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DREAM Module Identification Challenge – Consensus modules

PPI-STRING_Consensus_mod170

Assigned name NA Network PPI-STRING Module ID PPI-STRING_Consensus_mod170 Module size 27 genes

Module genes

This module comprises the following genes:

Gene ID Gene Symbol Gene Name 79913 ACTR5 ARP5 actin related protein 5 homolog 81611 ANP32E acidic nuclear phosphoprotein 32 family member E 10902 BRD8 bromodomain containing 8 124944 C17orf49 chromosome 17 open reading frame 49 57680 CHD8 chromodomain helicase DNA binding protein 8 84661 DPY30 dpy-30, histone methyltransferase complex regulatory subunit 1876 E2F6 E2F transcription factor 6 3054 HCFC1 host cell factor C1 54985 HCFC1R1 host cell factor C1 regulator 1 83444 INO80B INO80 complex subunit B 125476 INO80C INO80 complex subunit C 54891 INO80D INO80 complex subunit D 283899 INO80E INO80 complex subunit E 284058 KANSL1 KAT8 regulatory NSL complex subunit 1 54934 KANSL2 KAT8 regulatory NSL complex subunit 2 55683 KANSL3 KAT8 regulatory NSL complex subunit 3 653657 MBD3L3 methyl-CpG binding domain protein 3 like 3 10445 MCRS1 microspherule protein 1 23269 MGA MGA, MAX dimerization protein 4297 MLL lysine methyltransferase 2A 4798 NFRKB nuclear factor related to kappaB binding protein 27043 PELP1 proline, glutamate and leucine rich protein 1 51230 PHF20 PHD finger protein 20 5929 RBBP5 RB binding protein 5, histone lysine methyltransferase complex subunit 26168 SENP3 SUMO specific peptidase 3 90326 THAP3 THAP domain containing 3 11091 WDR5 WD repeat domain 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 1.71e-01 1.38e-28 GO MLL1 complex cellular_component 1.59e-01 2.25e-14 GO Ino80 complex cellular_component 1.26e-01 3.36e-19 GO histone acetyltransferase activity (H4-K16 specific) molecular_function 1.25e-01 3.36e-19 GO histone acetyltransferase activity (H4-K8 specific) molecular_function 1.24e-01 3.36e-19 GO histone acetyltransferase activity (H4-K5 specific) molecular_function 3.99e-02 1.73e-09 GO Set1C/COMPASS complex cellular_component 1.62e-02 3.44e-07 GO MLL3/4 complex cellular_component 1.03e-02 1.79e-17 GO histone H4-K5 acetylation biological_process 1.00e-02 1.79e-17 GO histone H4-K8 acetylation 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 peptidyl-lysine modification 0e+00 0e+00 covalent chromatin modification 0e+00 0e+00 chromatin organization 0e+00 0e+00 histone modification 0e+00 0e+00 histone H4 acetylation 0e+00 0e+00 internal protein amino acid acetylation 0e+00 0e+00 histone H4-K5 acetylation 0e+00 0e+00 protein acetylation 0e+00 0e+00 histone H4-K8 acetylation 0e+00 0e+00 histone H4-K16 acetylation 0e+00 0e+00 peptidyl-lysine acetylation 0e+00 0e+00 internal peptidyl-lysine acetylation 0e+00 0e+00 histone acetylation 0e+00 0e+00 transferase complex 0e+00 0e+00 histone methyltransferase complex 0e+00 0e+00 MLL1 complex 0e+00 0e+00 histone acetyltransferase complex 0e+00 0e+00 histone acetyltransferase activity (H4-K16 specific) 0e+00 0e+00 histone acetyltransferase activity (H4-K8 specific) 0e+00 0e+00 H4 histone acetyltransferase activity

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

²FDR corrected p-value (Benjamini-Hochberg)

Mouse mutant phenotypes

P-value1 FDR2 Term 3.74e-03 1e+00 increased ectoderm apoptosis 5.33e-03 1e+00 decreased bone trabecula number 9.33e-03 1e+00 embryonic lethality 1.12e-02 1e+00 cervical vertebral transformation 1.12e-02 1e+00 Leydig cell hyperplasia 1.12e-02 1e+00 abnormal auditory brainstem response 1.31e-02 1e+00 decreased circulating alkaline phosphatase level 1.32e-02 1e+00 abnormal cranium morphology 1.42e-02 1e+00 complete preweaning lethality 1.47e-02 1e+00 vertebral fusion 1.49e-02 1e+00 lumbar vertebral transformation 1.50e-02 1e+00 thoracic vertebral transformation 1.50e-02 1e+00 abnormal eye development 1.53e-02 1e+00 preweaning lethality 1.86e-02 1e+00 failure of primitive streak formation 1.87e-02 1e+00 abnormal craniofacial development 1.87e-02 1e+00 increased circulating alanine transaminase level 1.87e-02 1e+00 increased circulating aspartate transaminase level 2.23e-02 1e+00 increased mean platelet volume 2.24e-02 1e+00 increased circulating HDL cholesterol level

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

²FDR corrected p-value (Benjamini-Hochberg)