JASPAR: an open-access database for eukaryotic transcription factor binding profiles.

Nucleic acids research ·Vol. 32 ·No. Database issue ·2004-01-01 ·Pages D91-4

Sandelin A, Alkema W, Engström P, Wasserman WW, Lenhard B

Abstract

The analysis of regulatory regions in genome sequences is strongly based on the detection of potential transcription factor binding sites. The preferred models for representation of transcription factor binding specificity have been termed position-specific scoring matrices. JASPAR is an open-access database of annotated, high-quality, matrix-based transcription factor binding site profiles for multicellular eukaryotes. The profiles were derived exclusively from sets of nucleotide sequences experimentally demonstrated to bind transcription factors. The database is complemented by a web interface for browsing, searching and subset selection, an online sequence analysis utility and a suite of programming tools for genome-wide and comparative genomic analysis of regulatory regions. JASPAR is available at http://jaspar. cgb.ki.se.

MeSH Terms

Animals Base Sequence Binding Sites Computational Biology DNA/genetics,metabolism Databases, Nucleic Acid Eukaryotic Cells/metabolism Humans Information Storage and Retrieval Internet Molecular Sequence Data Response Elements/genetics Software Transcription Factors/metabolism Transcription, Genetic User-Computer Interface

Chemicals

Transcription Factors DNA

Authors & Affiliations

5 authors, click to expand affiliations / ORCID

Sandelin Albin

Center for Genomics and Bioinformatics, Karolinska Institutet, Berzelius väg 35, S-17177 Stockholm, Sweden.

Alkema Wynand

Engström Pär

Wasserman Wyeth W

Lenhard Boris

References (19)

19 references, click to expand

DNA binding sites: representation and discovery.
Bioinformatics. 2000 Jan;16(1):16-23 PMID: 10812473
ANN-Spec: a method for discovering transcription factor binding sites with improved specificity.
Pac Symp Biocomput. 2000;:467-78 PMID: 10902194
A predictive model for regulatory sequences directing liver-specific transcription.
Genome Res. 2001 Sep;11(9):1559-66 PMID: 11544200
TFBS: Computational framework for transcription factor binding site analysis.
Bioinformatics. 2002 Aug;18(8):1135-6 PMID: 12176838
Computational prediction of eukaryotic protein-coding genes.
Nat Rev Genet. 2002 Sep;3(9):698-709 PMID: 12209144
TRANSFAC: transcriptional regulation, from patterns to profiles.
Nucleic Acids Res. 2003 Jan 1;31(1):374-8 PMID: 12520026
Phylogenetic shadowing of primate sequences to find functional regions of the human genome.
Science. 2003 Feb 28;299(5611):1391-4 PMID: 12610304
In silico identification of metazoan transcriptional regulatory regions.
Naturwissenschaften. 2003 Apr;90(4):156-66 PMID: 12712249
YMF: A program for discovery of novel transcription factor binding sites by statistical overrepresentation.
Nucleic Acids Res. 2003 Jul 1;31(13):3586-8 PMID: 12824371
Cluster-Buster: Finding dense clusters of motifs in DNA sequences.
Nucleic Acids Res. 2003 Jul 1;31(13):3666-8 PMID: 12824389
Understanding the language of gene regulation.
Genome Biol. 2003;4(7):327 PMID: 12844355
Identification of functional clusters of transcription factor binding motifs in genome sequences: the MSCAN algorithm.
Bioinformatics. 2003;19 Suppl 1:i169-76 PMID: 12855453
Integrated analysis of yeast regulatory sequences for biologically linked clusters of genes.
Funct Integr Genomics. 2003 Jul;3(3):125-34 PMID: 12827523
Searching for statistically significant regulatory modules.
Bioinformatics. 2003 Oct;19 Suppl 2:ii16-25 PMID: 14534166
Identification of conserved regulatory elements by comparative genome analysis.
J Biol. 2003;2(2):13 PMID: 12760745
A general method applicable to the search for similarities in the amino acid sequence of two proteins.
J Mol Biol. 1970 Mar;48(3):443-53 PMID: 5420325
Sequence logos: a new way to display consensus sequences.
Nucleic Acids Res. 1990 Oct 25;18(20):6097-100 PMID: 2172928
A sensitive method for the determination of protein-DNA binding specificities.
Nucleic Acids Res. 1990 Nov 11;18(21):6197-204 PMID: 2243767
Meta-MEME: motif-based hidden Markov models of protein families.
Comput Appl Biosci. 1997 Aug;13(4):397-406 PMID: 9283754

Article Info

Journal

Nucleic acids research

Abbr.

Nucleic Acids Res

ISSN

1362-4962

DOI

10.1093/nar/gkh012

Published

2004-01-01

Pages

D91-4

Language

English

Region

England

NLM ID

0411011

PMCID

PMC308747

Subset

External Links

PubMed source DOI: 10.1093/nar/gkh012 PMC Full Text View journal details

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