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DREAM Module Identification Challenge – Consensus modules

PPI-STRING_Consensus_mod262

Assigned name NA Network PPI-STRING Module ID PPI-STRING_Consensus_mod262 Module size 49 genes

Module genes

This module comprises the following genes:

Gene ID Gene Symbol Gene Name 104 ADARB1 adenosine deaminase, RNA specific B1 312 ANXA13 annexin A13 51637 C14orf166 RNA transcription, translation and transport factor 51493 C22orf28 RNA 2',3'-cyclic phosphate and 5'-OH ligase 79074 C2orf49 chromosome 2 open reading frame 49 50854 C6orf48 chromosome 6 open reading frame 48 115098 CCDC124 coiled-coil domain containing 124 8531 CSDA Y-box binding protein 3 7812 CSDE1 cold shock domain containing E1 1653 DDX1 DEAD-box helicase 1 23644 EDC4 enhancer of mRNA decapping 4 5610 EIF2AK1 eukaryotic translation initiation factor 2 alpha kinase 2 26523 EIF2C1 argonaute 1, RISC catalytic component 27161 EIF2C2 argonaute 2, RISC catalytic component 192669 EIF2C3 argonaute 3, RISC catalytic component 192670 EIF2C4 argonaute 4, RISC catalytic component 25940 FAM98A family with sequence similarity 98 member A 283742 FAM98B family with sequence similarity 98 member B 147965 FAM98C family with sequence similarity 98 member C 8087 FXR1 FMR1 autosomal homolog 1 9513 FXR2 FMR1 autosomal homolog 2 154150 HDGFL1 HDGF like 1 10642 IGF2BP1 insulin like growth factor 2 mRNA binding protein 1 10644 IGF2BP2 insulin like growth factor 2 mRNA binding protein 2 10643 IGF2BP3 insulin like growth factor 2 mRNA binding protein 3 3608 ILF2 interleukin enhancer binding factor 2 9208 LRRFIP1 LRR binding FLII interacting protein 1 293719 MAP7 UBX domain protein 1 51320 MEX3C mex-3 RNA binding family member C 4343 MOV10 Mov10 RISC complex RNA helicase 4495 MT1M metallothionein 1G 80331 NCL DnaJ heat shock protein family (Hsp40) member C5 4836 NMT1 N-myristoyltransferase 1 92736 OTOP2 otopetrin 2 8575 PRKRA protein activator of interferon induced protein kinase EIF2AK2 79912 PYROXD1 pyridine nucleotide-disulphide oxidoreductase domain 1 27293 SMPDL3B sphingomyelin phosphodiesterase acid like 3B 6780 STAU1 staufen double-stranded RNA binding protein 1 27067 STAU2 staufen double-stranded RNA binding protein 2 55342 STRBP spermatid perinuclear RNA binding protein 10492 SYNCRIP synaptotagmin binding cytoplasmic RNA interacting protein 6895 TARBP2 TARBP2, RISC loading complex RNA binding subunit 11022 TDRKH tudor and KH domain containing 27327 TNRC6A trinucleotide repeat containing 6A 23112 TNRC6B trinucleotide repeat containing 6B 131405 TRIM71 tripartite motif containing 71 339487 ZBTB8OS zinc finger and BTB domain containing 8 opposite strand 64393 ZMAT3 zinc finger matrin-type 3 23567 ZNF346 zinc finger protein 346

