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DREAM Module Identification Challenge – Consensus modules

PPI-STRING_Consensus_mod91

Assigned name NA Network PPI-STRING Module ID PPI-STRING_Consensus_mod91 Module size 79 genes

Module genes

This module comprises the following genes:

Gene ID Gene Symbol Gene Name 10189 ALYREF Aly/REF export factor 55749 CCAR1 cell division cycle and apoptosis regulator 1 10421 CD2BP2 CD2 cytoplasmic tail binding protein 2 51362 CDC40 cell division cycle 40 10614 CLP1 hexamethylene bisacetamide inducible 1 53981 CPSF2 cleavage and polyadenylation specific factor 2 51692 CPSF3 cleavage and polyadenylation specific factor 3 79869 CPSF7 cleavage and polyadenylation specific factor 7 1477 CSTF1 cleavage stimulation factor subunit 1 1478 CSTF2 cleavage stimulation factor subunit 2 1479 CSTF3 cleavage stimulation factor subunit 3 9416 DDX23 DEAD-box helicase 23 9785 DHX38 DEAH-box helicase 38 1660 DHX9 DExH-box helicase 9 22826 DNAJC8 DnaJ heat shock protein family (Hsp40) member C8 2521 FUS FUS RNA binding protein 10949 HNRNPA0 heterogeneous nuclear ribonucleoprotein A0 3178 HNRNPA1 heterogeneous nuclear ribonucleoprotein A1 3181 HNRNPA2B1 heterogeneous nuclear ribonucleoprotein A2/B1 220988 HNRNPA3 heterogeneous nuclear ribonucleoprotein A3 3183 HNRNPC heterogeneous nuclear ribonucleoprotein C (C1/C2) 3184 HNRNPD heterogeneous nuclear ribonucleoprotein D 3185 HNRNPF heterogeneous nuclear ribonucleoprotein F 3187 HNRNPH1 heterogeneous nuclear ribonucleoprotein H1 3190 HNRNPK heterogeneous nuclear ribonucleoprotein K 3191 HNRNPL heterogeneous nuclear ribonucleoprotein L 4670 HNRNPM heterogeneous nuclear ribonucleoprotein M 10236 HNRNPR heterogeneous nuclear ribonucleoprotein R 3192 HNRNPU heterogeneous nuclear ribonucleoprotein U 11100 HNRNPUL1 heterogeneous nuclear ribonucleoprotein U like 1 4799 NFX1 nuclear transcription factor, X-box binding 1 11051 NUDT21 nudix hydrolase 21 8106 PABPN1 poly(A) binding protein nuclear 1 10914 PAPOLA poly(A) polymerase alpha 5093 PCBP1 poly(rC) binding protein 1 5094 PCBP2 poly(rC) binding protein 2 51585 PCF11 PCF11, cleavage and polyadenylation factor subunit 84844 PHF5A PHD finger protein 5A 9128 PRPF4 pre-mRNA processing factor 4 24148 PRPF6 pre-mRNA processing factor 6 10594 PRPF8 pre-mRNA processing factor 8 5725 PTBP1 polypyrimidine tract binding protein 1 10181 RBM5 RNA binding motif protein 5 27316 RBMX RNA binding motif protein X-linked 10921 RNPS1 RNA binding protein with serine rich domain 1 10291 SF3A1 splicing factor 3a subunit 1 8175 SF3A2 splicing factor 3a subunit 2 10946 SF3A3 splicing factor 3a subunit 3 23451 SF3B1 splicing factor 3b subunit 1 10992 SF3B2 splicing factor 3b subunit 2 23450 SF3B3 splicing factor 3b subunit 3 83443 SF3B5 splicing factor 3b subunit 5 23020 SNRNP200 small nuclear ribonucleoprotein U5 subunit 200 9410 SNRNP40 small nuclear ribonucleoprotein U5 subunit 40 6625 SNRNP70 small nuclear ribonucleoprotein U1 subunit 70 6626 SNRPA small nuclear ribonucleoprotein polypeptide A 6627 SNRPA1 small nuclear ribonucleoprotein polypeptide A' 6628 SNRPB small nuclear ribonucleoprotein polypeptides B and B1 6629 SNRPB2 small nuclear ribonucleoprotein polypeptide B2 6632 SNRPD1 small nuclear ribonucleoprotein D1 polypeptide 6633 SNRPD2 small nuclear ribonucleoprotein D2 polypeptide 6634 SNRPD3 small nuclear ribonucleoprotein D3 polypeptide 6635 SNRPE small nuclear ribonucleoprotein polypeptide E 6637 SNRPG small nuclear ribonucleoprotein polypeptide G 10250 SRRM1 serine and arginine repetitive matrix 1 6426 SRSF1 serine and arginine rich splicing factor 1 9295 SRSF11 serine and arginine rich splicing factor 11 6427 SRSF2 serine and arginine rich splicing factor 2 6428 SRSF3 serine and arginine rich splicing factor 3 6429 SRSF4 serine and arginine rich splicing factor 4 6430 SRSF5 serine and arginine rich splicing factor 5 6431 SRSF6 serine and arginine rich splicing factor 6 6432 SRSF7 serine and arginine rich splicing factor 7 8683 SRSF9 serine and arginine rich splicing factor 9 57794 SUGP1 SURP and G-patch domain containing 1 10907 TXNL4A thioredoxin like 4A 7307 U2AF1 U2 small nuclear RNA auxiliary factor 1 65109 UPF3B UPF3B, regulator of nonsense mediated mRNA decay 4904 YBX1 Y-box binding 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 2.62e-01 3.42e-28 GO U5 snRNP cellular_component 2.07e-01 5.26e-162 Reactome mRNA Splicing - Major Pathway Metabolism of RNA 1.64e-01 4.44e-28 GO U2 snRNP cellular_component 1.39e-01 6.17e-09 GO mRNA cleavage factor complex cellular_component 1.28e-01 2.91e-29 GO RNA metabolic process biological_process 9.30e-02 1.81e-50 GO mRNA 3'-end processing biological_process 8.86e-02 2.17e-159 Reactome mRNA Splicing Metabolism of RNA 8.27e-02 9.28e-17 GO negative regulation of mRNA splicing, via spliceosome biological_process 4.06e-02 1.36e-17 GO U2-type precatalytic spliceosome cellular_component 2.73e-02 6.61e-50 Reactome mRNA 3'-end processing Metabolism of RNA 2.50e-02 3.99e-20 GO RNA splicing, via transesterification reactions biological_process 2.36e-02 1.19e-15 GO RNA processing biological_process 2.19e-02 2.25e-57 Reactome Cleavage of Growing Transcript in the Termination Region Gene expression (Transcription) 2.17e-02 2.25e-57 Reactome RNA Polymerase II Transcription Termination Gene expression (Transcription) 1.81e-02 5.92e-65 GO catalytic step 2 spliceosome cellular_component 1.33e-02 1.68e-22 GO regulation of alternative mRNA splicing, via spliceosome 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 0e+00 0e+00 RNA splicing 0e+00 0e+00 mRNA processing 0e+00 0e+00 mRNA splicing, via spliceosome 0e+00 0e+00 RNA splicing, via transesterification reactions 0e+00 0e+00 mRNA metabolic process 0e+00 0e+00 negative regulation of mRNA splicing, via spliceosome 0e+00 0e+00 negative regulation of RNA splicing 0e+00 0e+00 spliceosomal snRNP assembly 0e+00 0e+00 U12-type spliceosomal complex 0e+00 0e+00 intracellular ribonucleoprotein complex 0e+00 0e+00 spliceosomal complex 0e+00 0e+00 ribonucleoprotein complex 0e+00 0e+00 spliceosomal snRNP complex 0e+00 0e+00 small nuclear ribonucleoprotein complex 0e+00 0e+00 U1 snRNP 0e+00 0e+00 U2 snRNP 0e+00 0e+00 catalytic step 2 spliceosome 0e+00 0e+00 U5 snRNP 0e+00 0e+00 precatalytic spliceosome 0e+00 0e+00 spliceosomal tri-snRNP complex

