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DREAM Module Identification Challenge – Consensus modules

PPI-STRING_Consensus_mod290

Assigned name NA Network PPI-STRING Module ID PPI-STRING_Consensus_mod290 Module size 29 genes

Module genes

This module comprises the following genes:

Gene ID Gene Symbol Gene Name 296312 AAR2 AAR2 splicing factor homolog 90799 CEP95 centrosomal protein 95 115265 DDIT4L DNA damage inducible transcript 4 like 340168 DPPA5 developmental pluripotency associated 5 27257 LSM1 LSM1 homolog, mRNA degradation associated 84967 LSM10 LSM10, U7 small nuclear RNA associated 57819 LSM2 LSM2 homolog, U6 small nuclear RNA and mRNA degradation associated 27258 LSM3 LSM3 homolog, U6 small nuclear RNA and mRNA degradation associated 25804 LSM4 LSM4 homolog, U6 small nuclear RNA and mRNA degradation associated 23658 LSM5 LSM5 homolog, U6 small nuclear RNA and mRNA degradation associated 11157 LSM6 LSM6 homolog, U6 small nuclear RNA and mRNA degradation associated 51690 LSM7 LSM7 homolog, U6 small nuclear RNA and mRNA degradation associated 56257 MEPCE methylphosphate capping enzyme 84316 NAA38 N(alpha)-acetyltransferase 38, NatC auxiliary subunit 219988 PATL1 PAT1 homolog 1, processing body mRNA decay factor 286187 PPP1R42 protein phosphatase 1 regulatory subunit 42 9129 PRPF3 pre-mRNA processing factor 3 55015 PRPF39 pre-mRNA processing factor 39 25766 PRPF40B pre-mRNA processing factor 40 homolog B 58517 RBM25 RNA binding motif protein 25 9092 SART1 spliceosome associated factor 1, recruiter of U4/U6.U5 tri-snRNP 9733 SART3 spliceosome associated factor 3, U4/U6 recycling protein 728492 SERF1B small EDRK-rich factor 1B 6631 SNRPC small nuclear ribonucleoprotein polypeptide C 6638 SNRPN small nuclear ribonucleoprotein polypeptide N 54957 TXNL4B thioredoxin like 4B 164781 WDR69 dynein assembly factor with WD repeats 1 153527 ZMAT2 zinc finger matrin-type 2 55954 ZMAT5 zinc finger matrin-type 5

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 3.00e-01 5.33e-20 Reactome mRNA decay by 5' to 3' exoribonuclease Metabolism of RNA 2.13e-01 2.79e-23 GO U4/U6 x U5 tri-snRNP complex cellular_component 6.83e-02 5.57e-09 GO U2-type prespliceosome cellular_component 2.82e-02 8.61e-10 GO U6 snRNA binding molecular_function 8.54e-03 1.57e-08 GO U1 snRNP cellular_component

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 0.00e+00 0.00e+00 mRNA splicing, via spliceosome 0.00e+00 0.00e+00 mRNA metabolic process 0.00e+00 0.00e+00 ribonucleoprotein complex assembly 0.00e+00 0.00e+00 mRNA processing 0.00e+00 0.00e+00 RNA splicing, via transesterification reactions 0.00e+00 0.00e+00 nuclear-transcribed mRNA catabolic process, exonucleolytic 0.00e+00 0.00e+00 exonucleolytic nuclear-transcribed mRNA catabolic process involved in deadenylation-dependent decay 0.00e+00 0.00e+00 nuclear-transcribed mRNA catabolic process, deadenylation-dependent decay 0.00e+00 0.00e+00 intracellular ribonucleoprotein complex 0.00e+00 0.00e+00 U4/U6 x U5 tri-snRNP complex 0.00e+00 0.00e+00 spliceosomal tri-snRNP complex 0.00e+00 0.00e+00 spliceosomal snRNP complex 0.00e+00 0.00e+00 spliceosomal complex 0.00e+00 0.00e+00 ribonucleoprotein complex 0.00e+00 0.00e+00 small nuclear ribonucleoprotein complex 0.00e+00 0.00e+00 snRNA binding 1.69e-11 1.51e-08 ribonucleoprotein complex biogenesis 1.40e-10 7.07e-08 U6 snRNP 1.69e-10 1.37e-07 nuclear-transcribed mRNA catabolic process

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 DEADENYLATION DEPENDENT MRNA DECAY 0.00e+00 0.00e+00 MRNA DECAY BY 5 TO 3 EXORIBONUCLEASE 0.00e+00 0.00e+00 MRNA DECAY BY 5 TO 3 EXORIBONUCLEASE 5.10e-11 1.43e-08 DEADENYLATION DEPENDENT MRNA DECAY 5.16e-10 1.75e-07 METABOLISM OF MRNA 1.03e-09 3.40e-07 METABOLISM OF RNA 4.20e-09 9.54e-07 METABOLISM OF MRNA 4.97e-09 1.12e-06 METABOLISM OF RNA 7.22e-03 5.62e-01 SLBP DEPENDENT PROCESSING OF REPLICATION DEPENDENT HISTONE PRE MRNAS 7.98e-03 6.71e-01 MRNA PROCESSING 1.71e-02 1.00e+00 SLBP DEPENDENT PROCESSING OF REPLICATION DEPENDENT HISTONE PRE MRNAS 1.74e-02 1.00e+00 MRNA PROCESSING 2.33e-02 1.00e+00 PROCESSING OF CAPPED INTRONLESS PRE MRNA 3.55e-02 1.00e+00 PROCESSING OF CAPPED INTRONLESS PRE MRNA 4.96e-02 1.00e+00 CLEAVAGE OF GROWING TRANSCRIPT IN THE TERMINATION REGION

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

²FDR corrected p-value (Benjamini-Hochberg)

Mouse mutant phenotypes

P-value1 FDR2 Term 1.42e-03 1e+00 increased body weight 1.87e-03 1e+00 genetic imprinting 3.74e-03 1e+00 abnormal imprinting 3.75e-03 1e+00 abnormal stationary movement 5.61e-03 1e+00 maternal imprinting 5.62e-03 1e+00 increased body size 7.48e-03 1e+00 abnormal DNA methylation 9.41e-03 1e+00 dehydration 1.69e-02 1e+00 abnormal retinal pigment epithelium morphology 1.84e-02 1e+00 corneal opacity 1.86e-02 1e+00 decreased circulating chloride level 1.87e-02 1e+00 retinal degeneration 2.24e-02 1e+00 absent gastric milk in neonates 2.42e-02 1e+00 increased circulating HDL cholesterol level 2.58e-02 1e+00 abnormal suckling behavior 2.98e-02 1e+00 decreased birth weight 2.98e-02 1e+00 increased total body fat amount 3.16e-02 1e+00 weakness 3.34e-02 1e+00 increased lean body mass 4.39e-02 1e+00 postnatal lethality

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

²FDR corrected p-value (Benjamini-Hochberg)