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DREAM Module Identification Challenge – Consensus modules

PPI-STRING_Consensus_mod344

Assigned name NA Network PPI-STRING Module ID PPI-STRING_Consensus_mod344 Module size 33 genes

Module genes

This module comprises the following genes:

Gene ID Gene Symbol Gene Name 83638 C11orf68 chromosome 11 open reading frame 68 100506380 C7orf13 long intergenic non-protein coding RNA 1006 10283 CWC27 CWC27 spliceosome associated protein homolog 55837 EAPP E2F associated phosphoprotein 80153 EDC3 enhancer of mRNA decapping 3 26017 FAM32A family with sequence similarity 32 member A 9130 FAM50A family with sequence similarity 50 member A 26240 FAM50B family with sequence similarity 50 member B 303741 FRG1 fascin actin-bundling protein 2, retinal 284802 FRG1B FSHD region gene 1 family member B, pseudogene 6936 GCFC2 GC-rich sequence DNA-binding factor 2 22889 KIAA0907 KH domain containing 4, pre-mRNA splicing factor 57456 KIAA1143 KIAA1143 4236 MFAP1 microfibril associated protein 1 80218 NAA50 N(alpha)-acetyltransferase 50, NatE catalytic subunit 222698 NKAPL NFKB activating protein like 55051 NRDE2 NRDE-2, necessary for RNA interference, domain containing 51645 PPIL1 peptidylprolyl isomerase like 1 23759 PPIL2 peptidylprolyl isomerase like 2 53938 PPIL3 peptidylprolyl isomerase like 3 85313 PPIL4 peptidylprolyl isomerase like 4 79706 PRKRIP1 PRKR interacting protein 1 378948 RBMY1B RNA binding motif protein, Y-linked, family 1, member B 378949 RBMY1D RNA binding motif protein, Y-linked, family 1, member D 378950 RBMY1E RNA binding motif protein, Y-linked, family 1, member E 378951 RBMY1J RNA binding motif protein, Y-linked, family 1, member J 10169 SERF2 small EDRK-rich factor 2 79753 SNIP1 Smad nuclear interacting protein 1 51066 SSUH2 ssu-2 homolog (C. elegans) 199745 THAP8 THAP domain containing 8 59286 UBL5 ubiquitin like 5 79650 USB1 U6 snRNA biogenesis phosphodiesterase 1 23217 ZFR2 zinc finger RNA binding protein 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 3.55e-02 1.54e-09 GO protein peptidyl-prolyl isomerization 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 6.39e-11 5.41e-08 mRNA metabolic process 1.15e-10 9.49e-08 RNA splicing 3.62e-10 2.84e-07 mRNA processing 4.68e-10 2.62e-07 peptidyl-prolyl cis-trans isomerase activity 5.23e-09 3.53e-06 protein peptidyl-prolyl isomerization 2.11e-08 8.01e-06 spliceosomal complex 2.46e-08 9.27e-06 catalytic step 2 spliceosome 2.91e-07 1.02e-04 isomerase activity 2.78e-06 7.50e-04 intracellular ribonucleoprotein complex 2.82e-06 7.59e-04 ribonucleoprotein complex 3.52e-06 1.50e-03 mRNA splicing, via spliceosome 3.79e-06 1.61e-03 RNA splicing, via transesterification reactions 7.55e-06 3.01e-03 protein folding 1.42e-04 3.93e-02 posttranscriptional gene silencing by RNA 1.42e-04 3.93e-02 posttranscriptional gene silencing 1.01e-03 1.99e-01 positive regulation of protein targeting to mitochondrion 1.13e-03 1.62e-01 intercellular bridge 1.36e-03 2.54e-01 regulation of protein targeting to mitochondrion 1.47e-03 2.70e-01 gene silencing by RNA 2.15e-03 3.61e-01 positive regulation of mitochondrion organization

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

²FDR corrected p-value (Benjamini-Hochberg)

Reactome

P-value1 FDR2 Term 1.08e-03 1.26e-01 BASIGIN INTERACTIONS 8.21e-03 6.85e-01 MRNA DECAY BY 5 TO 3 EXORIBONUCLEASE 8.29e-03 6.30e-01 BASIGIN INTERACTIONS 1.60e-02 1.00e+00 MRNA DECAY BY 5 TO 3 EXORIBONUCLEASE 1.68e-02 1.00e+00 CELL SURFACE INTERACTIONS AT THE VASCULAR WALL 2.10e-02 1.00e+00 CELL SURFACE INTERACTIONS AT THE VASCULAR WALL 2.29e-02 1.00e+00 DEADENYLATION DEPENDENT MRNA DECAY 3.48e-02 1.00e+00 DEADENYLATION DEPENDENT MRNA DECAY 3.73e-02 1.00e+00 METABOLISM OF MRNA 4.55e-02 1.00e+00 METABOLISM OF MRNA 4.90e-02 1.00e+00 METABOLISM OF RNA

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

²FDR corrected p-value (Benjamini-Hochberg)

Mouse mutant phenotypes

P-value1 FDR2 Term 3.74e-03 1e+00 abnormal placement of pupils 5.40e-03 1e+00 preweaning lethality 9.38e-03 1e+00 vertebral transformation 9.38e-03 1e+00 decreased oxygen consumption 1.32e-02 1e+00 abnormal rib morphology 1.68e-02 1e+00 abnormal epidermis stratum basale morphology 1.68e-02 1e+00 abnormal metabolism 1.86e-02 1e+00 decreased lumbar vertebrae number 2.23e-02 1e+00 increased sacral vertebrae number 2.62e-02 1e+00 decreased lean body mass 2.78e-02 1e+00 increased rib number 2.99e-02 1e+00 abnormal behavior 3.52e-02 1e+00 other aberrant phenotype

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

²FDR corrected p-value (Benjamini-Hochberg)