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DREAM Module Identification Challenge – Consensus modules

PPI-STRING_Consensus_mod332

Assigned name NA Network PPI-STRING Module ID PPI-STRING_Consensus_mod332 Module size 49 genes

Module genes

This module comprises the following genes:

Gene ID Gene Symbol Gene Name 86 ACTL6A actin like 6A 93973 ACTR8 ARP8 actin related protein 8 homolog 55252 ASXL2 ASXL transcriptional regulator 2 23476 BRD4 bromodomain containing 4 676 BRDT bromodomain testis associated 121053 C12orf45 chromosome 12 open reading frame 45 80304 C2orf44 WD repeat and coiled coil containing 51755 CDK12 cyclin dependent kinase 12 8621 CDK13 cyclin dependent kinase 13 1460 CSNK2B casein kinase 2 beta 25911 DPCD deleted in primary ciliary dyskinesia homolog (mouse) 8726 EED embryonic ectoderm development 283229 EFCAB4A calcium release activated channel regulator 2B 84337 ELOF1 elongation factor 1 homolog 54826 GIN1 gypsy retrotransposon integrase 1 94239 H2AFV H2A histone family member V 8479 HIRIP3 HIRA interacting protein 3 3621 ING1 inhibitor of growth family member 1 55677 IWS1 IWS1, SUPT6H interacting protein 65094 JMJD4 jumonji domain containing 4 339123 JMJD8 jumonji domain containing 8 56243 KIAA1217 KIAA1217 124751 KRBA2 KRAB-A domain containing 2 123169 LEO1 LEO1 homolog, Paf1/RNA polymerase II complex component 26046 LTN1 listerin E3 ubiquitin protein ligase 1 54531 MIER2 MIER family member 2 166968 MIER3 MIER family member 3 4298 MLLT1 MLLT1, super elongation complex subunit 8028 MLLT10 MLLT10, histone lysine methyltransferase DOT1L cofactor 4300 MLLT3 MLLT3, super elongation complex subunit 4302 MLLT6 MLLT6, PHD finger containing 339287 MSL1 male specific lethal 1 homolog 55167 MSL2 MSL complex subunit 2 26012 NELF NMDA receptor synaptonuclear signaling and neuronal migration factor 79447 PAGR1 PAXIP1 associated glutamate rich protein 1 9678 PHF14 PHD finger protein 14 23338 PHF15 jade family PHD finger 2 9767 PHF16 jade family PHD finger 3 5757 PTMA prothymosin alpha 56254 RNF20 ring finger protein 20 9810 RNF40 ring finger protein 40 388015 RTL1 retrotransposon Gag like 1 29072 SETD2 SET domain containing 2 22933 SIRT2 sirtuin 2 8614 STC2 stanniocalcin 2 6920 TCEA3 transcription elongation factor A3 127428 TCEANC2 transcription elongation factor A N-terminal and central domain containing 2 80185 TTI2 TELO2 interacting protein 2 80335 WDR82 WD repeat domain 82

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 1.52e-01 4.25e-05 GO MSL complex cellular_component 1.21e-01 7.04e-07 GO histone H2B ubiquitination biological_process 3.56e-02 6.75e-06 GO lysine-acetylated histone binding molecular_function 3.49e-02 8.91e-05 GO phosphorylation of RNA polymerase II C-terminal domain biological_process 3.44e-02 4.87e-08 GO positive regulation of transcription elongation from RNA polymerase II promoter biological_process 2.56e-02 1.97e-12 GO transcription elongation from RNA polymerase II promoter biological_process 2.02e-02 1.19e-04 GO cyclin/CDK positive transcription elongation factor complex cellular_component 1.33e-02 2.78e-04 GO transcription factor activity, transcription factor binding molecular_function 8.50e-03 1.88e-05 GO nucleosome binding 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 chromatin organization 0.00e+00 0.00e+00 transcription elongation from RNA polymerase II promoter 6.82e-11 5.76e-08 DNA-templated transcription, elongation 1.00e-10 5.15e-08 transcription elongation factor complex 2.49e-10 1.98e-07 covalent chromatin modification 3.37e-09 2.34e-06 histone modification 3.01e-08 1.12e-05 transferase complex 2.55e-07 8.14e-05 chromatin 1.51e-06 4.65e-04 RNA polymerase II core binding 2.32e-06 1.03e-03 regulation of DNA-templated transcription, elongation 2.59e-06 1.13e-03 histone H2B ubiquitination 6.39e-06 1.73e-03 RNA polymerase core enzyme binding 8.25e-06 2.19e-03 basal RNA polymerase II transcription machinery binding 1.00e-05 3.87e-03 regulation of mRNA 3'-end processing 2.04e-05 4.70e-03 heterochromatin 2.62e-05 9.11e-03 peptidyl-lysine modification 3.08e-05 1.05e-02 histone monoubiquitination 3.59e-05 8.40e-03 RNA polymerase binding 3.69e-05 1.23e-02 regulation of mRNA processing 3.87e-05 1.28e-02 regulation of mRNA export from nucleus

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

²FDR corrected p-value (Benjamini-Hochberg)

Reactome

P-value1 FDR2 Term 1.03e-02 8.15e-01 SIGNAL TRANSDUCTION BY L1 2.23e-02 1.00e+00 L1CAM INTERACTIONS

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

²FDR corrected p-value (Benjamini-Hochberg)

Mouse mutant phenotypes

P-value1 FDR2 Term 1.18e-04 2.51e-01 delayed cellular replicative senescence 8.29e-04 8.09e-01 abnormal sternum ossification 1.67e-03 1.00e+00 increased B cell derived lymphoma incidence 1.87e-03 1.00e+00 increased prostate gland tumor incidence 2.58e-03 1.00e+00 increased fibroblast proliferation 2.98e-03 1.00e+00 thoracic vertebral transformation 3.75e-03 1.00e+00 mammary gland hyperplasia 5.61e-03 1.00e+00 impaired placental function 5.61e-03 1.00e+00 increased pancreas tumor incidence 5.61e-03 1.00e+00 weaving 5.61e-03 1.00e+00 absent intervertebral disk 7.09e-03 1.00e+00 vertebral transformation 7.47e-03 1.00e+00 split vertebrae 7.48e-03 1.00e+00 altered tumor susceptibility 7.48e-03 1.00e+00 abnormal physical strength 8.67e-03 1.00e+00 abnormal placenta labyrinth morphology 1.12e-02 1.00e+00 abnormal nucleus pulposus morphology 1.15e-02 1.00e+00 increased lean body mass 1.30e-02 1.00e+00 increased placenta weight 1.30e-02 1.00e+00 abnormal placenta size

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

²FDR corrected p-value (Benjamini-Hochberg)