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DREAM Module Identification Challenge – Consensus modules

PPI-STRING_Consensus_mod99

Assigned name NA Network PPI-STRING Module ID PPI-STRING_Consensus_mod99 Module size 39 genes

Module genes

This module comprises the following genes:

Gene ID Gene Symbol Gene Name 8086 AAAS aladin WD repeat nucleoporin 11183 GCKR mitogen-activated protein kinase kinase kinase kinase 5 8487 GEMIN2 gem nuclear organelle associated protein 2 50628 GEMIN4 gem nuclear organelle associated protein 4 25929 GEMIN5 gem nuclear organelle associated protein 5 79833 GEMIN6 gem nuclear organelle associated protein 6 79760 GEMIN7 gem nuclear organelle associated protein 7 54960 GEMIN8 gem nuclear organelle associated protein 8 500697 GLE1 similar to GLE1-like, RNA export mediator isoform 1 57727 NCOA5 nuclear receptor coactivator 5 91754 NEK9 NIMA related kinase 9 9972 NUP153 nucleoporin 153 9631 NUP155 nucleoporin 155 23511 NUP188 nucleoporin 188 23165 NUP205 nucleoporin 205 23225 NUP210 nucleoporin 210 8021 NUP214 nucleoporin 214 129401 NUP35 nucleoporin 35 25497 NUP50 nucleoporin 50 53371 NUP54 nucleoporin 54 23636 NUP62 nucleoporin 62 4927 NUP88 nucleoporin 88 9688 NUP93 nucleoporin 93 4928 NUP98 nucleoporin 98 9818 NUPL1 nucleoporin 58 11097 NUPL2 nucleoporin like 2 10482 NXF1 nuclear RNA export factor 1 56001 NXF2 nuclear RNA export factor 2 728343 NXF2B nuclear RNA export factor 2B 56000 NXF3 nuclear RNA export factor 3 55998 NXF5 nuclear RNA export factor 5 29107 NXT1 nuclear transport factor 2 like export factor 1 55916 NXT2 nuclear transport factor 2 like export factor 2 51808 PHAX phosphorylated adaptor for RNA export 8480 RAE1 ribonucleic acid export 1 126638 RPTN repetin 7884 SLBP stem-loop binding protein 10073 SNUPN snurportin 1 7175 TPR translocated promoter region, nuclear basket protein

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 2.67e-01 1.37e-42 Reactome Regulation of Glucokinase by Glucokinase Regulatory Protein Metabolism 1.84e-01 2.99e-14 GO Gemini of coiled bodies cellular_component 1.76e-01 5.14e-13 GO poly(A)+ mRNA export from nucleus biological_process 1.17e-01 3.01e-41 Reactome Nuclear Pore Complex (NPC) Disassembly Cell Cycle 1.15e-01 5.97e-14 GO SMN complex cellular_component 9.70e-02 4.00e-16 GO nuclear pore central transport channel cellular_component 5.65e-02 9.87e-17 Reactome Metabolism of non-coding RNA Metabolism of RNA 5.65e-02 9.87e-17 Reactome snRNP Assembly Metabolism of RNA 3.59e-02 2.97e-46 GO mRNA export from nucleus biological_process 2.44e-02 1.44e-09 GO nucleocytoplasmic transport biological_process 1.70e-02 1.34e-14 GO import into nucleus biological_process 1.48e-02 6.74e-05 Reactome Transport of the SLBP Dependant Mature mRNA Metabolism of RNA 1.36e-02 1.33e-38 Reactome Viral Messenger RNA Synthesis Disease 1.33e-02 1.33e-38 Reactome SUMOylation of SUMOylation proteins Metabolism of proteins 1.24e-02 3.52e-24 GO protein import into nucleus biological_process 1.21e-02 6.63e-39 Reactome Nuclear import of Rev protein Disease 6.11e-03 2.66e-31 GO nuclear pore cellular_component 4.65e-03 1.33e-38 Reactome Rev-mediated nuclear export of HIV RNA Disease

