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DREAM Module Identification Challenge – Consensus modules

PPI-STRING_Consensus_mod322

Assigned name NA Network PPI-STRING Module ID PPI-STRING_Consensus_mod322 Module size 82 genes

Module genes

This module comprises the following genes:

Gene ID Gene Symbol Gene Name 29123 ANKRD11 ankyrin repeat domain 11 23253 ANKRD12 ankyrin repeat domain 12 84164 ASCC2 activating signal cointegrator 1 complex subunit 2 80063 ATF7IP2 activating transcription factor 7 interacting protein 2 54971 BANP BTG3 associated nuclear protein 192197 BCAS3 breast carcinoma amplified sequence 3 7832 BTG2 BTG anti-proliferation factor 2 23523 CABIN1 calcineurin binding protein 1 865 CBFB core-binding factor subunit beta 64753 CCDC136 coiled-coil domain containing 136 159989 CCDC67 deuterosome assembly protein 1 55118 CEP68 cartilage acidic protein 1 1616 DAXX death domain associated protein 1761 DMRT1 doublesex and mab-3 related transcription factor 1 63946 DMRTC2 DMRT like family C2 133418 EMB embigin 2033 EP300 E1A binding protein p300 2118 ETV4 ETS variant 4 2274 FHL2 four and a half LIM domains 2 1647 GADD45A growth arrest and DNA damage inducible alpha 84253 GARNL3 GTPase activating Rap/RanGAP domain like 3 65056 GPBP1 GC-rich promoter binding protein 1 2874 GPS2 G protein pathway suppressor 2 100912262 GTF2I general transcription factor II-I repeat domain-containing protein 1-like 338328 HBP1 glycosylphosphatidylinositol anchored high density lipoprotein binding protein 1 3159 HMGA1 high mobility group AT-hook 1 8091 HMGA2 high mobility group AT-hook 2 3150 HMGN1 high mobility group nucleosome binding domain 1 3151 HMGN2 high mobility group nucleosomal binding domain 2 9592 IER2 immediate early response 2 26145 IRF2BP1 interferon regulatory factor 2 binding protein 1 3713 IVL involucrin 133746 JMY junction mediating and regulatory protein, p53 cofactor 3725 JUN Jun proto-oncogene, AP-1 transcription factor subunit 55818 KDM3A lysine demethylase 3A 688 KLF5 Kruppel like factor 5 23641 LDOC1 LDOC1, regulator of NFKB signaling 79884 MAP9 microtubule associated protein 9 4149 MAX MYC associated factor X 57591 MKL1 myocardin related transcription factor A 57496 MKL2 myocardin related transcription factor B 4330 MN1 MN1 proto-oncogene, transcriptional regulator 4332 MNDA myeloid cell nuclear differentiation antigen 92140 MTDH metadherin 10608 MXD4 MAX dimerization protein 4 4609 MYC MYC proto-oncogene, bHLH transcription factor 80177 MYCT1 MYC target 1 93649 MYOCD myocardin 57447 NDRG2 NDRG family member 2 137814 NKX2-6 NK2 homeobox 6 26257 NKX2-8 NK2 homeobox 8 4824 NKX3-1 NK3 homeobox 1 26471 NUPR1 nuclear protein 1, transcriptional regulator 389493 NUPR1L nuclear protein 2, transcriptional regulator 401 PHOX2A paired like homeobox 2A 5570 PKIB cAMP-dependent protein kinase inhibitor beta 55269 PSPC1 paraspeckle component 1 295953 RAG2 recombination activating 2 10741 RBBP9 RB binding protein 9, serine hydrolase 56475 RPRM reprimo, TP53 dependent G2 arrest mediator homolog 861 RUNX1 runt related transcription factor 1 6278 S100A7 S100 calcium binding protein A7 29950 SERTAD1 SERTA domain containing 1 23411 SIRT1 sirtuin 1 54861 SNRK SNF related kinase 6660 SOX5 SRY-box 5 6667 SP1 Sp1 transcription factor 25803 SPDEF SAM pointed domain containing ETS transcription factor 6688 SPI1 Spi-1 proto-oncogene 153443 SRFBP1 serum response factor binding protein 1 6760 SS18 SS18, nBAF chromatin remodeling complex subunit 26039 SS18L1 