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DREAM Module Identification Challenge – Consensus modules

PPI-STRING_Consensus_mod184

Assigned name NA Network PPI-STRING Module ID PPI-STRING_Consensus_mod184 Module size 50 genes

Module genes

This module comprises the following genes:

Gene ID Gene Symbol Gene Name 326 AIRE autoimmune regulator 9070 ASH2L ASH2 like, histone lysine methyltransferase complex subunit 80816 ASXL3 ASXL transcriptional regulator 3 10951 CBX1 chromobox 1 11335 CBX3 chromobox 3 30827 CXXC1 CXXC finger protein 1 203522 DDX26B integrator complex subunit 6 like 11083 DIDO1 death inducer-obliterator 1 84444 DOT1L DOT1 like histone lysine methyltransferase 2145 EZH1 enhancer of zeste 1 polycomb repressive complex 2 subunit 2146 EZH2 enhancer of zeste 2 polycomb repressive complex 2 subunit 285596 FAM153A family with sequence similarity 153 member A 79709 GLT25D1 collagen beta(1-O)galactosyltransferase 1 23127 GLT25D2 collagen beta(1-O)galactosyltransferase 2 8350 HIST1H3A histone cluster 1 H3 family member a 8290 HIST3H3 histone cluster 3 H3 221656 KDM1B lysine demethylase 1B 9682 KDM4A lysine demethylase 4A 23030 KDM4B lysine demethylase 4B 23081 KDM4C lysine demethylase 4C 9757 MLL2 lysine methyltransferase 2B 58508 MLL3 lysine methyltransferase 2C 55904 MLL5 lysine methyltransferase 2E 64324 NSD1 nuclear receptor binding SET domain protein 1 51131 PHF11 PHD finger protein 11 51533 PHF7 PHD finger protein 7 5351 PLOD1 procollagen-lysine,2-oxoglutarate 5-dioxygenase 1 5352 PLOD2 procollagen-lysine,2-oxoglutarate 5-dioxygenase 2 8985 PLOD3 procollagen-lysine,2-oxoglutarate 5-dioxygenase 3 26040 SETBP1 SET binding protein 1 9739 SETD1A SET domain containing 1A 23067 SETD1B SET domain containing 1B 80854 SETD7 SET domain containing lysine methyltransferase 7 9869 SETDB1 SET domain bifurcated 1 83852 SETDB2 SET domain bifurcated 2 6419 SETMAR SET domain and mariner transposase fusion gene 150572 SMYD1 SET and MYND domain containing 1 56950 SMYD2 SET and MYND domain containing 2 64754 SMYD3 SET and MYND domain containing 3 114826 SMYD4 SET and MYND domain containing 4 10322 SMYD5 SMYD family member 5 6839 SUV39H1 suppressor of variegation 3-9 homolog 1 79723 SUV39H2 suppressor of variegation 3-9 homolog 2 51111 SUV420H1 lysine methyltransferase 5B 84787 SUV420H2 lysine methyltransferase 5C 170082 TCEANC transcription elongation factor A N-terminal and central domain containing 5728 TEP1 phosphatase and tensin homolog 1787 TRDMT1 tRNA aspartic acid methyltransferase 1 7468 WHSC1 nuclear receptor binding SET domain protein 2 54904 WHSC1L1 nuclear receptor binding SET domain protein 3

