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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Walking pathways with positive feedback loops reveal DNA methylation biomarkers of colorectal cancer.
Alexander E. Kel,Ulyana A. Boyarskikh,Philip Stegmaier,Leonid S. Leskov,Andrey Sokolov,Ivan S. Yevshin,Nikita Mandrik,Daria Stelmashenko,Jeannette Koschmann,Olga V. Kel-Margoulis,Mathias Krull,Anna Martínez-Cardús,Sebastian Moran,Manel Esteller,Fedor A. Kolpakov,Maxim L. Filipenko,Edgar Wingender +16 more
TL;DR: In this paper, a method for finding potential causal relationships between epigenetic changes (DNA methylations) in gene regulatory regions that affect transcription factor binding sites (TFBS) and gene expression changes was proposed.
Journal ArticleDOI
Machine learning for regulatory analysis and transcription factor target prediction in yeast.
TL;DR: A supervised learning approach to site identification using support vector machines (SVMs) to combine 26 different data types and finds that SVM-based classifiers provide a robust framework for analysis of regulatory networks.
Journal ArticleDOI
Characterization of three distinct metallothionein genes of the Ag-hyperaccumulating ectomycorrhizal fungus Amanita strobiliformis.
Kateřina Hložková,Michaela Matěnová,Petra Žáčková,Hynek Strnad,Hana Hršelová,Miluše Hroudová,Pavel Kotrba +6 more
TL;DR: The data indicate that A. strobiliformis can specifically employ different MT genes for functions in the cellular handling of Ag and Cu (As MT1s) and Zn (AsMT3) and that AsMT3 can protect the yeasts against Zn toxicity.
Journal ArticleDOI
Predicting tissue specific transcription factor binding sites
Shan Zhong,Xin He,Ziv Bar-Joseph +2 more
TL;DR: A new computational approach, PIPES, is developed, which integrates in vitro protein binding microarrays, sequence conservation and tissue-specific epigenetic information, and improves over existing methods on distinguishing between in vivo bound and unbound sequences.
Journal ArticleDOI
Orphan nuclear receptor NR2F6 acts as an essential gatekeeper of Th17 CD4 + T cell effector functions
TL;DR: The NR2F6 target gene repertoire thus identifies a general anti-inflammatory gatekeeper role for this orphan receptor, and will enable a greater knowledge of the genetic, immune, and environmental mechanisms that lead to chronic inflammation and of certain autoimmune disorders in a given individual.
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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