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      TFCat: the curated catalog of mouse and human transcription factors

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          Abstract

          TFCat is a catalog of mouse and human transcription factors based on a reliable core collection of annotations obtained by expert review of the scientific literature

          Abstract

          Unravelling regulatory programs governed by transcription factors (TFs) is fundamental to understanding biological systems. TFCat is a catalog of mouse and human TFs based on a reliable core collection of annotations obtained by expert review of the scientific literature. The collection, including proven and homology-based candidate TFs, is annotated within a function-based taxonomy and DNA-binding proteins are organized within a classification system. All data and user-feedback mechanisms are available at the TFCat portal http://www.tfcat.ca.

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          Gene Ontology: tool for the unification of biology

          Michael Ashburner, Catherine A. Ball, Judith Blake … (2002)
          Genomic sequencing has made it clear that a large fraction of the genes specifying the core biological functions are shared by all eukaryotes. Knowledge of the biological role of such shared proteins in one organism can often be transferred to other organisms. The goal of the Gene Ontology Consortium is to produce a dynamic, controlled vocabulary that can be applied to all eukaryotes even as knowledge of gene and protein roles in cells is accumulating and changing. To this end, three independent ontologies accessible on the World-Wide Web (http://www.geneontology.org) are being constructed: biological process, molecular function and cellular component.
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            JASPAR: an open-access database for eukaryotic transcription factor binding profiles.

            Albin Sandelin, Wynand Alkema, Pär G. Engström … (2004)
            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.
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              SMART 4.0: towards genomic data integration.

              Ivica Letunic, Richard Copley, Steffen Schmidt … (2004)
              SMART (Simple Modular Architecture Research Tool) is a web tool (http://smart.embl.de/) for the identification and annotation of protein domains, and provides a platform for the comparative study of complex domain architectures in genes and proteins. The January 2004 release of SMART contains 685 protein domains. New developments in SMART are centred on the integration of data from completed metazoan genomes. SMART now uses predicted proteins from complete genomes in its source sequence databases, and integrates these with predictions of orthology. New visualization tools have been developed to allow analysis of gene intron-exon structure within the context of protein domain structure, and to align these displays to provide schematic comparisons of orthologous genes, or multiple transcripts from the same gene. Other improvements include the ability to query SMART by Gene Ontology terms, improved structure database searching and batch retrieval of multiple entries.
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                Author and article information

                Journal
                Journal ID (nlm-ta): Genome Biol
                Title: Genome Biology
                Publisher: BioMed Central
                ISSN (Print): 1465-6906
                ISSN (Electronic): 1465-6914
                Publication date (Print): 2009
                Publication date (Electronic): 12 March 2009
                Volume: 10
                Issue: 3
                Page: R29
                Affiliations
                [1 ]Department of Medical Genetics, Centre for Molecular Medicine and Therapeutics - Child and Family Research Institute, University of British Columbia, West 28th Avenue, Vancouver, V5Z 4H4, Canada
                [2 ]Departments of Medicine and Human Genetics, McGill University and Genome Quebec Innovation Centre, Dr. Penfield Avenue, Montreal, H3A 1A4, Canada
                [3 ]Banting and Best Department of Medical Research, University of Toronto, College Street, Toronto, M5S 3E1, Canada
                [4 ]Center for Developmental Therapeutics, Seattle Children's Research Institute, Olive Way, Seattle, 98101, USA
                Article
                Publisher ID: gb-2009-10-3-r29
                DOI: 10.1186/gb-2009-10-3-r29
                PMC ID: 2691000
                PubMed ID: 19284633
                SO-VID: 72c58e7c-de76-4d76-a3f8-5fb360ec36bd
                Copyright © Copyright © 2009 Fulton et al.; licensee BioMed Central Ltd.
                License:

                This is an open access article distributed under the terms of the Creative Commons Attribution License ( http://creativecommons.org/licenses/by/2.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.

                History
                Date received : 5 December 2008
                Date revision received : 26 February 2009
                Date accepted : 12 March 2009
                Categories
                Subject: Software

                ScienceOpen disciplines: Genetics
                Data availability:
                ScienceOpen disciplines: Genetics

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