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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Fas Promotes T Helper 17 Cell Differentiation and Inhibits T Helper 1 Cell Development by Binding and Sequestering Transcription Factor STAT1
Gerd Meyer zu Hörste,Dariusz Przybylski,Markus A. Schramm,Chao Wang,Alexandra Schnell,Youjin Lee,Raymond A. Sobel,Aviv Regev,Vijay K. Kuchroo,Vijay K. Kuchroo +9 more
TL;DR: Fas is identified as a regulator of the Th17‐to‐Th1 cell balance by controlling the availability of opposing STAT1 and STAT3 to have a direct impact on autoimmunity.
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GAPWM: a genetic algorithm method for optimizing a position weight matrix.
TL;DR: GAPWM substantially increased the sensitivity/specificity of a poorly estimated PWM and further improved the quality of a good PWM, and provides an alternative for obtaining high-quality PWMs for genome-wide identification of transcription factor binding sites.
Journal ArticleDOI
OnTheFly: a database of Drosophila melanogaster transcription factors and their binding sites
TL;DR: OnTheFly, a database comprising a systematic collection of transcription factors of Drosophila melanogaster and their DNA-binding sites, provides a comprehensive view of TFs and their binding sites that will be a valuable resource for deciphering non-coding regulatory DNA.
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Proteomics: from technology developments to biological applications.
Mohamed Abu-Farha,Fred Elisma,Houjiang Zhou,Ruijun Tian,Hu Zhou,Mehmet Selim Asmer,Daniel Figeys +6 more
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The rs6983267 SNP is associated with MYC transcription efficiency, which promotes progression and worsens prognosis of colorectal cancer.
Yasushi Takatsuno,Koshi Mimori,Ken Yamamoto,Tetsuya Sato,Atsushi Niida,Hiroshi Inoue,Seiya Imoto,Shuhei Kawano,Rui Yamaguchi,Hiroyuki Toh,Hisae Iinuma,Shinya Ishimaru,Shinya Ishimaru,Hideshi Ishii,Hideshi Ishii,Sadao Suzuki,Shinkan Tokudome,Masahiko Watanabe,Jun Ichi Tanaka,Shin-ei Kudo,Hidetaka Mochizuki,Masato Kusunoki,Kazutaka Yamada,Yasuhiro Shimada,Yoshihiro Moriya,Satoru Miyano,Kenichi Sugihara,Masaki Mori +27 more
TL;DR: The presence of the minor allele of rs6983267 at 8q24.21 worsened the prognosis of CRC through up-regulation of MYC transcription and progression of CRC may require global CNA in the presence ofThe major allele and with lack of MyC transcription.
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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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