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 protein export from nucleus 0e+00 0e+00 RNA localization 0e+00 0e+00 mRNA export from nucleus 0e+00 0e+00 nuclear transport 0e+00 0e+00 nucleocytoplasmic transport 0e+00 0e+00 RNA export from nucleus 0e+00 0e+00 nuclear export 0e+00 0e+00 ribonucleoprotein complex localization 0e+00 0e+00 RNA transport 0e+00 0e+00 mRNA transport 0e+00 0e+00 ribonucleoprotein complex export from nucleus 0e+00 0e+00 nucleobase-containing compound transport 0e+00 0e+00 single-organism nuclear import 0e+00 0e+00 mitotic cell cycle process 0e+00 0e+00 protein sumoylation 0e+00 0e+00 regulation of cellular response to stress 0e+00 0e+00 nuclear import 0e+00 0e+00 viral transcription 0e+00 0e+00 nuclear envelope organization 0e+00 0e+00 intracellular transport of virus

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

²FDR corrected p-value (Benjamini-Hochberg)

Reactome

P-value1 FDR2 Term 0e+00 0e+00 PROCESSING OF CAPPED INTRON CONTAINING PRE MRNA 0e+00 0e+00 MRNA PROCESSING 0e+00 0e+00 TRANSPORT OF MATURE TRANSCRIPT TO CYTOPLASM 0e+00 0e+00 METABOLISM OF NON CODING RNA 0e+00 0e+00 SLC MEDIATED TRANSMEMBRANE TRANSPORT 0e+00 0e+00 REGULATION OF GLUCOKINASE BY GLUCOKINASE REGULATORY PROTEIN 0e+00 0e+00 INTERACTIONS OF VPR WITH HOST CELLULAR PROTEINS 0e+00 0e+00 METABOLISM OF CARBOHYDRATES 0e+00 0e+00 NEP NS2 INTERACTS WITH THE CELLULAR EXPORT MACHINERY 0e+00 0e+00 GLUCOSE TRANSPORT 0e+00 0e+00 ANTIVIRAL MECHANISM BY IFN STIMULATED GENES 0e+00 0e+00 TRANSMEMBRANE TRANSPORT OF SMALL MOLECULES 0e+00 0e+00 INFLUENZA LIFE CYCLE 0e+00 0e+00 TRANSPORT OF MATURE MRNA DERIVED FROM AN INTRONLESS TRANSCRIPT 0e+00 0e+00 HIV LIFE CYCLE 0e+00 0e+00 LATE PHASE OF HIV LIFE CYCLE 0e+00 0e+00 METABOLISM OF RNA 0e+00 0e+00 INTERFERON SIGNALING 0e+00 0e+00 HOST INTERACTIONS OF HIV FACTORS 0e+00 0e+00 TRANSPORT OF RIBONUCLEOPROTEINS INTO THE HOST NUCLEUS

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

²FDR corrected p-value (Benjamini-Hochberg)

Mouse mutant phenotypes

P-value1 FDR2 Term 1.25e-04 2.61e-01 early reproductive senescence 3.87e-04 5.22e-01 abnormal spermatogonia proliferation 8.14e-04 7.99e-01 abnormal spermatogonia morphology 3.42e-03 1.00e+00 small seminiferous tubules 3.63e-03 1.00e+00 abnormal male meiosis 3.74e-03 1.00e+00 abnormal MHC II cell surface expression on macrophages 3.78e-03 1.00e+00 abnormal blastocoele morphology 5.00e-03 1.00e+00 decreased male germ cell number 5.61e-03 1.00e+00 abnormal RR interval 6.30e-03 1.00e+00 insulin resistance 6.44e-03 1.00e+00 arrest of male meiosis 1.02e-02 1.00e+00 complete perinatal lethality 1.12e-02 1.00e+00 atrial fibrillation 1.31e-02 1.00e+00 decreased pancreatic islet number 1.31e-02 1.00e+00 abnormal level of surface class II molecules 1.42e-02 1.00e+00 abnormal male germ cell apoptosis 1.48e-02 1.00e+00 complete embryonic lethality between implantation and somite formation 1.67e-02 1.00e+00 increased fasted circulating glucose level 1.86e-02 1.00e+00 increased hepatocyte proliferation 1.87e-02 1.00e+00 kinked neural tube

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

²FDR corrected p-value (Benjamini-Hochberg)