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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Flow-dependent regulation of genome-wide mRNA and microRNA expression in endothelial cells in vivo
TL;DR: These microarray results were used to identify novel mechanosensitive genes such as DNA methyltransferase-1 and miR-712 that play key roles in atherosclerosis and report on in-depth information on experimental procedures along with an example of usage of these data.
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Differential regulation of human hepatic flavin containing monooxygenase 3 (FMO3) by CCAAT/enhancer-binding protein β (C/EBPβ) liver inhibitory and liver activating proteins
TL;DR: Transcription factor transient expression and treatment with histone deacetylase or DNA methylase inhibitors identified decreased hepatic nuclear factor levels and DNA hypermethylation as mechanisms suppressing HepG2 FMO3 expression and the absence of major deficiencies in transcriptional machinery suggested that within limits, the HepG 2 model is suitable for the study of F MO3 regulation.
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Epigenomes of Human Hearts Reveal New Genetic Variants Relevant for Cardiac Disease and Phenotype
Wilson Lek Wen Tan,Wilson Lek Wen Tan,Chukwuemeka George Anene-Nzelu,Chukwuemeka George Anene-Nzelu,Eleanor Wong,Eleanor Wong,Chang Jie Mick Lee,Chang Jie Mick Lee,Hui San Tan,Hui San Tan,Sze Jing Tang,Arnaud Perrin,Arnaud Perrin,Kan Xing Wu,Wenhao Zheng,Wenhao Zheng,Robert John Ashburn,Bangfen Pan,Bangfen Pan,May Yin Lee,Matias Ilmari Autio,Matias Ilmari Autio,Michael Morley,Wai Leong Tam,Wai Leong Tam,Christine Cheung,Christine Cheung,Kenneth B. Margulies,Leilei Chen,Thomas P. Cappola,Marie Loh,Marie Loh,Marie Loh,John C. Chambers,Shyam Prabhakar,Roger Foo,Roger Foo +36 more
TL;DR: 62 unique loci were identified by colocalization of haQTLs with the subthreshold loci of heart-related genome-wide association studies datasets, implying a surprising direct association between these specific TF and local histone acetylation in human hearts.
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Genome-wide analysis of the transcription factor binding preference of human bi-directional promoters and functional annotation of related gene pairs
TL;DR: Insight is provided into the function constraints of bi-directional genes and found that paired genes are biased toward functional similarities, as well as proposed a set of putative regulatory motifs in the bi- Directional promoters for further experimental studies to investigate transcriptional regulation ofBi-directionAL genes.
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Mutant IDH Inhibits IFNγ–TET2 Signaling to Promote Immunoevasion and Tumor Maintenance in Cholangiocarcinoma
TL;DR: Zhu et al. as discussed by the authors showed that mIDH1 supports cholangiocarcinoma tumor maintenance through an immuno-evasion program centered on dual (R)-2-hydroxyglutarate-mediated mechanisms: suppression of CD8+ T-cell activity and tumor cell-autonomous inactivation of TET2 DNA demethylase.
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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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