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 5.15e-01 3.01e-15 GO tRNA-splicing ligase complex cellular_component 1.67e-01 1.04e-10 GO translation regulator activity molecular_function 1.23e-01 5.26e-05 GO pre-miRNA binding molecular_function 1.06e-01 6.50e-07 Reactome Insulin-like Growth Factor-2 mRNA Binding Proteins (IGF2BPs/IMPs/VICKZs) bind RNA Metabolism of RNA 9.65e-02 1.39e-06 GO posttranscriptional gene silencing by RNA biological_process 5.31e-02 4.98e-16 GO double-stranded RNA binding molecular_function 2.99e-02 4.65e-03 Reactome C6 deamination of adenosine Metabolism of RNA 2.88e-02 4.65e-03 Reactome Formation of editosomes by ADAR proteins Metabolism of RNA 2.64e-02 3.93e-12 GO negative regulation of translation biological_process 1.68e-02 4.65e-03 Reactome mRNA Editing: A to I Conversion Metabolism of RNA 1.14e-02 3.29e-06 GO miRNA mediated inhibition of translation biological_process 4.10e-03 2.16e-07 GO mRNA 5'-UTR 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 0.00e+00 0.00e+00 regulation of translation 0.00e+00 0.00e+00 posttranscriptional regulation of gene expression 0.00e+00 0.00e+00 negative regulation of translation 0.00e+00 0.00e+00 ribonucleoprotein granule 0.00e+00 0.00e+00 tRNA-splicing ligase complex 0.00e+00 0.00e+00 double-stranded RNA binding 1.61e-10 1.31e-07 gene silencing by miRNA 2.23e-10 1.79e-07 posttranscriptional gene silencing by RNA 2.26e-10 1.11e-07 cytoplasmic ribonucleoprotein granule 2.92e-10 1.41e-07 intracellular ribonucleoprotein complex 2.98e-10 2.36e-07 posttranscriptional gene silencing 3.03e-10 1.46e-07 ribonucleoprotein complex 3.13e-10 2.47e-07 tRNA splicing, via endonucleolytic cleavage and ligation 2.74e-09 1.93e-06 gene silencing by RNA 8.47e-08 4.85e-05 gene silencing 1.13e-06 3.29e-04 CRD-mediated mRNA stability complex 1.16e-06 3.64e-04 translation regulator activity 1.74e-06 5.28e-04 mRNA 5'-UTR binding 2.15e-06 6.41e-04 mRNA binding 2.47e-06 1.09e-03 miRNA mediated inhibition of translation

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 PRE NOTCH TRANSCRIPTION AND TRANSLATION 0.00e+00 0.00e+00 REGULATORY RNA PATHWAYS 0.00e+00 0.00e+00 PRE NOTCH EXPRESSION AND PROCESSING 0.00e+00 0.00e+00 PRE NOTCH TRANSCRIPTION AND TRANSLATION 0.00e+00 0.00e+00 REGULATORY RNA PATHWAYS 0.00e+00 0.00e+00 PRE NOTCH EXPRESSION AND PROCESSING 7.41e-11 2.72e-08 SIGNALING BY NOTCH 1.65e-10 4.42e-08 SIGNALING BY NOTCH 2.55e-10 6.66e-08 MICRORNA MIRNA BIOGENESIS 6.15e-10 2.07e-07 MICRORNA MIRNA BIOGENESIS 6.37e-04 7.93e-02 DIABETES PATHWAYS 2.38e-03 2.17e-01 DIABETES PATHWAYS 1.92e-02 1.00e+00 LATE PHASE OF HIV LIFE CYCLE 2.10e-02 1.00e+00 HIV LIFE CYCLE 2.58e-02 1.00e+00 INTRINSIC PATHWAY FOR APOPTOSIS 3.34e-02 1.00e+00 HIV INFECTION 4.73e-02 1.00e+00 MRNA DECAY BY 5 TO 3 EXORIBONUCLEASE

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

²FDR corrected p-value (Benjamini-Hochberg)

Mouse mutant phenotypes

P-value1 FDR2 Term 2.00e-03 1e+00 abnormal seminiferous tubule epithelium morphology 5.61e-03 1e+00 everted embryonic neuroepithelium 5.62e-03 1e+00 abnormal insulin-like growth factor I level 5.63e-03 1e+00 turbinate hypoplasia 5.63e-03 1e+00 abnormal intestinal smooth muscle morphology 7.39e-03 1e+00 abnormal spermiogenesis 7.50e-03 1e+00 decreased hematopoietic cell number 7.50e-03 1e+00 abnormal small intestinal microvillus morphology 7.50e-03 1e+00 increased aggression 7.50e-03 1e+00 premature neuronal precursor differentiation 7.52e-03 1e+00 abnormal liver lobule morphology 1.03e-02 1e+00 small testis 1.05e-02 1e+00 short snout 1.12e-02 1e+00 abnormal mean corpuscular hemoglobin 1.24e-02 1e+00 decreased brain size 1.31e-02 1e+00 decreased length of allograft survival 1.47e-02 1e+00 decreased small intestinal villus size 1.50e-02 1e+00 abnormal mandibular coronoid process morphology 1.68e-02 1e+00 delayed intestine development 1.86e-02 1e+00 abnormal AMPA-mediated synaptic currents

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

²FDR corrected p-value (Benjamini-Hochberg)