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DREAM Module Identification Challenge – Consensus modules

PPI-STRING_Consensus_mod242

Assigned name NA Network PPI-STRING Module ID PPI-STRING_Consensus_mod242 Module size 59 genes

Module genes

This module comprises the following genes:

Gene ID Gene Symbol Gene Name 121536 AEBP2 AE binding protein 2 64919 BCL11B B cell CLL/lymphoma 11B 604 BCL6 B cell CLL/lymphoma 6 84312 BRMS1 BRMS1 like transcriptional repressor 90135 BTBD6 BTB domain containing 6 388272 C16orf87 chromosome 16 open reading frame 87 51267 CLEC1A C-type lectin domain family 1 member A 2117 ETV3 ETS variant 3 50943 FOXP3 forkhead box P3 83856 FSD1L fibronectin type III and SPRY domain containing 1 like 2626 GATA4 GATA binding protein 4 2735 GLI1 GLI family zinc finger 1 2736 GLI2 GLI family zinc finger 2 2737 GLI3 GLI family zinc finger 3 3065 HDAC1 histone deacetylase 1 83933 HDAC10 histone deacetylase 10 79885 HDAC11 histone deacetylase 11 3066 HDAC2 histone deacetylase 2 8841 HDAC3 histone deacetylase 3 9759 HDAC4 histone deacetylase 4 10014 HDAC5 histone deacetylase 5 10013 HDAC6 histone deacetylase 6 51564 HDAC7 histone deacetylase 7 55869 HDAC8 histone deacetylase 8 9734 HDAC9 histone deacetylase 9 139324 HDX highly divergent homeobox 64376 IKZF5 IKAROS family zinc finger 5 116842 LEAP2 liver enriched antimicrobial peptide 2 163175 LGI4 leucine rich repeat LGI family member 4 96626 LIMS3 LIM zinc finger domain containing 3 2122 MECOM MDS1 and EVI1 complex locus 4205 MEF2A myocyte enhancer factor 2A 4208 MEF2C myocyte enhancer factor 2C 4209 MEF2D myocyte enhancer factor 2D 4664 NAB1 NGFI-A binding protein 1 4776 NFATC4 nuclear factor of activated T cells 4 116337 PANX3 pannexin 3 57595 PDZD4 PDZ domain containing 4 114825 PWWP2A PWWP domain containing 2A 55472 RBM12B-AS1 RBM12B antisense RNA 1 283248 RCOR2 REST corepressor 2 92129 RIPPLY1 ripply transcriptional repressor 1 79628 SH3TC2 SH3 domain and tetratricopeptide repeats 2 390598 SKOR1 SKI family transcriptional corepressor 1 56731 SLC2A4RG SLC2A4 regulator 54345 SOX18 SRY-box 18 6658 SOX3 SRY-box 3 6662 SOX9 SRY-box 9 6670 SP3 Sp3 transcription factor 6736 SRY sex determining region Y 361769 SUFU SUFU negative regulator of hedgehog signaling 319100 TAAR6 trace amine associated receptor 6 7050 TGIF1 TGFB induced factor homeobox 1 128488 WFDC12 WAP four-disulfide core domain 12 7528 YY1 YY1 transcription factor 7704 ZBTB16 zinc finger and BTB domain containing 16 92999 ZBTB47 zinc finger and BTB domain containing 47 7546 ZIC2 Zic family member 2 7764 ZNF217 zinc finger protein 217

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 7.33e-01 6.30e-29 GO NAD-dependent histone deacetylase activity (H3-K14 specific) molecular_function 1.94e-01 9.08e-07 Reactome GLI proteins bind promoters of Hh responsive genes to promote transcription Signal Transduction 8.90e-02 6.74e-09 GO nuclear transcription factor complex cellular_component 6.09e-02 5.23e-08 GO negative regulation of pri-miRNA transcription by RNA polymerase II biological_process 3.95e-02 6.16e-12 GO activating transcription factor binding molecular_function 3.90e-02 4.25e-06 GO prostate gland development biological_process 2.73e-02 1.79e-22 GO histone deacetylase complex cellular_component 1.81e-02 2.28e-21 GO histone deacetylase binding molecular_function 9.67e-03 2.88e-05 GO enhancer sequence-specific DNA binding molecular_function 6.36e-03 5.82e-04 GO co-SMAD binding molecular_function 5.95e-03 3.24e-06 GO ciliary base cellular_component 3.84e-03 6.48e-05 GO endochondral ossification biological_process 1.36e-03 5.11e-06 GO chondrocyte differentiation 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 0.00e+00 0.00e+00 negative regulation of transcription from RNA polymerase II promoter 0.00e+00 0.00e+00 protein deacetylation 0.00e+00 0.00e+00 histone deacetylation 0.00e+00 0.00e+00 histone H3 deacetylation 0.00e+00 0.00e+00 histone deacetylase complex 0.00e+00 0.00e+00 transcriptional repressor complex 0.00e+00 0.00e+00 hydrolase activity, acting on carbon-nitrogen (but not peptide) bonds 0.00e+00 0.00e+00 hydrolase activity, acting on carbon-nitrogen (but not peptide) bonds, in linear amides 0.00e+00 0.00e+00 histone deacetylase activity 0.00e+00 0.00e+00 deacetylase activity 0.00e+00 0.00e+00 protein deacetylase activity 0.00e+00 0.00e+00 NAD-dependent histone deacetylase activity (H3-K14 specific) 0.00e+00 0.00e+00 NAD-dependent protein deacetylase activity 0.00e+00 0.00e+00 NAD-dependent histone deacetylase activity 1.64e-10 9.77e-08 transcription regulatory region DNA binding 1.65e-10 9.82e-08 regulatory region DNA binding 5.82e-10 4.46e-07 chromatin organization 7.82e-10 5.90e-07 histone modification 8.96e-10 6.71e-07 covalent chromatin modification 1.39e-09 7.21e-07 histone deacetylase binding

