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DREAM Module Identification Challenge – Consensus modules

PPI-STRING_Consensus_mod336

Assigned name NA Network PPI-STRING Module ID PPI-STRING_Consensus_mod336 Module size 30 genes

Module genes

This module comprises the following genes:

Gene ID Gene Symbol Gene Name 54487 DGCR8 DGCR8, microprocessor complex subunit 8446 DUSP11 dual specificity phosphatase 11 56339 METTL3 methyltransferase like 3 64219 PJA1 praja ring finger ubiquitin ligase 1 9867 PJA2 praja ring finger ubiquitin ligase 2 5430 POLR2A RNA polymerase II subunit A 5431 POLR2B RNA polymerase II subunit B 5432 POLR2C RNA polymerase II subunit C 51132 RLIM ring finger protein, LIM domain interacting 7844 RNF103 ring finger protein 103 79845 RNF122 ring finger protein 122 55819 RNF130 ring finger protein 130 284996 RNF149 ring finger protein 149 57484 RNF150 ring finger protein 150 494470 RNF165 ring finger protein 165 51255 RNF181 ring finger protein 181 200312 RNF215 ring finger protein 215 11237 RNF24 ring finger protein 24 140545 RNF32 ring finger protein 32 152006 RNF38 ring finger protein 38 54894 RNF43 ring finger protein 43 22838 RNF44 ring finger protein 44 6049 RNF6 ring finger protein 6 8732 RNGTT RNA guanylyltransferase and 5'-phosphatase 8731 RNMT RNA guanine-7 methyltransferase 79871 RPAP2 RNA polymerase II associated protein 2 84138 SLC7A6OS solute carrier family 7 member 6 opposite strand 8725 URI1 URI1, prefoldin like chaperone 84133 ZNRF3 zinc and ring finger 3 151112 ZSWIM2 zinc finger SWIM-type containing 2

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 5.86e-02 8.45e-12 GO 7-methylguanosine mRNA capping biological_process 4.07e-02 1.24e-08 GO RNA polymerase II, core complex cellular_component 2.35e-02 9.84e-05 GO primary miRNA processing biological_process 2.32e-02 5.04e-07 GO RNA polymerase II activity molecular_function 2.10e-02 4.53e-03 GO mRNA (2'-O-methyladenosine-N6-)-methyltransferase activity molecular_function

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 protein modification by small protein conjugation 0.00e+00 0.00e+00 protein catabolic process 0.00e+00 0.00e+00 protein ubiquitination 0.00e+00 0.00e+00 ubiquitin-protein transferase activity 0.00e+00 0.00e+00 ubiquitin protein ligase activity 0.00e+00 0.00e+00 ubiquitin-like protein transferase activity 5.15e-11 4.40e-08 ubiquitin-dependent protein catabolic process 7.51e-11 6.31e-08 modification-dependent protein catabolic process 1.80e-10 1.46e-07 proteolysis involved in cellular protein catabolic process 2.34e-10 1.87e-07 cellular protein catabolic process 1.30e-09 9.54e-07 proteasome-mediated ubiquitin-dependent protein catabolic process 1.39e-09 1.01e-06 proteasomal protein catabolic process 3.96e-08 2.37e-05 7-methylguanosine mRNA capping 5.51e-08 3.24e-05 7-methylguanosine RNA capping 6.68e-08 2.35e-05 DNA-directed RNA polymerase II, core complex 1.14e-07 3.85e-05 DNA-directed RNA polymerase II, holoenzyme 7.13e-07 3.49e-04 protein polyubiquitination 1.28e-06 5.96e-04 gene silencing by RNA 3.39e-06 1.45e-03 protein ubiquitination involved in ubiquitin-dependent protein catabolic process 3.73e-06 1.06e-03 RNA polymerase II activity

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

²FDR corrected p-value (Benjamini-Hochberg)

Reactome

P-value1 FDR2 Term 8.23e-08 2.14e-05 MRNA CAPPING 1.12e-07 2.17e-05 MRNA CAPPING 2.22e-07 5.50e-05 MRNA PROCESSING 4.22e-07 1.00e-04 MICRORNA MIRNA BIOGENESIS 4.38e-07 1.04e-04 REGULATORY RNA PATHWAYS 6.13e-07 1.42e-04 RNA POL II TRANSCRIPTION 1.06e-06 1.83e-04 MICRORNA MIRNA BIOGENESIS 1.10e-06 1.89e-04 REGULATORY RNA PATHWAYS 1.41e-06 2.39e-04 MRNA PROCESSING 1.45e-06 3.19e-04 TRANSCRIPTION 7.65e-06 1.49e-03 LATE PHASE OF HIV LIFE CYCLE 1.14e-05 2.16e-03 HIV LIFE CYCLE 2.53e-05 3.56e-03 RNA POL II TRANSCRIPTION 2.63e-05 3.68e-03 LATE PHASE OF HIV LIFE CYCLE 3.53e-05 6.11e-03 VIRAL MESSENGER RNA SYNTHESIS 3.99e-05 5.44e-03 VIRAL MESSENGER RNA SYNTHESIS 4.03e-05 5.48e-03 HIV LIFE CYCLE 5.75e-05 9.47e-03 ABORTIVE ELONGATION OF HIV1 TRANSCRIPT IN THE ABSENCE OF TAT 7.14e-05 1.15e-02 ELONGATION ARREST AND RECOVERY 7.77e-05 1.24e-02 MRNA SPLICING MINOR PATHWAY

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

²FDR corrected p-value (Benjamini-Hochberg)

Mouse mutant phenotypes

P-value1 FDR2 Term 1.87e-03 1e+00 decreased dentate gyrus size 3.74e-03 1e+00 abnormal dosage compensation, by inactivation of X chromosome 3.74e-03 1e+00 abnormal optic placode morphology 5.62e-03 1e+00 aphakia 7.48e-03 1e+00 impaired spatial learning 7.52e-03 1e+00 abnormal neural tube closure 7.54e-03 1e+00 enhanced contextual conditioning behavior 9.35e-03 1e+00 behavioral despair 9.35e-03 1e+00 abnormal brain interneuron morphology 1.12e-02 1e+00 abnormal nest building behavior 1.68e-02 1e+00 abnormal neuronal precursor proliferation 1.84e-02 1e+00 increased prepulse inhibition 1.86e-02 1e+00 transmission ratio distortion 1.99e-02 1e+00 enhanced long term potentiation 2.04e-02 1e+00 increased B cell number 2.33e-02 1e+00 abnormal dendrite morphology 2.63e-02 1e+00 decreased fetal size 2.97e-02 1e+00 abnormal spatial working memory 3.14e-02 1e+00 abnormal neuronal migration 3.17e-02 1e+00 decreased startle reflex

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

²FDR corrected p-value (Benjamini-Hochberg)