ࡱ > { } z $ bjbj,(,( 4T NB NB B B ( ( ( ( ( < < < < D | < y 4 3 W Y Y Y Y Y Y , " % F ( O y y O O ( ( O v ( ( G O W ː : 3 0 % % ( 4 O O O O O O % O O O O O O O O O X :
Table S6
Regulatory featuresFold-enrichment in
methylation desertsp-valueTranscription factor coding sequence ADDIN EN.CITE Vaquerizas2009200[1]20020017Vaquerizas, J. M.Kummerfeld, S. K.Teichmann, S. A.Luscombe, N. M.EMBL-European Bioinformatics Institute, Wellcome Trust Genome Campus, Cambridge, UK. jvaquerizas@ebi.ac.ukA census of human transcription factors: function, expression and evolutionNat Rev GenetNat Rev Genet252-631042009/03/11*Evolution, MolecularGene ExpressionGenome, HumanHumansTranscription Factors/*genetics/*metabolism2009Apr1471-0064 (Electronic)
1471-0056 (Linking)19274049http://www.ncbi.nlm.nih.gov/pubmed/19274049nrg2538 [pii]
10.1038/nrg2538eng[ HYPERLINK \l "_ENREF_1" \o "Vaquerizas, 2009 #200" 1]3.75< 1e-3Two fast-evolving transcription factor clusters ADDIN EN.CITE Vaquerizas2009200[1]20020017Vaquerizas, J. M.Kummerfeld, S. K.Teichmann, S. A.Luscombe, N. M.EMBL-European Bioinformatics Institute, Wellcome Trust Genome Campus, Cambridge, UK. jvaquerizas@ebi.ac.ukA census of human transcription factors: function, expression and evolutionNat Rev GenetNat Rev Genet252-631042009/03/11*Evolution, MolecularGene ExpressionGenome, HumanHumansTranscription Factors/*genetics/*metabolism2009Apr1471-0064 (Electronic)
1471-0056 (Linking)19274049http://www.ncbi.nlm.nih.gov/pubmed/19274049nrg2538 [pii]
10.1038/nrg2538eng[ HYPERLINK \l "_ENREF_1" \o "Vaquerizas, 2009 #200" 1]15< 1e-3Genomic regulatory blocks(GRB) ADDIN EN.CITE ADDIN EN.CITE.DATA [ HYPERLINK \l "_ENREF_2" \o "Akalin, 2009 #199" 2]2.8< 1e-10GRB target genes ADDIN EN.CITE ADDIN EN.CITE.DATA [ HYPERLINK \l "_ENREF_2" \o "Akalin, 2009 #199" 2] vs. random segments12< 1e-10GRB target genes vs. 'bystander' genes ADDIN EN.CITE ADDIN EN.CITE.DATA [ HYPERLINK \l "_ENREF_2" \o "Akalin, 2009 #199" 2]9.21.42E-43GRB target genes vs. other CpG island-overlapping genes outside GRBs ADDIN EN.CITE ADDIN EN.CITE.DATA [ HYPERLINK \l "_ENREF_2" \o "Akalin, 2009 #199" 2]331.41E-146Hyperconserved CpG domains with low COCAD scores ADDIN EN.CITE Tanay2007201[3]20120117Tanay, A.O'Donnell, A. H.Damelin, M.Bestor, T. H.Center for Studies in Physics and Biology, The Rockefeller University, New York, NY 10021, USA. atanay@mail.rockefeller.eduHyperconserved CpG domains underlie Polycomb-binding sitesProc Natl Acad Sci U S AProc Natl Acad Sci U S A5521-6104132007/03/23AnimalsBinding SitesConserved Sequence*CpG IslandsEmbryonic Stem Cells/metabolismEpigenesis, GeneticEvolution, MolecularGenomeGenome, HumanHumansPan troglodytesProtein Structure, TertiaryRepressor Proteins/*geneticsSpecies SpecificityTranscription Factors/metabolism2007Mar 270027-8424 (Print)
0027-8424 (Linking)17376869http://www.ncbi.nlm.nih.gov/pubmed/1737686918384900609746104 [pii]
10.1073/pnas.0609746104eng[ HYPERLINK \l "_ENREF_3" \o "Tanay, 2007 #201" 3]37.6<1e-4Promoters with high CpG content1.1<1e-3Promoters with low CpG content0.65<1e-4Promoters with intermediate CpG content3.1<1e-4Bivalent promoters (H3K27me3 and H3K4me2) ADDIN EN.CITE ADDIN EN.CITE.DATA [ HYPERLINK \l "_ENREF_4" \o "Ku, 2008 #202" 4]2.6<1e-3Bivalent promoters with intermediate CpG content ADDIN EN.CITE ADDIN EN.CITE.DATA [ HYPERLINK \l "_ENREF_4" \o "Ku, 2008 #202" 4]4<1e-3
Reference:
ADDIN EN.REFLIST 1. Vaquerizas JM, Kummerfeld SK, Teichmann SA, Luscombe NM (2009) A census of human transcription factors: function, expression and evolution. Nat Rev Genet 10: 252-263.
2. Akalin A, Fredman D, Arner E, Dong X, Bryne JC, et al. (2009) Transcriptional features of genomic regulatory blocks. Genome Biol 10: R38.
3. Tanay A, O'Donnell AH, Damelin M, Bestor TH (2007) Hyperconserved CpG domains underlie Polycomb-binding sites. Proc Natl Acad Sci U S A 104: 5521-5526.
4. Ku M, Koche RP, Rheinbay E, Mendenhall EM, Endoh M, et al. (2008) Genomewide analysis of PRC1 and PRC2 occupancy identifies two classes of bivalent domains. PLoS Genet 4: e1000242.
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5HaBp yt. D Akalin2009199[2]19919917Akalin, A.Fredman, D.Arner, E.Dong, X.Bryne, J. C.Suzuki, H.Daub, C. O.Hayashizaki, Y.Lenhard, B.Computational Biology Unit, Bergen Center for Computational Science, and Sars Centre for Marine Molecular Biology, University of Bergen, 5008 Bergen, Norway.Transcriptional features of genomic regulatory blocksGenome BiolGenome BiolR381042009/04/21AcetylationBase SequenceCell Differentiation/geneticsConserved SequenceCpG IslandsEpigenesis, Genetic*Gene Expression RegulationGene Regulatory NetworksGenome, Human/*geneticsHumansMacrophages/cytology/metabolismModels, GeneticPromoter Regions, Genetic/geneticsRegulatory Sequences, Nucleic AcidTranscription Initiation SiteTranscription, Genetic/*genetics20091465-6914 (Electronic)
1465-6906 (Linking)19374772http://www.ncbi.nlm.nih.gov/pubmed/193747722688929gb-2009-10-4-r38 [pii]
10.1186/gb-2009-10-4-r38eng