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DREAM Module Identification Challenge – Consensus modules

PPI-STRING_Consensus_mod6

Assigned name NA Network PPI-STRING Module ID PPI-STRING_Consensus_mod6 Module size 55 genes

Module genes

This module comprises the following genes:

Gene ID Gene Symbol Gene Name 55129 ANO10 anoctamin 10 57719 ANO8 anoctamin 8 9716 AQR aquarius intron-binding spliceosomal factor 66037 BOLL boule homolog, RNA binding protein 84811 BUD13 BUD13 homolog 79169 C1orf35 chromosome 1 open reading frame 35 1153 CIRBP cold inducible RNA binding protein 57396 CLK4 CDC like kinase 4 55280 CWF19L1 CWF19 like cell cycle control factor 1 143884 CWF19L2 CWF19 like cell cycle control factor 2 1617 DAZ1 deleted in azoospermia 1 57055 DAZ2 deleted in azoospermia 2 57054 DAZ3 deleted in azoospermia 3 57135 DAZ4 deleted in azoospermia 4 26528 DAZAP1 DAZ associated protein 1 1618 DAZL deleted in azoospermia like 8220 DGCR14 ess-2 splicing factor homolog 7458 EIF4H eukaryotic translation initiation factor 4H 55094 GPATCH1 G-patch domain containing 1 144983 HNRNPA1L2 heterogeneous nuclear ribonucleoprotein A1-like 2 3182 HNRNPAB heterogeneous nuclear ribonucleoprotein A/B 343069 HNRNPCL1 heterogeneous nuclear ribonucleoprotein C-like 1 202559 KHDRBS2 KH RNA binding domain containing, signal transduction associated 2 10656 KHDRBS3 KH RNA binding domain containing, signal transduction associated 3 221496 LEMD2 LEM domain containing 2 23592 LEMD3 LEM domain containing 3 124801 LSM12 LSM12 homolog 55692 LUC7L LUC7 like 51631 LUC7L2 LUC7 like 2, pre-mRNA splicing factor 51747 LUC7L3 LUC7 like 3 pre-mRNA splicing factor 4440 MSI1 musashi RNA binding protein 1 124540 MSI2 musashi RNA binding protein 2 392517 NCBP2L nuclear cap binding protein subunit 2 like 55660 PRPF40A pre-mRNA processing factor 40 homolog A 22913 RALY RALY heterogeneous nuclear ribonucleoprotein 138046 RALYL RALY RNA binding protein like 146713 RBFOX3 RNA binding fox-1 homolog 3 221662 RBM24 RNA binding motif protein 24 5935 RBM3 RNA binding motif protein 3 55544 RBM38 RNA binding motif protein 38 51634 RBMX2 RNA binding motif protein X-linked 2 139804 RBMXL3 RBMX like 3 7737 RNF113A ring finger protein 113A 140432 RNF113B ring finger protein 113B 55599 RNPC3 RNA binding region (RNP1, RRM) containing 3 7536 SF1 splicing factor 1 10262 SF3B4 splicing factor 3b subunit 4 81892 SLIRP SRA stem-loop interacting RNA binding protein 10569 SLU7 SLU7 homolog, splicing factor 11066 SNRNP35 small nuclear ribonucleoprotein U11/U12 subunit 35 26576 SRPK3 SRSF protein kinase 3 23524 SRRM2 serine/arginine repetitive matrix 2 10772 SRSF10 serine and arginine rich splicing factor 10 135295 SRSF12 serine and arginine rich splicing factor 12 54952 TRNAU1AP tRNA selenocysteine 1 associated protein 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 2.23e-01 3.87e-13 GO translation activator activity molecular_function 9.41e-02 5.49e-08 GO U2-type prespliceosome cellular_component 9.26e-02 6.68e-05 Reactome PTK6 Regulates Proteins Involved in RNA Processing Signal Transduction 9.08e-02 6.05e-12 GO positive regulation of translational initiation biological_process 8.08e-02 1.40e-04 Reactome Clearance of Nuclear Envelope Membranes from Chromatin Cell Cycle 6.30e-02 8.25e-11 GO poly(U) RNA binding molecular_function 4.26e-02 2.38e-07 GO positive regulation of mRNA splicing, via spliceosome biological_process 3.97e-02 1.93e-07 GO mRNA splice site selection biological_process 3.68e-02 4.72e-06 GO regulation of mRNA splicing, via spliceosome biological_process 3.07e-02 5.39e-17 GO mRNA 3'-UTR binding molecular_function 2.68e-02 1.55e-07 GO U1 snRNP cellular_component 1.77e-02 2.40e-10 GO germ cell development biological_process 1.18e-02 1.64e-13 GO mRNA binding molecular_function 8.25e-03 2.39e-04 GO small ribosomal subunit rRNA binding molecular_function 4.86e-03 1.22e-13 GO ribonucleoprotein complex cellular_component 3.89e-03 4.36e-04 GO spliceosomal tri-snRNP complex assembly biological_process 1.41e-03 3.71e-05 GO RNA splicing, via transesterification reactions 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 intracellular ribonucleoprotein complex 0.00e+00 0.00e+00 spliceosomal complex 0.00e+00 0.00e+00 ribonucleoprotein complex 0.00e+00 0.00e+00 U2-type spliceosomal complex 1.90e-12 1.75e-09 mRNA splice site selection 7.50e-12 6.78e-09 spliceosomal complex assembly 2.57e-11 2.26e-08 regulation of RNA splicing 5.32e-11 4.54e-08 ribonucleoprotein complex assembly 2.15e-10 1.73e-07 regulation of mRNA processing 5.51e-10 3.05e-07 mRNA binding 2.74e-09 1.93e-06 regulation of mRNA splicing, via spliceosome 2.90e-08 1.08e-05 small nuclear ribonucleoprotein complex 4.03e-08 1.48e-05 U2-type prespliceosome 5.81e-08 2.08e-05 catalytic step 2 spliceosome 6.30e-08 2.23e-05 prespliceosome

