ABS: a database of Annotated regulatory Binding Sites from orthologous promoters E. Blanco, D. Farré, M. Albà, X. Messeguer and R. Guigó. ABS: a database of Annotated regulatory Binding Sites from orthologous promoters. Nucleic Acids Research 34:D63-D67 (2006). http://genome.imim.es/datasets/abs2005 http://nar.oxfordjournals.org/cgi/content/full/34/suppl_1/D63

The ARE project contains twenty active antioxidant responsive elements (AREs) that are a subset of the AREs originally curated in Wang et al, 2007, Table S1 (PMID: 17409198). Active AREs were selected by Chou and Wasserman (unpublished results) and bulk-uploaded with the interacting transcription factor labeled as human NFE2L2 (NRF2). Consult each original publication to determine the actual species source of TF used in the experiments. The NFE2L2 protein interacts with one of the small Maf proteins to form a functional complex.

Compilation of binding sites for the HIF1 transcription factor complex composed of HIF1A and ARNT. The data was extracted from the following review: [DOI: 10.1126/stke.3062005re12] Roland H. Wenger, Daniel P. Stiehl and Gieri Camenisch. Integration of oxygen signaling at the consensus HRE. (2005) Sci STKE. 306:re12.

The HNF4 project houses data from the Sladek lab at UC Riverside (http://www.sladeklab.ucr.edu/). The project includes 107 expert curated TFBS that were bulk-uploaded with the interacting transcription factor labeled as human HNF4A. Consult each original publication to determine the actual species source of TF used in the experiments. H4 numbers assigned to regulatory sequences refer to specific binding sites.

The JASPAR CORE database contains a curated, non-redundant set of 123 transcription factor binding profiles from published articles. JASPAR website is : http://jaspar.genereg.net

Set of predicted motifs remapped from Xie et al., 2005. This set was originally generated by comparative analysis of the human, mouse, rat and dog genomes to create a systematic catalogue of common regulatory motifs in promoters and 3' untranslated regions. We remapped it to the current human genome build NCBI 36 (using ensembl release 45). The original chromosome coordinates, provided by the authors in the supplementary information does not always match the current release. The other data, through which we could identify the site in question is the RefSeq identifier and the IUPAC consenus sequence (also provided), which are not sufficient to find unique hit in most cases. Therefore we used GERP scores (Cooper et al., 2005) to select the best hit. Xie X, Lu J, Kulbokas EJ, Golub TR, Mootha V, Lindblad-Toh K, Lander ES, Kellis M. (2005) Systematic discovery of regulatory motifs in human promoters and 3' UTRs by comparison of several mammals. Nature 434(7031):338-45. Cooper GM, Stone EA, Asimenos G, Green ED, Batzoglou S and Sidow A. (2005) Distribution and intensity of constraint in mammalian genomic sequence. Genome Res 15(7):901-13. !!! Please be patient when working with this dataset as it contains over 100,000 sequences and pages might take a long time to load !!!

Set of liver-specific regulatory regions and transcription factor binding sites curated from the literature

Sequences regulating the transcription of the Mucin 5AC MUC5AC gene.

Set of muscle-specific regulatory regions and transcription factor binding sites curated from the literature.

The NFIRegulomeDB is a database of genes regulated by the Nuclear Factor I transcription factor family compiled by the Gronostajski Lab. The long-term goal is to provide a generic annotation and search system that individual labs focussed on specific transcription factors or transcription factor families can use to keep databases on genes that their factors regulate. Eventually we'd like to link these individual databases into a distributed RegulomeDB for all known regulated genes and their associated transcription factors. http://nfiregulome.ccr.buffalo.edu

Collection of binding sites for Olf/Ebf proteins from the literature.

ORegAnno Dataset. The Open REGulatory ANNOtation database (ORegAnno) is an open database for the curation of known regulatory elements from scientific literature. Annotation is collected from users worldwide for various biological assays. http://www.oreganno.org Montgomery SB, Griffith OL, Sleumer MC, Bergman CM, Bilenky M, Pleasance ED, Prychyna Y, Zhang X and Jones SJM. (2006) ORegAnno: An open access database and curation system for literature-derived promoters, transcription factor binding sites and regulatory variation. Bioinformatics 22(5):637-40.