SS18L1, nBAF chromatin remodeling complex subunit 6759 SSX4 SSX family member 4 55809 TRERF1 transcriptional regulating factor 1 10346 TRIM22 tripartite motif containing 22 23650 TRIM29 tripartite motif containing 29 51592 TRIM33 tripartite motif containing 33 29855 UBN1 ubinuclein 1 7350 UCP1 uncoupling protein 1 7392 USF2 upstream transcription factor 2, c-fos interacting 55249 YY1AP1 YY1 associated protein 1 6935 ZEB1 zinc finger E-box binding homeobox 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 2.53e-01 5.48e-05 Reactome RUNX3 regulates RUNX1-mediated transcription Gene expression (Transcription) 1.49e-01 1.53e-07 Reactome Formation of Senescence-Associated Heterochromatin Foci (SAHF) Cellular responses to external stimuli 8.82e-02 1.64e-05 GO smooth muscle cell differentiation biological_process 8.43e-02 1.24e-05 GO positive regulation of response to DNA damage stimulus biological_process 7.53e-02 9.01e-06 GO positive regulation of cellular senescence biological_process 5.87e-02 4.23e-06 Reactome RUNX3 regulates p14-ARF Gene expression (Transcription) 4.87e-02 5.04e-04 GO negative regulation of cAMP-dependent protein kinase activity biological_process 3.35e-02 5.00e-05 GO positive regulation by host of viral transcription biological_process 2.86e-02 8.06e-04 GO response to UV-B biological_process 2.64e-02 1.82e-04 Reactome RUNX1 regulates expression of components of tight junctions Gene expression (Transcription) 2.64e-02 1.82e-04 Reactome RUNX1 regulates transcription of genes involved in interleukin signaling Gene expression (Transcription) 1.91e-02 8.06e-04 GO ventricular cardiac muscle cell development biological_process 1.87e-02 1.10e-06 GO protein-DNA complex cellular_component 1.03e-02 1.28e-04 GO positive regulation of pri-miRNA transcription by RNA polymerase II biological_process 8.00e-03 1.28e-04 GO R-SMAD binding molecular_function 3.20e-03 8.10e-06 GO p53 binding molecular_function 3.03e-03 1.65e-04 GO bHLH transcription factor binding molecular_function 2.65e-03 4.14e-05 GO androgen receptor signaling pathway biological_process 2.15e-03 3.45e-05 GO androgen receptor binding molecular_function 8.70e-04 4.92e-05 GO E-box binding molecular_function 8.06e-04 1.28e-04 GO nuclear hormone receptor 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 2.20e-09 1.10e-06 transcription cofactor activity 3.38e-09 1.65e-06 transcription factor activity, transcription factor binding 3.92e-09 1.90e-06 transcription factor activity, protein binding 5.68e-09 3.81e-06 transcription from RNA polymerase II promoter 3.22e-08 1.34e-05 transcription coactivator activity 7.81e-08 3.05e-05 RNA polymerase II transcription factor activity, sequence-specific DNA binding 1.47e-07 4.84e-05 chromatin 6.44e-07 3.18e-04 negative regulation of transcription from RNA polymerase II promoter 2.09e-06 6.24e-04 transcription regulatory region DNA binding 2.12e-06 6.33e-04 regulatory region DNA binding 3.27e-06 9.41e-04 core promoter binding 4.25e-06 1.20e-03 transcription factor binding 6.61e-06 2.66e-03 chromatin organization 1.98e-05 4.88e-03 double-stranded DNA binding 2.12e-05 4.87e-03 nuclear body 3.36e-05 1.13e-02 positive regulation of cellular senescence 4.20e-05 9.68e-03 transcriptional activator activity, RNA polymerase II transcription regulatory region sequence-specific binding 4.67e-05 1.51e-02 covalent chromatin modification 5.22e-05 1.67e-02 positive regulation of cell aging 6.66e-05 1.45e-02 transcription regulatory region sequence-specific DNA binding

