TRANSFAC® and its module TRANSCompel®: transcriptional gene regulation in eukaryotes
V. Matys,Olga V. Kel-Margoulis,Ellen Fricke,Ines Liebich,Sigrid Land,A. Barre-Dirrie,Ingmar Reuter,D. Chekmenev,Mathias Krull,Klaus Hornischer,Nico Voss,Philip Stegmaier,Birgit Lewicki-Potapov,H. Saxel,Alexander E. Kel,Edgar Wingender +15 more
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TLDR
The TRANSFAC® database on transcription factors, their binding sites, nucleotide distribution matrices and regulated genes as well as the complementing database TRANSCompel® on composite elements have been further enhanced on various levels.Abstract:
The TRANSFAC database on transcription factors, their binding sites, nucleotide distribution matrices and regulated genes as well as the complementing database TRANSCompel on composite elements have been further enhanced on various levels. A new web interface with different search options and integrated versions of Match and Patch provides increased functionality for TRANSFAC. The list of databases which are linked to the common GENE table of TRANSFAC and TRANSCompel has been extended by: Ensembl, UniGene, EntrezGene, HumanPSD and TRANSPRO. Standard gene names from HGNC, MGI and RGD, are included for human, mouse and rat genes, respectively. With the help of InterProScan, Pfam, SMART and PROSITE domains are assigned automatically to the protein sequences of the transcription factors. TRANSCompel contains now, in addition to the COMPEL table, a separate table for detailed information on the experimental EVIDENCE on which the composite elements are based. Finally, for TRANSFAC, in respect of data growth, in particular the gain of Drosophila transcription factor binding sites (by courtesy of the Drosophila DNase I footprint database) and of Arabidopsis factors (by courtesy of DATF, Database of Arabidopsis Transcription Factors) has to be stressed. The here described public releases, TRANSFAC 7.0 and TRANSCompel 7.0, are accessible under http://www.gene-regulation.com/pub/databases.html.read more
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Systematic localization of common disease-associated variation in regulatory DNA.
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References
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Journal ArticleDOI
Genew: the Human Gene Nomenclature Database, 2004 updates
TL;DR: Genew, the Human Gene Nomenclature Database http://www.gene.pl is the only resource that provides data for all human genes that have approved symbols, containing over 22 000 records, 75% of which are represented online by a publicly searchable text file.
Journal ArticleDOI
TRANSCompel: a database on composite regulatory elements in eukaryotic genes.
TL;DR: The TRANSCompel database emphasizes the key role of specific interactions between transcription factors binding to their target sites providing specific features of gene regulation in a particular cellular content, and has developed the program CATCH for searching potential CEs in DNA sequences.
Journal ArticleDOI
TRANSPATH: an integrated database on signal transduction and a tool for array analysis.
TL;DR: TRANSPATH is a database system about gene regulatory networks that combines encyclopedic information on signal transduction with tools for visualization and analysis and the integration with TRANSFAC provides the possibility to obtain complete signaling pathways from ligand to target genes and their products.
Journal ArticleDOI
The TRANSPATH signal transduction database: a knowledge base on signal transduction networks
TL;DR: UNLABELLED TRANSPATH is an information system on gene-regulatory pathways, and an extension module to the TRANSFAC database system, that focuses on pathways involved in the regulation of transcription factors in different species, mainly human, mouse and rat.
Journal ArticleDOI
Annotating the human proteome: the Human Proteome Survey Database (HumanPSD™) and an in-depth target database for G protein-coupled receptors (GPCR-PD™) from Incyte Genomics
Peter E. Hodges,Pauline M. Carrico,Jennifer D. Hogan,Kathy E. O'Neill,J. J. Owen,Mary E. Mangan,Brian P. Davis,Joan E. Brooks,James I. Garrels +8 more
TL;DR: GPCR-PD contains more than 3200 Protein Reports from the three mammalian species for G protein-coupled receptors, their protein ligands, associated G-proteins and their downstream signaling proteins that displays annotations of experimental findings from over 10 000 publications.
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