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 PROCESSING OF CAPPED INTRON CONTAINING PRE MRNA 0.00e+00 0.00e+00 MRNA SPLICING 0.00e+00 0.00e+00 MRNA PROCESSING 0.00e+00 0.00e+00 PROCESSING OF INTRONLESS PRE MRNAS 0.00e+00 0.00e+00 PROCESSING OF CAPPED INTRON CONTAINING PRE MRNA 0.00e+00 0.00e+00 MRNA SPLICING 0.00e+00 0.00e+00 MRNA PROCESSING 0.00e+00 0.00e+00 PROCESSING OF INTRONLESS PRE MRNAS 3.32e-43 1.33e-40 CLEAVAGE OF GROWING TRANSCRIPT IN THE TERMINATION REGION 4.77e-41 1.43e-38 CLEAVAGE OF GROWING TRANSCRIPT IN THE TERMINATION REGION 1.59e-37 6.38e-35 MRNA 3 END PROCESSING 3.23e-36 9.66e-34 MRNA 3 END PROCESSING 1.29e-31 5.16e-29 RNA POL II TRANSCRIPTION 1.32e-28 5.27e-26 MRNA SPLICING MINOR PATHWAY 4.15e-26 1.24e-23 RNA POL II TRANSCRIPTION 1.94e-25 5.78e-23 MRNA SPLICING MINOR PATHWAY 3.53e-22 1.41e-19 TRANSCRIPTION 2.54e-21 1.01e-18 TRANSPORT OF MATURE TRANSCRIPT TO CYTOPLASM 1.34e-20 5.32e-18 PROCESSING OF CAPPED INTRONLESS PRE MRNA 1.41e-19 4.20e-17 PROCESSING OF CAPPED INTRONLESS PRE MRNA

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

²FDR corrected p-value (Benjamini-Hochberg)

Mouse mutant phenotypes

P-value1 FDR2 Term 1.85e-04 3.32e-01 abnormal ectoplacental cone morphology 1.12e-03 9.61e-01 complete embryonic lethality between implantation and somite formation 1.14e-03 9.71e-01 complete embryonic lethality before implantation 1.17e-03 9.85e-01 abnormal ectoderm development 1.73e-03 1.00e+00 abnormal gastrulation 7.39e-03 1.00e+00 decreased birth weight 7.48e-03 1.00e+00 delayed gastrulation 7.48e-03 1.00e+00 increased ectoderm apoptosis 9.29e-03 1.00e+00 respiratory failure 1.12e-02 1.00e+00 complete lethality during fetal growth through weaning 1.12e-02 1.00e+00 kidney hemorrhage 1.31e-02 1.00e+00 abnormal parietal endoderm morphology 1.31e-02 1.00e+00 abnormal phrenic nerve innervation pattern to diaphragm 1.49e-02 1.00e+00 abnormal Reichert's membrane morphology 1.68e-02 1.00e+00 skeletal muscle atrophy 2.04e-02 1.00e+00 abnormal redox activity 2.05e-02 1.00e+00 progressive muscle weakness 2.23e-02 1.00e+00 failure of blastocyst formation 2.23e-02 1.00e+00 motor neuron degeneration 2.23e-02 1.00e+00 abnormal sciatic nerve morphology

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

²FDR corrected p-value (Benjamini-Hochberg)