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A new generation of JASPAR, the open-access repository for transcription factor binding site profiles

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      Abstract

      JASPAR is the most complete open-access collection of transcription factor binding site (TFBS) matrices. In this new release, JASPAR grows into a meta-database of collections of TFBS models derived by diverse approaches. We present JASPAR CORE—an expanded version of the original, non-redundant collection of annotated, high-quality matrix-based transcription factor binding profiles, JASPAR FAM—a collection of familial TFBS models and JASPAR phyloFACTS—a set of matrices computationally derived from statistically overrepresented, evolutionarily conserved regulatory region motifs from mammalian genomes. JASPAR phyloFACTS serves as a non-redundant extension to JASPAR CORE, enhancing the overall breadth of JASPAR for promoter sequence analysis. The new release of JASPAR is available at .

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      Most cited references 15

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      TRANSFAC: transcriptional regulation, from patterns to profiles.

      The TRANSFAC database on eukaryotic transcriptional regulation, comprising data on transcription factors, their target genes and regulatory binding sites, has been extended and further developed, both in number of entries and in the scope and structure of the collected data. Structured fields for expression patterns have been introduced for transcription factors from human and mouse, using the CYTOMER database on anatomical structures and developmental stages. The functionality of Match, a tool for matrix-based search of transcription factor binding sites, has been enhanced. For instance, the program now comes along with a number of tissue-(or state-)specific profiles and new profiles can be created and modified with Match Profiler. The GENE table was extended and gained in importance, containing amongst others links to LocusLink, RefSeq and OMIM now. Further, (direct) links between factor and target gene on one hand and between gene and encoded factor on the other hand were introduced. The TRANSFAC public release is available at http://www.gene-regulation.com. For yeast an additional release including the latest data was made available separately as TRANSFAC Saccharomyces Module (TSM) at http://transfac.gbf.de. For CYTOMER free download versions are available at http://www.biobase.de:8080/index.html.
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        Systematic discovery of regulatory motifs in human promoters and 3' UTRs by comparison of several mammals.

        Comprehensive identification of all functional elements encoded in the human genome is a fundamental need in biomedical research. Here, we present a 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 (3' UTRs). The promoter analysis yields 174 candidate motifs, including most previously known transcription-factor binding sites and 105 new motifs. The 3'-UTR analysis yields 106 motifs likely to be involved in post-transcriptional regulation. Nearly one-half are associated with microRNAs (miRNAs), leading to the discovery of many new miRNA genes and their likely target genes. Our results suggest that previous estimates of the number of human miRNA genes were low, and that miRNAs regulate at least 20% of human genes. The overall results provide a systematic view of gene regulation in the human, which will be refined as additional mammalian genomes become available.
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          The ENCODE (ENCyclopedia Of DNA Elements) Project.

          The ENCyclopedia Of DNA Elements (ENCODE) Project aims to identify all functional elements in the human genome sequence. The pilot phase of the Project is focused on a specified 30 megabases (approximately 1%) of the human genome sequence and is organized as an international consortium of computational and laboratory-based scientists working to develop and apply high-throughput approaches for detecting all sequence elements that confer biological function. The results of this pilot phase will guide future efforts to analyze the entire human genome.
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            Author and article information

            Affiliations
            simpleDepartment for Molecular Biomedical Research (DMBR), VIB—Ghent University Technologiepark 927 B-9052 Ghent (Zwijnaarde), Belgium
            1simpleGenome Exploration Research Group, RIKEN Genomic Sciences Center (GSC), RIKEN Yokohama Institute 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama, Kanagawa 230-0045, Japan
            2simpleCentre for Molecular Medicine and Therapeutics, Department of Medical Genetics, University of British Columbia Vancouver, BC, Canada
            3simpleComputational Biology Unit, Bergen Center for Computational Science, University of Bergen Thormøhlensgate 55, N-5008 Bergen, Norway
            Author notes
            *To whom correspondence should be addressed. Tel: +47 55 84362; Fax: +47 555 84295; Email: Boris.Lenhard@ 123456bccs.uib.no

            The authors wish it to be known that, in their opinion, the first two authors should be regarded as joint First Authors

            Journal
            Nucleic Acids Res
            Nucleic Acids Research
            Nucleic Acids Research
            Oxford University Press
            0305-1048
            1362-4962
            01 January 2006
            01 January 2006
            28 December 2005
            : 34
            : Database issue
            : D95-D97
            1347477
            10.1093/nar/gkj115
            16381983
            © The Author 2006. Published by Oxford University Press. All rights reserved

            The online version of this article has been published under an open access model. Users are entitled to use, reproduce, disseminate, or display the open access version of this article for non-commercial purposes provided that: the original authorship is properly and fully attributed; the Journal and Oxford University Press are attributed as the original place of publication with the correct citation details given; if an article is subsequently reproduced or disseminated not in its entirety but only in part or as a derivative work this must be clearly indicated. For commercial re-use, please contact journals.permissions@ 123456oxfordjournals.org

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            Genetics

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