Compiled by Ross Hardison, from work of many groups, as referenced here. All are on the Mar. 2006 human genome assembly, hg18. If you publish work resulting from the use of these datasets, please cite the listed reference(s).
Noncoding DNA segments with high regulatory potential
RP score of at least 0.05 for at least 200bp, remove KnownGenes exons.
James Taylor, Svitlana Tyekucheva, David C. King, Ross C. Hardison, Webb Miller, and Francesca Chiaromonte (2006) ESPERR: Learning strong and weak signals in genomic sequence alignments to identify functional elements. Genome Res. 16 : 1596-1604. Full text of publication.
PRPs: Intersection of the High RP segments and the PReMods (clusters of conserved transcription factor binding site motifs)
Blanchette M, Bataille AR, Chen X, Poitras C, Laganiere J, Lefebvre C, Deblois G, Giguere V, Ferretti V, Bergeron D, Coulombe B, Robert F. (2006) Genome-wide computational prediction of transcriptional regulatory modules reveals new insights into human gene expression. Genome Res. 16 : 656-668 Full text of publication and website .
Miller W, Rosenbloom K, Hardison RC, Hou M, Taylor J, Raney B, Burhans R, King DC, Baertsch R, Blankenberg D, Kosakovsky Pond SL, Nekrutenko A, Giardine B, Harris RS, Tyekucheva S, Diekhans M, Pringle TH, Murphy WJ, Lesk A, Weinstock GM, Lindblad-Toh K, Gibbs RA, Lander ES, Siepel A, Haussler D, Kent WJ. (2007) 28-Way vertebrate alignment and conservation track in the UCSC Genome Browser. Genome Res. 17:1797-1808. Full text of publication.
Most constrained DNA segments, phastCons
Data in bed format. 68MB
Siepel A, Bejerano G, Pedersen JS, Hinrichs AS, Hou M, Rosenbloom K, Clawson H, Spieth J, Hillier LW, Richards S, Weinstock GM, Wilson RK, Gibbs RA, Kent WJ, Miller W, Haussler D. 2005 Evolutionarily conserved elements in vertebrate, insect, worm, and yeast genomes. Genome Res.15:1034-1050. Full text of publication.
DNase hypersensitive sites in CD4+ T cells
Boyle AP, Davis S, Shulha HP, Meltzer P, Margulies EH, Weng Z, Furey TS, Crawford GE (2008) High-resolution mapping and characterization of open chromatin across the genome. Cell 132:311-322.
DNA segments occupied by CTCF in primary fibroblasts
Kim TH, Abdullaev ZK, Smith AD, Ching KA, Loukinov DI, Green RD, Zhang MQ, Lobanenkov VV, Ren B. (2008) Analysis of the vertebrate insulator protein CTCF-binding sites in the human genome. Cell 128:1231-1245.
Preinitiation complexes (TAF1) in IMR90 cells
Kim TH, Barrera LO, Zheng M, Qu C, Singer MA, Richmond TA, Wu Y, Green RD, Ren B. (2005) A high-resolution map of active promoters in the human genome. Nature. 436:876-880.
Predicted erythroid cis-regulatory modules
High regulatory potential and constrained binding site motif.
Hao Wang, Ying Zhang, Yong Cheng, Yuepin Zhou, David C. King, James Taylor, Francesca Chiaromonte, Jyotsna Kasturi, Hanna Petrykowska, Bryan Gibb, Christine Dorman, Webb Miller, Louis C. Dore, John Welch, Mitchell J. Weiss, Ross C. Hardison (2006) Experimental Validation of Predicted Mammalian Erythroid Cis-Regulatory Modules. Genome Res. 16 : 1480-1492 Full text of publication.
Page created: Sunday 07-Sep-2008, updated 07-Sep-2008