediator 0e+00 0e+00 regulation of G1/S transition of mitotic cell cycle

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 DEADENYLATION DEPENDENT MRNA DECAY 0.00e+00 0.00e+00 METABOLISM OF RNA 0.00e+00 0.00e+00 DEADENYLATION OF MRNA 0.00e+00 0.00e+00 METABOLISM OF MRNA 0.00e+00 0.00e+00 DEADENYLATION DEPENDENT MRNA DECAY 0.00e+00 0.00e+00 METABOLISM OF RNA 0.00e+00 0.00e+00 DEADENYLATION OF MRNA 0.00e+00 0.00e+00 METABOLISM OF MRNA 5.88e-03 5.23e-01 ANTIVIRAL MECHANISM BY IFN STIMULATED GENES 7.26e-03 5.63e-01 ANTIVIRAL MECHANISM BY IFN STIMULATED GENES 1.03e-02 8.15e-01 MTORC1 MEDIATED SIGNALLING 1.08e-02 7.78e-01 MTORC1 MEDIATED SIGNALLING 1.45e-02 9.89e-01 PKB MEDIATED EVENTS 2.05e-02 1.00e+00 PKB MEDIATED EVENTS 2.26e-02 1.00e+00 BMAL1 CLOCK NPAS2 ACTIVATES CIRCADIAN EXPRESSION 2.38e-02 1.00e+00 INTERFERON SIGNALING 3.76e-02 1.00e+00 NONSENSE MEDIATED DECAY ENHANCED BY THE EXON JUNCTION COMPLEX 4.24e-02 1.00e+00 BMAL1 CLOCK NPAS2 ACTIVATES CIRCADIAN EXPRESSION

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

²FDR corrected p-value (Benjamini-Hochberg)

Mouse mutant phenotypes

P-value1 FDR2 Term 9.46e-05 2.18e-01 increased bone resorption 1.83e-04 3.30e-01 osteoporosis 3.89e-04 5.24e-01 increased osteoclast cell number 1.01e-03 9.05e-01 abnormal osteoclast differentiation 2.19e-03 1.00e+00 abnormal trabecular bone morphology 3.74e-03 1.00e+00 Sertoli cell hypoplasia 3.74e-03 1.00e+00 decreased brown fat cell size 3.74e-03 1.00e+00 decreased left ventricle developed pressure 7.48e-03 1.00e+00 increased heart left ventricle size 9.33e-03 1.00e+00 decreased fasted circulating glucose level 9.34e-03 1.00e+00 abnormal long term depression 9.34e-03 1.00e+00 abnormal adipose tissue morphology 9.34e-03 1.00e+00 decreased trabecular bone mass 1.31e-02 1.00e+00 abnormal sperm mitochondrial sheath morphology 1.31e-02 1.00e+00 abnormal spatial reference memory 1.31e-02 1.00e+00 abnormal adipose tissue amount 1.49e-02 1.00e+00 decreased trabecular bone thickness 1.49e-02 1.00e+00 increased osteoblast cell number 1.49e-02 1.00e+00 increased trabecular bone mass 2.05e-02 1.00e+00 decreased white fat cell size

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

²FDR corrected p-value (Benjamini-Hochberg)