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 3.35e-01 7.75e-09 GO procollagen-lysine 5-dioxygenase activity molecular_function 3.34e-01 7.75e-09 GO hydroxylysine biosynthetic process biological_process 2.24e-01 5.01e-32 GO histone-lysine N-methyltransferase activity molecular_function 8.14e-02 9.21e-07 GO histone H3-K36 demethylation biological_process 6.27e-02 1.54e-07 GO histone methyltransferase activity (H3-K36 specific) molecular_function 4.78e-02 2.04e-09 Reactome HDMs demethylate histones Chromatin organization 3.81e-02 1.02e-08 GO Set1C/COMPASS complex cellular_component 3.73e-02 3.44e-28 Reactome PKMTs methylate histone lysines Chromatin organization 3.35e-02 1.26e-06 GO histone methyltransferase activity molecular_function 7.54e-03 3.10e-04 GO site of DNA damage cellular_component 5.94e-03 1.26e-06 GO histone demethylase activity (H3-K36 specific) molecular_function 3.90e-03 2.78e-06 GO histone demethylase activity (H3-K9 specific) 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 methylation 0.00e+00 0.00e+00 covalent chromatin modification 0.00e+00 0.00e+00 chromatin organization 0.00e+00 0.00e+00 histone lysine methylation 0.00e+00 0.00e+00 histone modification 0.00e+00 0.00e+00 histone methylation 0.00e+00 0.00e+00 protein methylation 0.00e+00 0.00e+00 peptidyl-lysine methylation 0.00e+00 0.00e+00 peptidyl-lysine modification 0.00e+00 0.00e+00 chromatin 0.00e+00 0.00e+00 methyltransferase activity 0.00e+00 0.00e+00 S-adenosylmethionine-dependent methyltransferase activity 0.00e+00 0.00e+00 N-methyltransferase activity 0.00e+00 0.00e+00 protein methyltransferase activity 0.00e+00 0.00e+00 histone methyltransferase activity 0.00e+00 0.00e+00 histone-lysine N-methyltransferase activity 0.00e+00 0.00e+00 lysine N-methyltransferase activity 0.00e+00 0.00e+00 protein-lysine N-methyltransferase activity 2.37e-10 1.89e-07 peptidyl-lysine dimethylation 3.16e-09 1.33e-06 histone methyltransferase complex

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

²FDR corrected p-value (Benjamini-Hochberg)

Reactome

P-value1 FDR2 Term 1.70e-07 4.28e-05 COLLAGEN FORMATION 1.03e-06 1.78e-04 COLLAGEN FORMATION 1.23e-06 2.75e-04 EXTRACELLULAR MATRIX ORGANIZATION 6.40e-06 9.87e-04 EXTRACELLULAR MATRIX ORGANIZATION 8.00e-04 9.68e-02 MEIOSIS 8.08e-04 8.30e-02 MEIOSIS 2.22e-03 2.04e-01 MEIOTIC SYNAPSIS 2.32e-03 2.42e-01 RNA POL I TRANSCRIPTION 2.57e-03 2.64e-01 MEIOTIC SYNAPSIS 2.70e-03 2.42e-01 RNA POL I TRANSCRIPTION 5.37e-03 4.85e-01 MEIOTIC RECOMBINATION 6.99e-03 5.47e-01 MEIOTIC RECOMBINATION 7.25e-03 6.18e-01 CHROMOSOME MAINTENANCE 7.60e-03 5.86e-01 RNA POL I RNA POL III AND MITOCHONDRIAL TRANSCRIPTION 8.53e-03 6.45e-01 CHROMOSOME MAINTENANCE 1.20e-02 9.20e-01 PACKAGING OF TELOMERE ENDS 1.27e-02 8.92e-01 PACKAGING OF TELOMERE ENDS 1.43e-02 1.00e+00 RNA POL I RNA POL III AND MITOCHONDRIAL TRANSCRIPTION 2.88e-02 1.00e+00 TELOMERE MAINTENANCE 3.18e-02 1.00e+00 TELOMERE MAINTENANCE

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

²FDR corrected p-value (Benjamini-Hochberg)

Mouse mutant phenotypes

P-value1 FDR2 Term 1.95e-04 3.43e-01 increased B cell derived lymphoma incidence 7.05e-04 7.38e-01 preweaning lethality 1.43e-03 1.00e+00 paralysis 1.63e-03 1.00e+00 complete embryonic lethality between somite formation and embryo turning 2.12e-03 1.00e+00 abnormal cutaneous collagen fibril morphology 2.47e-03 1.00e+00 embryonic lethality 3.77e-03 1.00e+00 parotid gland inflammation 3.77e-03 1.00e+00 thyroid inflammation 5.61e-03 1.00e+00 abnormal splenocyte morphology 5.62e-03 1.00e+00 asymmetric snout 5.64e-03 1.00e+00 absent Hassall's corpuscle 5.64e-03 1.00e+00 prostate gland inflammation 5.65e-03 1.00e+00 decreased autoantibody level 5.65e-03 1.00e+00 submandibular gland inflammation 7.21e-03 1.00e+00 abnormal spine curvature 7.52e-03 1.00e+00 abnormal metallophilic macrophage morphology 8.12e-03 1.00e+00 aneuploidy 8.69e-03 1.00e+00 decreased NK cell number 9.35e-03 1.00e+00 uveitis 9.39e-03 1.00e+00 decreased tear production

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

²FDR corrected p-value (Benjamini-Hochberg)