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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Journal ArticleDOI
Regulation of Sec16 levels and dynamics links proliferation and secretion.
Kerstin D. Tillmann,Veronika Reiterer,Francesco Baschieri,Julia Hoffmann,Valentina Millarte,Mark A. Hauser,Arnon Mazza,Nir Atias,Daniel F. Legler,Roded Sharan,Matthias Weiss,Hesso Farhan +11 more
TL;DR: It is found that Sec16A is a short-lived protein that is regulated by growth factors in a manner dependent on Egr family transcription factors, which provides a mechanistic basis for the previously proposed link between secretion and proliferation.
Journal ArticleDOI
Psoriasis drug development and GWAS interpretation through in silico analysis of transcription factor binding sites
William R. Swindell,Mrinal K. Sarkar,Philip E. Stuart,John J. Voorhees,James T. Elder,Andrew Johnston,Johann E. Gudjonsson +6 more
TL;DR: An approach that connects transcriptome informatics to cdODN drug development and enhances the ability to interpret GWAS findings is developed, identifying new TF/uDBP candidates and showing that PREs are disproportionately disrupted by psoriasis risk alleles.
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A functional SNP in the regulatory region of the decay-accelerating factor gene associates with extraocular muscle pareses in myasthenia gravis.
Jeannine M. Heckmann,H Uwimpuhwe,R Ballo,Mandeep Kaur,Vladimir B. Bajic,Vladimir B. Bajic,Sharon Prince +6 more
TL;DR: The findings suggest that at critical periods during autoimmune MG, this SNP may result in inadequate DAF upregulation with consequent complement-mediated EOM damage, andceptible individuals may benefit from anti-complement therapy in addition to immunosuppression.
Journal ArticleDOI
Text-mining assisted regulatory annotation
Stein Aerts,Maximilian Haeussler,Steven Van Vooren,Obi L. Griffith,Paco Hulpiau,Steven J.M. Jones,Stephen B. Montgomery,Casey M. Bergman +7 more
TL;DR: It is demonstrated that text-mining technologies can be successfully integrated with genome annotation systems, thereby increasing the availability of annotated cis-regulatory data needed to catalyze advances in the field of gene regulation.
Journal ArticleDOI
The PAX258 gene subfamily: A comparative perspective
TL;DR: A comprehensive comparative overview of the vertebrate PAX2, PAX5 and PAX8 gene subfamily, derived from an ancient class of paired box genes and arose from whole genome duplication events, and their ancient and divergent roles.
References
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TRANSFAC®: transcriptional regulation, from patterns to profiles
V. Matys,Ellen Fricke,Robert Geffers,Ellen Gößling,Martin Haubrock,Reinhard Hehl,Klaus Hornischer,Dagmar Karas,Alexander E. Kel,Olga V. Kel-Margoulis,Dorothee-U. Kloos,Sigrid Land,Birgit Lewicki-Potapov,Holger Michael,Richard Münch,Ingmar Reuter,Stella Rotert,H. Saxel,Maurice Scheer,S. Thiele,Edgar Wingender +20 more
TL;DR: 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.
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