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

²FDR corrected p-value (Benjamini-Hochberg)

Reactome

P-value1 FDR2 Term 2.74e-03 2.78e-01 ACTIVATION OF THE MRNA UPON BINDING OF THE CAP BINDING COMPLEX AND EIFS AND SUBSEQUENT BINDING TO 43S 2.75e-03 2.79e-01 3 UTR MEDIATED TRANSLATIONAL REGULATION 2.08e-02 1.00e+00 MRNA SPLICING MINOR PATHWAY 2.13e-02 1.00e+00 MRNA SPLICING MINOR PATHWAY 2.19e-02 1.00e+00 TRANSLATION 2.33e-02 1.00e+00 ACTIVATION OF THE MRNA UPON BINDING OF THE CAP BINDING COMPLEX AND EIFS AND SUBSEQUENT BINDING TO 43S 2.35e-02 1.00e+00 3 UTR MEDIATED TRANSLATIONAL REGULATION 3.00e-02 1.00e+00 TRANSLATION 4.14e-02 1.00e+00 MRNA SPLICING 4.16e-02 1.00e+00 PROCESSING OF CAPPED INTRON CONTAINING PRE MRNA 4.86e-02 1.00e+00 MRNA SPLICING

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

²FDR corrected p-value (Benjamini-Hochberg)

Mouse mutant phenotypes

P-value1 FDR2 Term 5.21e-04 6.2e-01 decreased leukocyte cell number 3.13e-03 1.0e+00 small cerebellum 3.74e-03 1.0e+00 decreased DN3 thymocyte number 3.74e-03 1.0e+00 abnormal cranium size 5.18e-03 1.0e+00 thin myocardium 6.08e-03 1.0e+00 pale yolk sac 6.86e-03 1.0e+00 arrest of spermatogenesis 6.86e-03 1.0e+00 decreased fibroblast proliferation 7.47e-03 1.0e+00 decreased DN2 thymocyte number 7.48e-03 1.0e+00 absent embryonic telencephalon 7.48e-03 1.0e+00 decreased cranium width 9.33e-03 1.0e+00 abnormal ependyma morphology 1.12e-02 1.0e+00 dilated heart right atrium 1.26e-02 1.0e+00 abnormal cell cycle 1.30e-02 1.0e+00 impaired neuron differentiation 1.30e-02 1.0e+00 decreased embryonic neuroepithelial cell proliferation 1.31e-02 1.0e+00 decreased double-negative T cell number 1.49e-02 1.0e+00 abnormal common lymphocyte progenitor cell morphology 1.49e-02 1.0e+00 abnormal mesenchyme morphology 1.67e-02 1.0e+00 small pharyngeal arch

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

²FDR corrected p-value (Benjamini-Hochberg)