Back to main page

DREAM Module Identification Challenge – Consensus modules

PPI-STRING_Consensus_mod232

Assigned name NA Network PPI-STRING Module ID PPI-STRING_Consensus_mod232 Module size 34 genes

Module genes

This module comprises the following genes:

Gene ID Gene Symbol Gene Name 10438 C1D C1D nuclear receptor corepressor 100912393 DCP2 mRNA-decapping enzyme 2-like 22894 DIS3 DIS3 homolog, exosome endoribonuclease and 3'-5' exoribonuclease 115752 DIS3L DIS3 like exosome 3'-5' exoribonuclease 129563 DIS3L2 DIS3 like 3'-5' exoribonuclease 2 679140 EXOSC1 exosome component 1 5394 EXOSC10 exosome component 10 23404 EXOSC2 exosome component 2 51010 EXOSC3 exosome component 3 54512 EXOSC4 exosome component 4 56915 EXOSC5 exosome component 5 118460 EXOSC6 exosome component 6 23016 EXOSC7 exosome component 7 11340 EXOSC8 exosome component 8 5393 EXOSC9 exosome component 9 54707 GPN2 GPN-loop GTPase 2 9567 GTPBP1 GTP binding protein 1 8570 KHSRP KH-type splicing regulatory protein 114785 MBD6 methyl-CpG binding domain protein 6 10200 MPHOSPH6 M-phase phosphoprotein 6 5073 PARN poly(A)-specific ribonuclease 315045 POP1 POP1 homolog, ribonuclease P/MRP subunit 286430 POP4 NLR family pyrin domain containing 2B 51367 POP5 POP5 homolog, ribonuclease P/MRP subunit 10248 POP7 POP7 homolog, ribonuclease P/MRP subunit 361799 RAI1 decapping exoribonuclease 11102 RPP14 ribonuclease P/MRP subunit p14 79897 RPP21 ribonuclease P/MRP subunit p21 54913 RPP25 ribonuclease P and MRP subunit p25 10556 RPP30 ribonuclease P/MRP subunit p30 10799 RPP40 ribonuclease P/MRP subunit p40 288615 SBDS SBDS, ribosome maturation factor 6832 SUPV3L1 Suv3 like RNA helicase 54464 XRN1 5'-3' exoribonuclease 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 3.67e-01 5.91e-24 GO ribonuclease P activity molecular_function 2.29e-01 1.58e-39 GO exosome (RNase complex) cellular_component 2.23e-01 3.32e-21 GO tRNA 5'-leader removal biological_process 2.05e-01 2.50e-37 GO nuclear exosome (RNase complex) cellular_component 1.81e-01 7.50e-34 Reactome KSRP (KHSRP) binds and destabilizes mRNA Metabolism of RNA 1.50e-01 2.42e-30 GO cytoplasmic exosome (RNase complex) cellular_component 1.22e-01 2.17e-16 GO nucleolar ribonuclease P complex cellular_component 6.72e-02 6.65e-22 GO nuclear mRNA surveillance biological_process 5.10e-02 3.81e-23 GO RNA phosphodiester bond hydrolysis, exonucleolytic biological_process 3.92e-02 1.59e-30 Reactome Butyrate Response Factor 1 (BRF1) binds and destabilizes mRNA Metabolism of RNA 2.60e-02 1.59e-30 Reactome Tristetraprolin (TTP, ZFP36) binds and destabilizes mRNA Metabolism of RNA 1.09e-02 7.47e-05 GO miRNA catabolic process biological_process 1.05e-02 8.06e-08 GO telomerase RNA binding molecular_function 3.87e-03 3.93e-10 GO maturation of 5.8S rRNA 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 nucleic acid phosphodiester bond hydrolysis 0e+00 0e+00 aromatic compound catabolic process 0e+00 0e+00 RNA phosphodiester bond hydrolysis 0e+00 0e+00 tRNA 5'-leader removal 0e+00 0e+00 RNA catabolic process 0e+00 0e+00 RNA phosphodiester bond hydrolysis, exonucleolytic 0e+00 0e+00 nuclear-transcribed mRNA catabolic process 0e+00 0e+00 exonucleolytic nuclear-transcribed mRNA catabolic process involved in deadenylation-dependent decay 0e+00 0e+00 ribosome biogenesis 0e+00 0e+00 regulation of mRNA stability 0e+00 0e+00 ribonucleoprotein complex biogenesis 0e+00 0e+00 regulation of RNA stability 0e+00 0e+00 rRNA processing 0e+00 0e+00 mRNA catabolic process 0e+00 0e+00 nuclear-transcribed mRNA catabolic process, deadenylation-dependent decay 0e+00 0e+00 posttranscriptional regulation of gene expression 0e+00 0e+00 mRNA metabolic process 0e+00 0e+00 rRNA metabolic process 0e+00 0e+00 rRNA catabolic process 0e+00 0e+00 nuclear-transcribed mRNA catabolic process, exonucleolytic

