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DREAM Module Identification Challenge – Consensus modules

PPI-STRING_Consensus_mod194

Assigned name NA Network PPI-STRING Module ID PPI-STRING_Consensus_mod194 Module size 76 genes

Module genes

This module comprises the following genes:

Gene ID Gene Symbol Gene Name 22985 ACIN1 apoptotic chromatin condensation inducer 1 8227 AKAP17A A-kinase anchoring protein 17A 85016 C11orf70 cilia and flagella associated protein 300 29105 C16orf80 cilia and flagella associated protein 20 79002 C19orf43 telomerase RNA component interacting RNase 389203 C4orf52 small integral membrane protein 20 100499483 C9orf174 coiled-coil domain containing 180 26093 CCDC9 coiled-coil domain containing 9 90324 CCDC97 coiled-coil domain containing 97 201134 CEP112 centrosomal protein 112 11052 CPSF6 cleavage and polyadenylation specific factor 6 9993 DGCR2 DiGeorge syndrome critical region gene 2 9343 EFTUD2 elongation factor Tu GTP binding domain containing 2 84691 FAM71F1 family with sequence similarity 71 member F1 8880 FUBP1 far upstream element binding protein 1 155038 GIMAP8 GTPase, IMAP family member 8 63906 GPATCH3 G-patch domain containing 3 83550 GPR101 G protein-coupled receptor 101 3188 HNRNPH2 heterogeneous nuclear ribonucleoprotein H2 3189 HNRNPH3 heterogeneous nuclear ribonucleoprotein H3 9987 HNRPDL heterogeneous nuclear ribonucleoprotein D like 92906 HNRPLL heterogeneous nuclear ribonucleoprotein L like 27336 HTATSF1 HIV-1 Tat specific factor 1 25962 KIAA1429 vir like m6A methyltransferase associated 4116 MAGOH mago homolog, exon junction complex subunit 9782 MATR3 matrin 3 4154 MBNL1 muscleblind like splicing regulator 1 4809 NHP2L1 small nuclear ribonucleoprotein 13 4841 NONO non-POU domain containing octamer binding 4857 NOVA1 NOVA alternative splicing regulator 1 4858 NOVA2 NOVA alternative splicing regulator 2 56146 PCDHA2 protocadherin alpha 2 114770 PGLYRP2 peptidoglycan recognition protein 2 10084 PQBP1 polyglutamine binding protein 1 8899 PRPF4B pre-mRNA processing factor 4B 163154 PRR22 proline rich 22 58155 PTBP2 polypyrimidine tract binding protein 2 9991 PTBP3 polypyrimidine tract binding protein 3 22827 PUF60 poly(U) binding splicing factor 60 55225 RAVER2 ribonucleoprotein, PTB binding 2 23543 RBFOX2 RNA binding fox-1 homolog 2 8241 RBM10 RNA binding motif protein 10 5936 RBM4 RNA binding motif protein 4 55285 RBM41 RNA binding motif protein 41 166863 RBM46 RNA binding motif protein 46 54502 RBM47 RNA binding motif protein 47 83759 RBM4B RNA binding motif protein 4B 494115 RBMXL1 RBMX like 1 80196 RNF34 ring finger protein 34 6100 RP9 RP9, pre-mRNA splicing factor 6280 S100A9 S100 calcium binding protein A9 6294 SAFB scaffold attachment factor B 9667 SAFB2 scaffold attachment factor B2 58506 SCAF1 SR-related CTD associated factor 1 9169 SCAF11 SR-related CTD associated factor 11 6421 SFPQ splicing factor proline and glutamine rich 79811 SLTM SAFB like transcription modulator 10285 SMNDC1 survival motor neuron domain containing 1 55234 SMU1 SMU1, DNA replication regulator and spliceosomal factor 6651 SON SON DNA binding protein 54558 SPATA6 spermatogenesis associated 6 54466 SPIN2A spindlin family member 2A 140890 SREK1 splicing regulatory glutamic acid and lysine rich protein 1 23435 TARDBP TAR DNA binding protein 10915 TCERG1 transcription elongation regulator 1 374395 TMEM179B transmembrane protein 179B 6434 TRA2B transformer 2 beta homolog 79054 TRPM8 transient receptor potential cation channel subfamily M member 8 60385 TSKS testis specific serine kinase substrate 11338 U2AF2 U2 small nuclear RNA auxiliary factor 2 10713 USP39 ubiquitin specific peptidase 39 51729 WBP11 WW domain binding protein 11 11193 WBP4 WW domain binding protein 4 91746 YTHDC1 YTH domain containing 1 54439 ZC3H18 RNA binding motif protein 27 284695 ZNF326 zinc finger protein 326

