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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An α-smooth muscle actin (acta2/αsma) zebrafish transgenic line marking vascular mural cells and visceral smooth muscle cells.
Thomas Whitesell,Regan M. Kennedy,Alyson D. Carter,Evvi-Lynn Rollins,Sonja Georgijevic,Massimo Santoro,Sarah J. Childs +6 more
TL;DR: The data suggests that zebrafish mural cells develop relatively late, and have little mobility once they associate with vessels.
Journal ArticleDOI
Similarity regression predicts evolution of transcription factor sequence specificity.
Samuel A. Lambert,Ally Yang,Alexander Sasse,Gwendolyn Cowley,Mihai Albu,Mark X. Caddick,Quaid Morris,Matthew T. Weirauch,Matthew T. Weirauch,Timothy P. Hughes,Timothy P. Hughes +10 more
TL;DR: It is concluded that diversification in DNA-binding motifs is pervasive, and a new tool and updated resource to study TF diversity and gene regulation across eukaryotes is presented.
Journal ArticleDOI
Mapping and analysis of Caenorhabditis elegans transcription factor sequence specificities
Kamesh Narasimhan,Samuel A. Lambert,Ally Yang,Jeremy Riddell,Sanie Mnaimneh,Hong Zheng,Mihai Albu,Hamed S. Najafabadi,John S. Reece-Hoyes,Juan I. Fuxman Bass,Albertha J.M. Walhout,Matthew T. Weirauch,Timothy P. Hughes +12 more
TL;DR: In this article, protein binding microarray experiments on representatives of canonical TF families in C. elegans were performed, obtaining motifs for 129 TFs and increasing coverage of binding specificities to 292 of the estimated 763 sequence-specific transcription factors (TFs).
Journal ArticleDOI
Unipro UGENE NGS pipelines and components for variant calling, RNA-seq and ChIP-seq data analyses
Olga Golosova,Ross Henderson,Yuriy Vaskin,Andrei Gabrielian,German Grekhov,Vijayaraj Nagarajan,Andrew J. Oler,Mariam Quinones,Darrell E. Hurt,Mikhail Fursov,Yentram Huyen +10 more
TL;DR: This work presents NGS pipelines “Variant Calling with SAMtools”, “Tuxedo Pipeline for RNA-seq Data Analysis” and “Cistrome Pipeline for ChIP-seq data analysis” integrated into the Unipro UGENE desktop toolkit.
Journal ArticleDOI
Automated protein-DNA interaction screening of Drosophila regulatory elements
Korneel Hens,Jean-Daniel Feuz,Alina Isakova,Antonina Iagovitina,Andreas Massouras,Julien Bryois,Patrick Callaerts,Patrick Callaerts,Susan E. Celniker,Bart Deplancke +9 more
TL;DR: The development and validation of a high-throughput yeast one-hybrid platform, which enables screening of DNA elements versus an array of full-length, sequence-verified clones containing over 85% of predicted Drosophila transcription factors, and identifies two new regulators of sine oculis gene expression and hence eye development.
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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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