Stanford ENCODE Dataset. This set was generated by aligning full-length cDNA clones from the Mammalian Gene Collection to the human genome rough draft sequence to estimate the start sites of more than 10,000 human transcripts. Genomic sequence just upstream from the 5' end of these cDNA sequences was selected and designated as putative promoters. Random putative promoter were assayed in a luciferase-based transfection assay in multiple cultured cell types. This dataset was extracted from the ORegAnno database. http://www-shgc.stanford.edu/myerslab Trinklein N, Force Aldred S, Saldanha A, and Myers RM. (2003) Identification and functional analysis of human transcriptional promoters. Genome Research 13(2):308-312.

Mammalian Erythroid Cis-Regulatory Modules. A set of cis regulatory modules for mammalian genes expressed in red blood cells reported by Wang et al (2006) by the Hardison lab at PSU, extracted from the ORegAnno database. http://www.bx.psu.edu/~ross/dataset/DatasetHome.html Wang H, Zhang Y, Cheng Y, Zhou Y, King DC, Taylor J, Chiaromonte F, Kasturi J, Petrykowska H, Gibb B, Dorman C, Miller W, Dore LC, Welch J, Weiss MJ, Hardison RC. 2006. Experimental validation of predicted mammalian erythroid cis-regulatory modules. Genome Res. 16(12):1480-92.

STAT1 ChIP-Seq-derived Binding Sites. A set of transcription factor binding sites for STAT1, extracted from the ORegAnno database. Experimental determination of STAT1 binding sites by ChIP-TS (chromatin immunoprecipitation with tag sequencing by the Illumina 1G system, Bentley DR 2006, PMID: 17055251). Robertson G, Hirst M, Bainbridge M, Bilenky M, Zhao Y, Zeng T, Pandoh P, Fichter K, Tam A, Ma K, Prabhu AL, Moksa M, Lee S, Mah D, Sa D, McDonald H, Delaney A, Theissen N, Bernier B, Griffith O, He A, Varhol R, Euskirchen G, Snyder M, Marra M and Jones SJM. (2007) Genome-wide profiles of STAT1 DNA association in HeLa S3 cells using chromatin immunoprecipitation and massively parallel sequencing. Nat Methods.

STAT1 literature-derived Binding Sites. A set of transcription factor binding sites for STAT1, extracted from the ORegAnno database. These sites were collected from the scientific literature to serve as positive controls in support of the experimental determination of STAT1 binding sites by ChIP-TS (chromatin immunoprecipitation with tag sequencing by the Illumina 1G system, Bentley DR 2006, PMID: 17055251). Robertson G, Hirst M, Bainbridge M, Bilenky M, Zhao Y, Zeng T, Pandoh P, Fichter K, Tam A, Ma K, Prabhu AL, Moksa M, Lee S, Mah D, Sa D, McDonald H, Delaney A, Theissen N, Bernier B, Griffith O, He A, Varhol R, Euskirchen G, Snyder M, Marra M and Jones SJM. (2007) Genome-wide profiles of STAT1 DNA association in HeLa S3 cells using chromatin immunoprecipitation and massively parallel sequencing. Nat Methods. [Epub ahead of print]

Approved genes from the Pleiades project www.pleiades.org

Set of retinoic acid response elements (RARE) curated from the literature

The goal of the TFe (Transcription Factor Encyclopedia) project is to create an online encyclopedic collection of well-studied transcription factor proteins, combining a mixture of both hand-curated and automatically-generated content to provide users with a wide set of information relevant to a transcription factor protein of their interest. http://www.cisreg.ca/cgi-bin/tfe/home.pl

TRIM28 ChIP-chip dataset. Complete genomic analysis of KAP1 binding using a 38-array tiling set, identifying ~7,000 KAP1 binding sites. O'Geen H, Squazzo SL, Iyengar S, Blahnik K, Rinn JL, Chang HY, Green R, Farnham PJ. (2007) Genome-wide analysis of KAP1 binding suggests autoregulation of KRAB-ZNFs. PLoS Genet. 3(6):e89.

The Wasserman Lab Set is a special collection of binding sequences for selected sequences.