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DREAM Module Identification Challenge – Consensus modules

PPI-STRING_Consensus_mod258

Assigned name NA Network PPI-STRING Module ID PPI-STRING_Consensus_mod258 Module size 13 genes

Module genes

This module comprises the following genes:

Gene ID Gene Symbol Gene Name 64838 FNDC4 fibronectin type III domain containing 4 2962 GTF2F1 general transcription factor IIF subunit 1 2963 GTF2F2 general transcription factor IIF subunit 2 5433 POLR2D RNA polymerase II subunit D 5434 POLR2E RNA polymerase II subunit E 5435 POLR2F RNA polymerase II subunit F 5436 POLR2G RNA polymerase II subunit G 5437 POLR2H RNA polymerase II subunit H 5438 POLR2I RNA polymerase II subunit I 5439 POLR2J RNA polymerase II subunit J 5440 POLR2K RNA polymerase II subunit K 5441 POLR2L RNA polymerase II subunit L 90853 SPOCD1 SPOC domain containing 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 1.96e-01 6.15e-33 Reactome Signaling by FGFR2 IIIa TM Disease 6.92e-02 9.70e-26 GO RNA polymerase II, core complex cellular_component 6.87e-02 1.10e-31 Reactome Abortive elongation of HIV-1 transcript in the absence of Tat Disease 4.80e-02 8.16e-14 GO RNA polymerase I activity molecular_function 4.06e-02 1.06e-30 Reactome RNA Pol II CTD phosphorylation and interaction with CE Gene expression (Transcription) 4.05e-02 1.06e-30 Reactome RNA Pol II CTD phosphorylation and interaction with CE during HIV infection Disease 3.99e-02 1.74e-30 Reactome FGFR2 alternative splicing Signal Transduction 7.94e-03 6.22e-24 Reactome PIWI-interacting RNA (piRNA) biogenesis Gene expression (Transcription) 7.60e-03 6.22e-24 Reactome MicroRNA (miRNA) biogenesis Gene expression (Transcription) 7.50e-03 3.39e-29 Reactome Tat-mediated HIV elongation arrest and recovery Disease 7.03e-03 6.22e-24 GO regulation of gene silencing by miRNA biological_process 6.89e-03 3.39e-29 Reactome Pausing and recovery of Tat-mediated HIV elongation Disease 5.13e-03 4.50e-13 GO RNA polymerase III activity molecular_function 2.99e-03 1.33e-13 GO RNA polymerase I complex cellular_component 7.91e-04 4.88e-29 Reactome HIV elongation arrest and recovery Disease 2.31e-04 4.88e-29 Reactome Pausing and recovery of HIV elongation Disease

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 response to growth factor 0e+00 0e+00 transcription-coupled nucleotide-excision repair 0e+00 0e+00 fibroblast growth factor receptor signaling pathway 0e+00 0e+00 transcription from RNA polymerase II promoter 0e+00 0e+00 nucleotide-excision repair 0e+00 0e+00 ncRNA transcription 0e+00 0e+00 transcription initiation from RNA polymerase II promoter 0e+00 0e+00 transcription elongation from RNA polymerase II promoter 0e+00 0e+00 regulation of viral process 0e+00 0e+00 regulation of viral transcription 0e+00 0e+00 response to fibroblast growth factor 0e+00 0e+00 positive regulation of viral transcription 0e+00 0e+00 stem cell population maintenance 0e+00 0e+00 7-methylguanosine mRNA capping 0e+00 0e+00 positive regulation of viral process 0e+00 0e+00 cellular response to growth factor stimulus 0e+00 0e+00 7-methylguanosine RNA capping 0e+00 0e+00 snRNA transcription from RNA polymerase II promoter 0e+00 0e+00 positive regulation of viral life cycle

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

²FDR corrected p-value (Benjamini-Hochberg)

Reactome

P-value1 FDR2 Term 0e+00 0e+00 MRNA SPLICING 0e+00 0e+00 FORMATION OF THE HIV1 EARLY ELONGATION COMPLEX 0e+00 0e+00 FORMATION OF TRANSCRIPTION COUPLED NER TC NER REPAIR COMPLEX 0e+00 0e+00 FORMATION OF RNA POL II ELONGATION COMPLEX 0e+00 0e+00 RNA POL II TRANSCRIPTION PRE INITIATION AND PROMOTER OPENING 0e+00 0e+00 RNA POL II PRE TRANSCRIPTION EVENTS 0e+00 0e+00 ABORTIVE ELONGATION OF HIV1 TRANSCRIPT IN THE ABSENCE OF TAT 0e+00 0e+00 MRNA PROCESSING 0e+00 0e+00 REGULATORY RNA PATHWAYS 0e+00 0e+00 INFLUENZA LIFE CYCLE 0e+00 0e+00 HIV LIFE CYCLE 0e+00 0e+00 LATE PHASE OF HIV LIFE CYCLE 0e+00 0e+00 MRNA CAPPING 0e+00 0e+00 PROCESSING OF CAPPED INTRON CONTAINING PRE MRNA 0e+00 0e+00 MICRORNA MIRNA BIOGENESIS 0e+00 0e+00 VIRAL MESSENGER RNA SYNTHESIS 0e+00 0e+00 TRANSCRIPTION 0e+00 0e+00 RNA POL II TRANSCRIPTION 0e+00 0e+00 INFLUENZA VIRAL RNA TRANSCRIPTION AND REPLICATION 0e+00 0e+00 ELONGATION ARREST AND RECOVERY

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

²FDR corrected p-value (Benjamini-Hochberg)