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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DiscoverySpace: an interactive data analysis application
Neil Robertson,Mehrdad Oveisi-Fordorei,Scott Zuyderduyn,Richard Varhol,Christopher D. Fjell,Marco A. Marra,Steven J.M. Jones,Asim Siddiqui +7 more
TL;DR: DiscoverySpace is a graphical application for bioinformatics data analysis that can seamlessly traverse references between biological databases and draw together annotations in an intuitive tabular interface.
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Myofibril breakdown during atrophy is a delayed response requiring the transcription factor PAX4 and desmin depolymerization.
TL;DR: It is found that phosphorylation and ubiquitination of the desmin cytoskeleton precede its depolymerization, which eventually causes myofibril destruction, and a delayed phase in the atrophy process is uncovered, which involves the induction of genes that facilitate my ofibril breakdown by the transcription factor paired box 4 (PAX4).
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Search for Specific Biomarkers of IFNβ Bioactivity in Patients with Multiple Sclerosis
Sunny Malhotra,Marta F. Bustamante,Francisco Pérez-Miralles,Jordi Río,Mari Carmen Ruiz de Villa,Esteban Vegas,Lara Nonell,Florian Deisenhammer,Nicolás Fissolo,Ramil N. Nurtdinov,Xavier Montalban,Manuel Comabella +11 more
TL;DR: Specific biomarkers of IFNβ bioactivity are identified in order to compare their gene expression induction by type I IFNs with the MxA, and to investigate their potential role in MS pathogenesis.
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Genome-Wide Location Analysis Reveals Distinct Transcriptional Circuitry by Paralogous Regulators Foxa1 and Foxa2
Irina M. Bochkis,Jonathan Schug,Diana Z. Ye,Svitlana Kurinna,Sabrina A. Stratton,Michelle Craig Barton,Klaus H. Kaestner +6 more
TL;DR: In this article, a genome-wide location analysis (ChIP-Seq) was performed for the highly homologous paralogs Foxa1 and Foxa2 transcriptional regulators.
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Phosphatidylinositol 3-kinase signaling in proliferating cells maintains an anti-apoptotic transcriptional program mediated by inhibition of FOXO and non-canonical activation of NFκB transcription factors
Jolyon Terragni,Julie R. Graham,Kenneth W. Adams,Kenneth W. Adams,Michael E. Schaffer,Michael E. Schaffer,John W. Tullai,Geoffrey M. Cooper +7 more
TL;DR: PI 3-kinase signaling in proliferating cells regulates a novel transcriptional program that is highly enriched in genes that regulate apoptosis.
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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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