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 8.18e-02 2.66e-35 GO RNA splicing biological_process 6.40e-02 7.14e-07 GO activation of innate immune response biological_process 6.03e-02 9.63e-06 GO regulation of mRNA processing biological_process 3.62e-02 1.18e-09 GO regulation of RNA splicing biological_process 2.26e-02 2.94e-27 GO mRNA processing biological_process 1.42e-02 9.92e-13 GO regulation of alternative mRNA splicing, via spliceosome biological_process 1.12e-02 2.58e-14 GO spliceosomal complex cellular_component 6.86e-03 4.54e-04 GO regulation of DNA-templated transcription, elongation 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 0.00e+00 0.00e+00 RNA splicing, via transesterification reactions 0.00e+00 0.00e+00 RNA splicing 0.00e+00 0.00e+00 mRNA metabolic process 0.00e+00 0.00e+00 mRNA processing 0.00e+00 0.00e+00 mRNA splicing, via spliceosome 0.00e+00 0.00e+00 regulation of RNA splicing 0.00e+00 0.00e+00 regulation of mRNA processing 0.00e+00 0.00e+00 regulation of mRNA splicing, via spliceosome 0.00e+00 0.00e+00 spliceosomal complex 0.00e+00 0.00e+00 nuclear body 4.60e-21 2.73e-18 nuclear speck 4.29e-14 2.52e-11 intracellular ribonucleoprotein complex 4.37e-14 2.56e-11 ribonucleoprotein complex 2.62e-09 1.85e-06 regulation of alternative mRNA splicing, via spliceosome 1.15e-08 5.19e-06 pre-mRNA binding 9.36e-07 4.48e-04 negative regulation of RNA splicing 1.91e-06 5.74e-04 mRNA binding 4.08e-06 1.07e-03 paraspeckles 2.71e-05 9.39e-03 spliceosomal complex assembly 5.62e-05 1.25e-02 pre-mRNA intronic binding

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

²FDR corrected p-value (Benjamini-Hochberg)

Reactome

P-value1 FDR2 Term 4.50e-07 1.06e-04 MRNA SPLICING 5.25e-07 1.23e-04 PROCESSING OF CAPPED INTRON CONTAINING PRE MRNA 7.11e-07 1.26e-04 MRNA SPLICING 9.22e-07 2.09e-04 MRNA PROCESSING 2.16e-06 3.57e-04 PROCESSING OF CAPPED INTRON CONTAINING PRE MRNA 3.44e-06 5.52e-04 MRNA PROCESSING 5.64e-04 7.16e-02 TRANSPORT OF MATURE TRANSCRIPT TO CYTOPLASM 9.64e-04 1.14e-01 MRNA 3 END PROCESSING 1.36e-03 1.53e-01 CLEAVAGE OF GROWING TRANSCRIPT IN THE TERMINATION REGION 1.47e-03 1.42e-01 MRNA 3 END PROCESSING 1.61e-03 1.78e-01 MRNA SPLICING MINOR PATHWAY 2.05e-03 1.90e-01 CLEAVAGE OF GROWING TRANSCRIPT IN THE TERMINATION REGION 3.84e-03 3.28e-01 TRANSPORT OF MATURE TRANSCRIPT TO CYTOPLASM 4.01e-03 3.81e-01 RNA POL II TRANSCRIPTION 4.84e-03 4.00e-01 MRNA SPLICING MINOR PATHWAY 1.22e-02 8.65e-01 RNA POL II TRANSCRIPTION 2.04e-02 1.00e+00 SIGNALING BY FGFR1 MUTANTS 2.04e-02 1.00e+00 SIGNALING BY FGFR1 FUSION MUTANTS 2.38e-02 1.00e+00 SIGNALING BY FGFR MUTANTS 3.10e-02 1.00e+00 TRANSCRIPTION

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

²FDR corrected p-value (Benjamini-Hochberg)

Mouse mutant phenotypes

P-value1 FDR2 Term 3.56e-04 4.95e-01 decreased susceptibility to bacterial infection induced morbidity/mortality 1.24e-03 1.00e+00 small pancreatic islets 1.82e-03 1.00e+00 abnormal circadian rhythm 3.79e-03 1.00e+00 hyperglycemia 5.61e-03 1.00e+00 abnormal branching involved in seminal vesicle morphogenesis 8.93e-03 1.00e+00 decreased fetal size 9.34e-03 1.00e+00 increased circulating VLDL triglyceride level 9.34e-03 1.00e+00 abnormal thermosensation 9.34e-03 1.00e+00 premature neuronal precursor differentiation 9.35e-03 1.00e+00 small thoracic cage 1.12e-02 1.00e+00 abnormal muscle tone 1.12e-02 1.00e+00 ovary atrophy 1.12e-02 1.00e+00 abnormal cortical ventricular zone morphology 1.13e-02 1.00e+00 Sertoli cell hyperplasia 1.13e-02 1.00e+00 delayed cellular replicative senescence 1.31e-02 1.00e+00 reduced male mating frequency 1.31e-02 1.00e+00 abnormal neutrophil morphology 1.41e-02 1.00e+00 decreased survivor rate 1.44e-02 1.00e+00 complete lethality 1.49e-02 1.00e+00 abnormal gut flora balance

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

²FDR corrected p-value (Benjamini-Hochberg)