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

²FDR corrected p-value (Benjamini-Hochberg)

Reactome

P-value1 FDR2 Term 0e+00 0e+00 DIABETES PATHWAYS 0e+00 0e+00 PERK REGULATED GENE EXPRESSION 0e+00 0e+00 UNFOLDED PROTEIN RESPONSE 0e+00 0e+00 MRNA DECAY BY 3 TO 5 EXORIBONUCLEASE 0e+00 0e+00 REGULATION OF MRNA STABILITY BY PROTEINS THAT BIND AU RICH ELEMENTS 0e+00 0e+00 DESTABILIZATION OF MRNA BY KSRP 0e+00 0e+00 ACTIVATION OF GENES BY ATF4 0e+00 0e+00 DEADENYLATION DEPENDENT MRNA DECAY 0e+00 0e+00 DESTABILIZATION OF MRNA BY BRF1 0e+00 0e+00 METABOLISM OF RNA 0e+00 0e+00 DESTABILIZATION OF MRNA BY TRISTETRAPROLIN TTP 0e+00 0e+00 METABOLISM OF MRNA 0e+00 0e+00 ACTIVATION OF GENES BY ATF4 0e+00 0e+00 DIABETES PATHWAYS 0e+00 0e+00 UNFOLDED PROTEIN RESPONSE 0e+00 0e+00 PERK REGULATED GENE EXPRESSION 0e+00 0e+00 DEADENYLATION DEPENDENT MRNA DECAY 0e+00 0e+00 DESTABILIZATION OF MRNA BY BRF1 0e+00 0e+00 METABOLISM OF RNA 0e+00 0e+00 DESTABILIZATION OF MRNA BY TRISTETRAPROLIN TTP

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

²FDR corrected p-value (Benjamini-Hochberg)

Mouse mutant phenotypes

P-value1 FDR2 Term 3.19e-03 1e+00 decreased survivor rate 3.74e-03 1e+00 broad nasal bone 5.61e-03 1e+00 polyphalangy 5.61e-03 1e+00 abnormal vertebral arch development 5.61e-03 1e+00 fusion of atlas and odontoid process 7.47e-03 1e+00 increased interferon-beta secretion 7.48e-03 1e+00 abnormal thyroid cartilage morphology 9.33e-03 1e+00 failure to form egg cylinders 9.34e-03 1e+00 abnormal rib development 1.06e-02 1e+00 abnormal vertebral transverse process morphology 1.12e-02 1e+00 abnormal abdominal fat pad morphology 1.12e-02 1e+00 partial embryonic lethality between implantation and placentation 1.12e-02 1e+00 absent proamniotic cavity 1.31e-02 1e+00 abnormal nasal bone morphology 1.31e-02 1e+00 partial embryonic lethality between implantation and somite formation 1.47e-02 1e+00 complete prenatal lethality 1.54e-02 1e+00 preweaning lethality 1.68e-02 1e+00 abnormal circulating hormone level 1.68e-02 1e+00 increased white adipose tissue amount 1.68e-02 1e+00 short nasal bone

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

²FDR corrected p-value (Benjamini-Hochberg)