Literature DB >> 10592259

TRANSFAC: an integrated system for gene expression regulation.

E Wingender1, X Chen, R Hehl, H Karas, I Liebich, V Matys, T Meinhardt, M Prüss, I Reuter, F Schacherer.   

Abstract

TRANSFAC is a database on transcription factors, their genomic binding sites and DNA-binding profiles (http://transfac.gbf.de/TRANSFAC/). Its content has been enhanced, in particular by information about training sequences used for the construction of nucleotide matrices as well as by data on plant sites and factors. Moreover, TRANSFAC has been extended by two new modules: PathoDB provides data on pathologically relevant mutations in regulatory regions and transcription factor genes, whereas S/MARt DB compiles features of scaffold/matrix attached regions (S/MARs) and the proteins binding to them. Additionally, the databases TRANSPATH, about signal transduction, and CYTOMER, about organs and cell types, have been extended and are increasingly integrated with the TRANSFAC data sources.

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Year:  2000        PMID： 10592259      PMCID： PMC102445          DOI： 10.1093/nar/28.1.316

Source DB:  PubMed          Journal:  Nucleic Acids Res        ISSN： 0305-1048            Impact factor:   16.971


  19 in total

1.  A database for cell signaling networks.

Authors:  T Takai-Igarashi; Y Nadaoka; T Kaminuma
Journal:  J Comput Biol       Date:  1998       Impact factor: 1.479

2.  PlantCARE, a plant cis-acting regulatory element database.

Authors:  S Rombauts; P Déhais; M Van Montagu; P Rouzé
Journal:  Nucleic Acids Res       Date:  1999-01-01       Impact factor: 16.971

3.  Using views for retrieving data from extremely heterogeneous databanks.

Authors:  T Etzold; G Verde
Journal:  Pac Symp Biocomput       Date:  1997

4.  Reciprocal effect of Waardenburg syndrome mutations on DNA binding by the Pax-3 paired domain and homeodomain.

Authors:  A S Fortin; D A Underhill; P Gros
Journal:  Hum Mol Genet       Date:  1997-10       Impact factor: 6.150

Review 5.  Compilation of transcription regulating proteins.

Authors:  E Wingender
Journal:  Nucleic Acids Res       Date:  1988-03-25       Impact factor: 16.971

6.  A compilation of composite regulatory elements affecting gene transcription in vertebrates.

Authors:  O V Kel; A G Romaschenko; A E Kel; E Wingender; N A Kolchanov
Journal:  Nucleic Acids Res       Date:  1995-10-25       Impact factor: 16.971

7.  TRANSFAC: a database on transcription factors and their DNA binding sites.

Authors:  E Wingender; P Dietze; H Karas; R Knüppel
Journal:  Nucleic Acids Res       Date:  1996-01-01       Impact factor: 16.971

8.  MatInd and MatInspector: new fast and versatile tools for detection of consensus matches in nucleotide sequence data.

Authors:  K Quandt; K Frech; H Karas; E Wingender; T Werner
Journal:  Nucleic Acids Res       Date:  1995-12-11       Impact factor: 16.971

9.  Recognition of NFATp/AP-1 composite elements within genes induced upon the activation of immune cells.

Authors:  A Kel; O Kel-Margoulis; V Babenko; E Wingender
Journal:  J Mol Biol       Date:  1999-05-07       Impact factor: 5.469

10.  The Mouse Genome Database (MGD): genetic and genomic information about the laboratory mouse. The Mouse Genome Database Group.

Authors:  J A Blake; J E Richardson; M T Davisson; J T Eppig
Journal:  Nucleic Acids Res       Date:  1999-01-01       Impact factor: 16.971
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  424 in total

1.  Assessing clusters and motifs from gene expression data.

Authors:  L M Jakt; L Cao; K S Cheah; D K Smith
Journal:  Genome Res       Date:  2001-01       Impact factor: 9.043

2.  ACTIVITY: a database on DNA/RNA sites activity adapted to apply sequence-activity relationships from one system to another.

Authors:  J V Ponomarenko; D P Furman; A S Frolov; N L Podkolodny; G V Orlova; M P Ponomarenko; N A Kolchanov; A Sarai
Journal:  Nucleic Acids Res       Date:  2001-01-01       Impact factor: 16.971

3.  The TRANSFAC system on gene expression regulation.

Authors:  E Wingender; X Chen; E Fricke; R Geffers; R Hehl; I Liebich; M Krull; V Matys; H Michael; R Ohnhäuser; M Prüss; F Schacherer; S Thiele; S Urbach
Journal:  Nucleic Acids Res       Date:  2001-01-01       Impact factor: 16.971

4.  Mendel-GFDb and Mendel-ESTS: databases of plant gene families and ESTs annotated with gene family numbers and gene family names.

Authors:  D Lonsdale; M Crowe; B Arnold; B C Arnold
Journal:  Nucleic Acids Res       Date:  2001-01-01       Impact factor: 16.971

5.  rSNP_Guide, a database system for analysis of transcription factor binding to target sequences: application to SNPs and site-directed mutations.

Authors:  J V Ponomarenko; T I Merkulova; G V Vasiliev; Z B Levashova; G V Orlova; S V Lavryushev; O N Fokin; M P Ponomarenko; A S Frolov; A Sarai
Journal:  Nucleic Acids Res       Date:  2001-01-01       Impact factor: 16.971

6.  The EMBL nucleotide sequence database.

Authors:  G Stoesser; W Baker; A van den Broek; E Camon; M Garcia-Pastor; C Kanz; T Kulikova; V Lombard; R Lopez; H Parkinson; N Redaschi; P Sterk; P Stoehr; M A Tuli
Journal:  Nucleic Acids Res       Date:  2001-01-01       Impact factor: 16.971

7.  The Eukaryotic Promoter Database, EPD: new entry types and links to gene expression data.

Authors:  Viviane Praz; Rouaïda Périer; Claude Bonnard; Philipp Bucher
Journal:  Nucleic Acids Res       Date:  2002-01-01       Impact factor: 16.971

8.  Critical roles of PPAR beta/delta in keratinocyte response to inflammation.

Authors:  N S Tan; L Michalik; N Noy; R Yasmin; C Pacot; M Heim; B Flühmann; B Desvergne; W Wahli
Journal:  Genes Dev       Date:  2001-12-15       Impact factor: 11.361

9.  The EMBL Nucleotide Sequence Database.

Authors:  Guenter Stoesser; Wendy Baker; Alexandra van den Broek; Evelyn Camon; Maria Garcia-Pastor; Carola Kanz; Tamara Kulikova; Rasko Leinonen; Quan Lin; Vincent Lombard; Rodrigo Lopez; Nicole Redaschi; Peter Stoehr; Mary Ann Tuli; Katerina Tzouvara; Robert Vaughan
Journal:  Nucleic Acids Res       Date:  2002-01-01       Impact factor: 16.971

10.  PlantCARE, a database of plant cis-acting regulatory elements and a portal to tools for in silico analysis of promoter sequences.

Authors:  Magali Lescot; Patrice Déhais; Gert Thijs; Kathleen Marchal; Yves Moreau; Yves Van de Peer; Pierre Rouzé; Stephane Rombauts
Journal:  Nucleic Acids Res       Date:  2002-01-01       Impact factor: 16.971
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