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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Transcriptional regulation of gene expression clusters in motor neurons following spinal cord injury
Jesper Ryge,Ole Winther,Ole Winther,Jacob Wienecke,Albin Sandelin,Ann-Charlotte Westerdahl,Hans Hultborn,Ole Kiehn +7 more
TL;DR: This analysis provides important clues to the underlying mechanisms of transcriptional regulation responsible for the increased excitability observed in motor neurons in the late chronic phase of spinal Cord injury suggesting alternative targets for treatment of spinal cord injury.
Journal ArticleDOI
TransFind—predicting transcriptional regulators for gene sets
TL;DR: TransFind, a simple-to-use web servers able to combine state-of-the-art prediction methods with phylogenetic analysis and appropriate multiple testing corrected statistics, which returns the results within a short time, is developed.
Journal ArticleDOI
Motif discovery and motif finding from genome-mapped DNase footprint data
TL;DR: New motifs can recognize footprints with a greater sensitivity at the same false positive rate than existing models and possible overfitting of constructed motifs are discussed.
Journal ArticleDOI
Identification of Novel Nuclear Factor of Activated T Cell (NFAT)-associated Proteins in T Cells
Christian H. Gabriel,Fridolin Gross,Martin Karl,Heike Stephanowitz,Anna Floriane Hennig,Melanie Weber,Stefanie Gryzik,Ivo Bachmann,Katharina Hecklau,Jürgen Wienands,Johannes Schuchhardt,Hanspeter Herzel,Andreas Radbruch,Eberhard Krause,Ria Baumgrass +14 more
TL;DR: The computational analysis discovered that binding motifs for RUNX and CREB1 are found preferentially in the direct vicinity of NFAT-binding motifs and in a distinct orientation to them, providing evidence that mTOR and CHEK1 kinase activity influence NFAT's transcriptional potency.
Journal ArticleDOI
FOSL1 controls the assembly of endothelial cells into capillary tubes by direct repression of αv and β3 integrin transcription.
Sandrine Evellin,Federico Galvagni,Alessio Zippo,Francesco Neri,Maurizio Orlandini,Danny Incarnato,Daniela Dettori,Stefanie Neubauer,Horst Kessler,Horst Kessler,Erwin F. Wagner,Salvatore Oliviero +11 more
TL;DR: It is shown that Fosl1−/− embryonic stem cells differentiate into endothelial cells but fail to correctly assemble into primitive capillaries and to form tube-like structures, suggesting that FOSL1-dependent negative regulation of αvβ3 expression on endothelial Cells is required for endothelial assembly into vessel structures.
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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