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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Genome-wide prediction of transcription factor binding sites using an integrated model.
TL;DR: Chromia significantly outperforms other methods in the identification of 13 transcription factor binding sites in mouse embryonic stem cells, evaluated by both binding (ChIP-seq) and functional (RNA interference knockdown) experiments.
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A perspective of promoter architecture from the CCAAT box.
TL;DR: The new features of the CCAAT box and the link with the neighbouring elements will help in the functional classification of promoters, as well as validate the NF-Y-dependency of several promoters with functional assays.
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Combining tissue transcriptomics and urine metabolomics for breast cancer biomarker identification
TL;DR: Bomarkers identified by the present study have increased coherence and robustness because the significances of biomarkers are validated in both gene expression profiles and metabolic profiles, and showed consistency in pathways' gene expression as well as urine samples.
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Multi-Organ Expression Profiling Uncovers a Gene Module in Coronary Artery Disease Involving Transendothelial Migration of Leukocytes and LIM Domain Binding 2: The Stockholm Atherosclerosis Gene Expression (STAGE) Study
Sara Hägg,Sara Hägg,Josefin Skogsberg,Jesper Lundström,Jesper Lundström,Peri Noori,Roland Nilsson,Hua Zhong,Shohreh Maleki,Ming-Mei Shang,Björn Brinne,Maria Bradshaw,Maria Bradshaw,Vladimir B. Bajic,Vladimir B. Bajic,Ann Samnegård,Angela Silveira,Lee M. Kaplan,Bruna Gigante,Karin Leander,Ulf de Faire,Stefan Rosfors,Ulf Lockowandt,Ulf Lockowandt,Jan Liska,Jan Liska,Peter Konrad,Rabbe Takolander,Anders Franco-Cereceda,Anders Franco-Cereceda,Eric E. Schadt,Torbjörn Ivert,Torbjörn Ivert,Anders Hamsten,Jesper Tegnér,Jesper Tegnér,Johan Björkegren,Johan Björkegren +37 more
TL;DR: The transcription co-factor LIM domain binding 2 (LDB2) was identified as a potential high-hierarchy regulator of the A-module, a notion supported by subnetwork analysis, by cellular and lesion expression of LDB2, and by the expression of 13 TEML genes in Ldb2–deficient arterial wall.
Journal ArticleDOI
CiiiDER: A tool for predicting and analysing transcription factor binding sites.
Linden J. Gearing,Linden J. Gearing,Helen E. Cumming,Helen E. Cumming,Ross L Chapman,Ross L Chapman,Alexander M. Finkel,Alexander M. Finkel,Isaac B. Woodhouse,Isaac B. Woodhouse,Kevin Luu,Kevin Luu,Jodee Ann Gould,Jodee Ann Gould,Samuel C. Forster,Samuel C. Forster,Paul J. Hertzog,Paul J. Hertzog +17 more
TL;DR: CiiiDER, an integrated computational toolkit for transcription factor binding analysis, written in the Java programming language, is presented to make it independent of computer operating system.
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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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