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
Reads0
Chats0
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
Citations
More filters
Journal ArticleDOI
Widespread Alu repeat-driven expansion of consensus DR2 retinoic acid response elements during primate evolution
TL;DR: Mapping the positions of all consensus DR-type hormone response elements in the human genome found that DR2 motifs, recognized by retinoic acid receptors (RARs), are heavily overrepresented, providing strong support for the notion that Alu-mediated expansion of DR elements contributed to the evolution of gene regulation by RARs and other nuclear receptors in primates and humans.
Journal ArticleDOI
Using bioinformatics to predict the functional impact of SNVs
Melissa S. Cline,Rachel Karchin +1 more
TL;DR: The essential components of bioinformatics tools that predict functional SNVs are described and it is shown that the black box nature of many tools can be a pitfall for researchers.
Journal ArticleDOI
Proteomic Analyses of Human Regulatory T Cells Reveal Adaptations in Signaling Pathways that Protect Cellular Identity
Eloy Cuadrado,Maartje van den Biggelaar,Sander de Kivit,Yi-yen Chen,Manon C. Slot,Ihsane Doubal,Alexander B. Meijer,René A. W. van Lier,Jannie Borst,Derk Amsen +9 more
TL;DR: A molecular characterization of regulatory and conventional CD4+ T cell subsets is provided, yielding markers to distinguish cells with different properties and insights into mechanisms that prevent regulatory T cells from exhibiting undesirable functional activities of the related but functionally antithetical conventional T cells.
Journal ArticleDOI
An Epigenetic Memory of Pregnancy in the Mouse Mammary Gland
Camila O. dos Santos,Egor Dolzhenko,Emily Hodges,Emily Hodges,Andrew D. Smith,Gregory J. Hannon,Gregory J. Hannon +6 more
TL;DR: It is verified that the mouse mammary gland responds more robustly to a second pregnancy, indicating that the gland retains a long-term memory of pregnancy.
Journal ArticleDOI
FOG-1 and GATA-1 act sequentially to specify definitive megakaryocytic and erythroid progenitors.
Elena Mancini,Alejandra Sanjuan-Pla,Luisa Luciani,Susan Hardman Moore,Amit Grover,Agnes Zay,Kasper D. Rasmussen,Sidinh Luc,Daniel Bilbao,Dónal O'Carroll,Sten Eirik W. Jacobsen,Claus Nerlov,Claus Nerlov +12 more
TL;DR: C/EBPs and FOG‐1 exhibited transcriptional cross‐regulation in early myelo‐erythroid progenitors making their functional antagonism a potential mechanism for separation of the myeloid and Mk/E lineages.
References
More filters
Journal ArticleDOI
The Pfam protein families database
Marco Punta,Penny Coggill,Ruth Y. Eberhardt,Jaina Mistry,John Tate,Chris Boursnell,Ningze Pang,Kristoffer Forslund,Goran Ceric,Jody Clements,Andreas Heger,Liisa Holm,Erik L. L. Sonnhammer,Sean R. Eddy,Alex Bateman,Robert D. Finn +15 more
TL;DR: The definition and use of family-specific, manually curated gathering thresholds are explained and some of the features of domains of unknown function (also known as DUFs) are discussed, which constitute a rapidly growing class of families within Pfam.
Journal ArticleDOI
Database resources of the National Center for Biotechnology Information
David L. Wheeler,Deanna M. Church,Ron Edgar,Scott Federhen,Wolfgang Helmberg,Thomas L. Madden,Joan Pontius,Gregory D. Schuler,Lynn M. Schriml,Edwin Sequeira,Tugba O. Suzek,Tatiana Tatusova,Lukas Wagner +12 more
TL;DR: In addition to maintaining the GenBank(R) nucleic acid sequence database, the National Center for Biotechnology Information (NCBI) provides data analysis and retrieval resources for the data in GenBank and other biological data made available through NCBI’s website.
Journal ArticleDOI
Pfam: the protein families database.
Robert D. Finn,Alex Bateman,Jody Clements,Penelope Coggill,Ruth Y. Eberhardt,Sean R. Eddy,Andreas Heger,Kirstie Hetherington,Liisa Holm,Jaina Mistry,Erik L. L. Sonnhammer,John Tate,Marco Punta +12 more
TL;DR: Pfam as discussed by the authors is a widely used database of protein families, containing 14 831 manually curated entries in the current version, version 27.0, and has been updated several times since 2012.
Journal ArticleDOI
Entrez Gene: gene-centered information at NCBI
TL;DR: Entrez Gene is a step forward from NCBI's LocusLink, with both a major increase in taxonomic scope and improved access through the many tools associated with NCBI Entrez.
Journal ArticleDOI
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.
Related Papers (5)
An integrated encyclopedia of DNA elements in the human genome
Gene Ontology: tool for the unification of biology
M Ashburner,Catherine A. Ball,Judith A. Blake,David Botstein,Heather Butler,J. M. Cherry,Allan Peter Davis,Kara Dolinski,Selina S. Dwight,J.T. Eppig,Midori A. Harris,David P. Hill,Laurie Issel-Tarver,Andrew Kasarskis,Suzanna E. Lewis,John C. Matese,Joel E. Richardson,M. Ringwald,Gerald M. Rubin,Gavin Sherlock +19 more