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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FIREWACh: high-throughput functional detection of transcriptional regulatory modules in mammalian cells
Matthew Murtha,Zeynep Tokcaer-Keskin,Zuojian Tang,Francesco Strino,Xi Chen,Yatong Wang,Xiangmei Xi,Claudio Basilico,Stuart M. Brown,Richard Bonneau,Yuval Kluger,Lisa Dailey +11 more
TL;DR: A high-throughput functional assay for directly identifying active promoter and enhancer elements called FIREWACh (Functional Identification of Regulatory Elements Within Accessible Chromatin), which was used to simultaneously assess over 80,000 DNA fragments derived from nucleosome-free regions within the chromatin of embryonic stem cells and identify 6,364 active regulatory elements.
Journal ArticleDOI
Beyond microarrays: Finding key transcription factors controlling signal transduction pathways
TL;DR: A novel computational approach for revealing key transcription factors by knowledge-based analysis of gene expression data with the help of databases on gene regulatory networks (TRANSFAC® and TRANSPATH®).
Journal ArticleDOI
Novel mechanism of positive versus negative regulation by thyroid hormone receptor β1 (TRβ1) identified by genome-wide profiling of binding sites in mouse liver.
Preeti Ramadoss,Brian J. Abraham,Linus T.-Y. Tsai,Yiming Zhou,Ricardo H. Costa-e-Sousa,Felix D. Ye,Martin Bilban,Keji Zhao,Anthony N. Hollenberg +8 more
TL;DR: This study demonstrates that a mechanism other than differential co-regulator recruitment is involved in transcriptional regulation by TRβ1 Triiodothyronine (T3) regulates key metabolic processes in the liver through the thyroid hormone receptor, TR β1.
Journal ArticleDOI
Combining transcription factor binding affinities with open-chromatin data for accurate gene expression prediction
Florian Schmidt,Florian Schmidt,Nina Gasparoni,Gilles Gasparoni,Kathrin Gianmoena,Cristina Cadenas,Julia K. Polansky,Peter Ebert,Karl Nordström,Matthias Barann,Anupam Sinha,Sebastian Froehler,Jieyi Xiong,Azim Dehghani Amirabad,Azim Dehghani Amirabad,Fatemeh Behjati Ardakani,Fatemeh Behjati Ardakani,Barbara Hutter,Gideon Zipprich,Baerbel Felder,Jürgen Eils,Benedikt Brors,Wei Chen,Jan G. Hengstler,Alf Hamann,Thomas Lengauer,Philip Rosenstiel,Jörn Walter,Marcel H. Schulz +28 more
TL;DR: A novel segmentation-based method, TEPIC, is reported to predict TF binding by combining sets of OCRs with position weight matrices, and finds low affinity binding sites to improve the ability to explain gene expression variability compared to the standard presence/absence classification of binding sites.
Journal ArticleDOI
Enhancer Architecture and Essential Core Regulatory Circuitry of Chronic Lymphocytic Leukemia.
Christopher J. Ott,Alexander J. Federation,Logan Schwartz,Siddha Kasar,Josephine L. Klitgaard,Romina E. Lenci,Qiyuan Li,Qiyuan Li,Matthew A. Lawlor,Stacey M. Fernandes,Amanda Souza,Donald R. Polaski,Deepti Gadi,Matthew L. Freedman,Jennifer R. Brown,James E. Bradner +15 more
TL;DR: It is discovered that the essential super enhancer factor PAX5 dominates CLL regulatory nodes and is essential for CLL cell survival, and Targeting enhancer signaling via BET bromodomain inhibition disrupts super enhancers-dependent gene expression with selective effects on CLL core regulatory circuitry, conferring potent anti-tumor activity.
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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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