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

²FDR corrected p-value (Benjamini-Hochberg)

Reactome

P-value1 FDR2 Term 0.00e+00 0.00e+00 NOTCH1 INTRACELLULAR DOMAIN REGULATES TRANSCRIPTION 0.00e+00 0.00e+00 SIGNALING BY NOTCH 0.00e+00 0.00e+00 SIGNALING BY NOTCH1 0.00e+00 0.00e+00 NOTCH1 INTRACELLULAR DOMAIN REGULATES TRANSCRIPTION 0.00e+00 0.00e+00 SIGNALING BY NOTCH 0.00e+00 0.00e+00 SIGNALING BY NOTCH1 7.24e-05 9.45e-03 MYOGENESIS 5.08e-04 6.52e-02 MYOGENESIS 8.28e-04 8.51e-02 CIRCADIAN CLOCK 2.03e-03 2.16e-01 CIRCADIAN CLOCK 2.64e-03 2.37e-01 DOWNREGULATION OF SMAD2 3 SMAD4 TRANSCRIPTIONAL ACTIVITY 3.30e-03 2.88e-01 SMAD2 SMAD3 SMAD4 HETEROTRIMER REGULATES TRANSCRIPTION 3.57e-03 3.09e-01 FACTORS INVOLVED IN MEGAKARYOCYTE DEVELOPMENT AND PLATELET PRODUCTION 4.43e-03 3.70e-01 P75 NTR RECEPTOR MEDIATED SIGNALLING 4.93e-03 4.06e-01 SIGNALLING BY NGF 7.51e-03 6.37e-01 DOWNREGULATION OF SMAD2 3 SMAD4 TRANSCRIPTIONAL ACTIVITY 8.41e-03 6.37e-01 TRANSCRIPTIONAL ACTIVITY OF SMAD2 SMAD3 SMAD4 HETEROTRIMER 9.49e-03 7.03e-01 ERK MAPK TARGETS 9.87e-03 7.93e-01 SMAD2 SMAD3 SMAD4 HETEROTRIMER REGULATES TRANSCRIPTION 1.07e-02 8.40e-01 ERK MAPK TARGETS

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

²FDR corrected p-value (Benjamini-Hochberg)

Mouse mutant phenotypes

P-value1 FDR2 Term 4.43e-04 5.65e-01 abnormal xiphoid process morphology 4.86e-04 5.98e-01 exencephaly 5.51e-04 6.44e-01 bowed radius 7.90e-04 7.85e-01 abnormal long bone morphology 1.09e-03 9.45e-01 abnormal metatarsal bone morphology 1.27e-03 1.00e+00 abnormal folding of telencephalic vesicles 1.44e-03 1.00e+00 hemimelia 1.79e-03 1.00e+00 abnormal ameloblast morphology 2.01e-03 1.00e+00 abnormal basisphenoid bone morphology 2.41e-03 1.00e+00 microcephaly 2.45e-03 1.00e+00 complete embryonic lethality 2.48e-03 1.00e+00 fused metatarsal bones 2.49e-03 1.00e+00 premature suture closure 2.84e-03 1.00e+00 abnormal head shape 3.12e-03 1.00e+00 polyphalangy 3.95e-03 1.00e+00 abnormal primary sex determination 4.03e-03 1.00e+00 fused tarsal bones 4.67e-03 1.00e+00 short sternum 4.77e-03 1.00e+00 abnormal DNA methylation 4.80e-03 1.00e+00 abnormal vibrissa number

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

²FDR corrected p-value (Benjamini-Hochberg)