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

²FDR corrected p-value (Benjamini-Hochberg)

Reactome

P-value1 FDR2 Term 8.28e-05 1.07e-02 TRANSCRIPTIONAL ACTIVITY OF SMAD2 SMAD3 SMAD4 HETEROTRIMER 3.23e-04 3.66e-02 SIGNALING BY TGF BETA RECEPTOR COMPLEX 8.10e-04 9.79e-02 TRANSCRIPTIONAL ACTIVITY OF SMAD2 SMAD3 SMAD4 HETEROTRIMER 1.05e-03 1.05e-01 PRE NOTCH TRANSCRIPTION AND TRANSLATION 1.28e-03 1.25e-01 SIGNALING BY NOTCH 1.63e-03 1.55e-01 SMAD2 SMAD3 SMAD4 HETEROTRIMER REGULATES TRANSCRIPTION 3.01e-03 3.02e-01 SIGNALING BY TGF BETA RECEPTOR COMPLEX 3.31e-03 2.89e-01 PRE NOTCH EXPRESSION AND PROCESSING 3.93e-03 3.34e-01 NOTCH1 INTRACELLULAR DOMAIN REGULATES TRANSCRIPTION 6.62e-03 5.75e-01 PRE NOTCH TRANSCRIPTION AND TRANSLATION 7.53e-03 6.38e-01 SMAD2 SMAD3 SMAD4 HETEROTRIMER REGULATES TRANSCRIPTION 9.31e-03 7.56e-01 SIGNALING BY NOTCH 1.00e-02 7.32e-01 TRANSCRIPTIONAL REGULATION OF WHITE ADIPOCYTE DIFFERENTIATION 1.01e-02 7.38e-01 SIGNALING BY NOTCH1 1.37e-02 1.00e+00 PRE NOTCH EXPRESSION AND PROCESSING 1.44e-02 9.84e-01 INTEGRATION OF PROVIRUS 1.56e-02 1.00e+00 NOTCH1 INTRACELLULAR DOMAIN REGULATES TRANSCRIPTION 1.60e-02 1.00e+00 APOBEC3G MEDIATED RESISTANCE TO HIV1 INFECTION 1.68e-02 1.00e+00 APOBEC3G MEDIATED RESISTANCE TO HIV1 INFECTION 1.72e-02 1.00e+00 PPARA ACTIVATES GENE EXPRESSION

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

²FDR corrected p-value (Benjamini-Hochberg)

Mouse mutant phenotypes

P-value1 FDR2 Term 1.38e-04 2.81e-01 increased fibroblast proliferation 1.78e-04 3.25e-01 internal hemorrhage 2.91e-04 4.41e-01 palate bone hypoplasia 7.77e-04 7.77e-01 decreased Paneth cell number 1.78e-03 1.00e+00 increased sensitivity to skin irradiation 2.11e-03 1.00e+00 increased T cell derived lymphoma incidence 3.57e-03 1.00e+00 decreased thymocyte number 3.66e-03 1.00e+00 abnormal T cell subpopulation ratio 3.72e-03 1.00e+00 abnormal testis development 3.82e-03 1.00e+00 hemoperitoneum 3.97e-03 1.00e+00 abnormal lymph organ development 3.99e-03 1.00e+00 lymph node hypoplasia 4.23e-03 1.00e+00 decreased CD8-positive, alpha-beta T cell number 4.23e-03 1.00e+00 abnormal chromosome number 4.24e-03 1.00e+00 abnormal leukopoiesis 4.27e-03 1.00e+00 pale yolk sac 4.32e-03 1.00e+00 abnormal inguinal fat pad morphology 5.02e-03 1.00e+00 exencephaly 5.08e-03 1.00e+00 absent mature B cells 5.37e-03 1.00e+00 decreased erythroid progenitor cell number

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

²FDR corrected p-value (Benjamini-Hochberg)