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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Podocyte-Specific Induction of Krüppel-Like Factor 15 Restores Differentiation Markers and Attenuates Kidney Injury in Proteinuric Kidney Disease.
Yiqing Guo,Jesse Pace,Zhengzhe Li,Avi Ma'ayan,Zichen Wang,Monica P. Revelo,Edward Y. Chen,Xiangchen Gu,Ahmed Attalah,Yaqi Yang,Chelsea Estrada,Vincent W. Yang,John Cijiang He,John Cijiang He,Sandeep K. Mallipattu +14 more
TL;DR: Inducing podocyte-specific KLF15 attenuates kidney injury by directly and indirectly upregulating genes critical for podocyte differentiation, suggesting that KLF 15 induction might be a potential strategy for treating proteinuric kidney disease.
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miR-200a-3p regulates TLR1 expression in bacterial challenged miiuy croaker.
TL;DR: Direct evidence is provided that miR-200a-3p is involved in TLR1 expression modulation in miiuy croaker, which will offer a basis for better understanding of miRNA regulation in fish TLR signaling pathways.
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The Transcription Factor Con7-1 Is a Master Regulator of Morphogenesis and Virulence in Fusarium oxysporum.
TL;DR: Comparative microarray-based gene expression analysis indicated that Con7-1 modulates the expression of a large number of genes involved in different biological functions, including host-pathogen interactions, morphogenesis and development, signal perception and transduction, transcriptional regulation, and primary and secondary metabolism.
Journal ArticleDOI
Regions of common inter-individual DNA methylation differences in human monocytes: genetic basis and potential function
Christopher Schröder,Elsa Leitão,Stefan Wallner,Gerd Schmitz,Ludger Klein-Hitpass,Anupam Sinha,Karl-Heinz Jöckel,Stefanie Heilmann-Heimbach,Per Hoffmann,Markus M. Nöthen,Michael Steffens,Peter Ebert,Sven Rahmann,Bernhard Horsthemke +13 more
TL;DR: Allele-specific DNA methylation occurs in discrete chromosomal regions and is driven by genetic variation in cis and trans, but in general has little effect on gene expression.
Journal ArticleDOI
Wigwams: identifying gene modules co-regulated across multiple biological conditions
Krzysztof Polanski,Johanna Rhodes,Claire Hill,Peijun Zhang,Dafyd J. Jenkins,Steven J. Kiddle,Aleksey Jironkin,Jim Beynon,Vicky Buchanan-Wollaston,Sascha Ott,Katherine J. Denby +10 more
TL;DR: Wigwams is a simple and efficient method to identify gene modules showing evidence for co-regulation in multiple time series of gene expression data, enabling gene network reconstruction to be focused on those gene modules and combinations of conditions that show evidence for shared regulatory mechanisms.
References
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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.
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