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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Complementary Post Transcriptional Regulatory Information is Detected by PUNCH-P and Ribosome Profiling
TL;DR: The results reported here support the conjecture that for gaining a full post-transcriptional regulation picture one should integrate the two approaches, and show that combining the approaches better predicts steady state changes in protein abundance.
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Prediction of cis-regulatory elements controlling genes differentially expressed by retinal and choroidal vascular endothelial cells
Dongseok Choi,Binoy Appukuttan,S. J. Binek,Stephen R. Planck,J. Timothy Stout,James T. Rosenbaum,Justine R. Smith +6 more
TL;DR: The findings raise the possibility of exploiting specific cis-regulatory motifs to target therapy at the ocular endothelial cells subtypes responsible for neovascular age-related macular degeneration or proliferative diabetic retinopathy.
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Identifying and Analyzing Novel Epilepsy-Related Genes Using Random Walk with Restart Algorithm
Wei Guo,Dong-Mei Shang,Jing-Hui Cao,Kai-Yan Feng,Yichun He,Yang Jiang,ShaoPeng Wang,Yufei Gao +7 more
TL;DR: A pioneering computational workflow was proposed to predict novel epilepsy-related genes using the random walk with restart (RWR) algorithm and it is believed that the proposed workflow can also be applied to identify genes related to other diseases and deepen the understanding of the mechanisms of these diseases.
Posted ContentDOI
High throughput screening identifies SOX2 as a Super Pioneer Factor that inhibits DNA methylation maintenance at its binding sites
TL;DR: While most SPFs induce TET-dependent active DNA dem methylation, SOX2 binding leads to passive demethylation by inhibition of the maintenance methyltransferase DNMT1 during replication, which suggests a novel mechanism allowing TFs to interfere with the epigenetic memory during DNA replication.
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Evolutionary conservation and divergence of the human brain transcriptome.
TL;DR: In this article, the authors compare 116 independent data sets derived from human, mouse, and non-human primate representing more than 15,000 total samples and identify robust co-expression modules reflecting whole-brain and regional patterns of gene expression.
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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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