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Literature DB >> 14681387

TrSDB: a proteome database of transcription factors.

Antoni Hermoso¹, Daniel Aguilar, Francesc X Aviles, Enrique Querol.

Abstract

TrSDB-TranScout Database-(http://ibb.uab.es/trsdb) is a proteome database of eukaryotic transcription factors based upon predicted motifs by TranScout and data sources such as InterPro and Gene Ontology Annotation. Nine eukaryotic proteomes are included in the current version. Extensive and diverse information for each database entry, different analyses considering TranScout classification and similarity relationships are offered for research on transcription factors or gene expression.

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Year: 2004 PMID： 14681387 PMCID： PMC308835 DOI： 10.1093/nar/gkh101

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

12 in total

1. Transcription factors: bound to activate or repress.

Authors: D S Latchman
Journal: Trends Biochem Sci Date: 2001-04 Impact factor: 13.807

2. Transcription-associated protein families are primarily taxon-specific.

Authors: R M Coulson; A J Enright; C A Ouzounis
Journal: Bioinformatics Date: 2001-01 Impact factor: 6.937

3. TranScout: prediction of gene expression regulatory proteins from their sequences.

Authors: Daniel Aguilar; Baldomero Oliva; Francesc X Aviles; Enrique Querol
Journal: Bioinformatics Date: 2002-04 Impact factor: 6.937

4. The Gene Ontology Annotation (GOA) project: implementation of GO in SWISS-PROT, TrEMBL, and InterPro.

Authors: Evelyn Camon; Michele Magrane; Daniel Barrell; David Binns; Wolfgang Fleischmann; Paul Kersey; Nicola Mulder; Tom Oinn; John Maslen; Anthony Cox; Rolf Apweiler
Journal: Genome Res Date: 2003-03-12 Impact factor: 9.043

5. The InterPro Database, 2003 brings increased coverage and new features.

Authors: Nicola J Mulder; Rolf Apweiler; Teresa K Attwood; Amos Bairoch; Daniel Barrell; Alex Bateman; David Binns; Margaret Biswas; Paul Bradley; Peer Bork; Phillip Bucher; Richard R Copley; Emmanuel Courcelle; Ujjwal Das; Richard Durbin; Laurent Falquet; Wolfgang Fleischmann; Sam Griffiths-Jones; Daniel Haft; Nicola Harte; Nicolas Hulo; Daniel Kahn; Alexander Kanapin; Maria Krestyaninova; Rodrigo Lopez; Ivica Letunic; David Lonsdale; Ville Silventoinen; Sandra E Orchard; Marco Pagni; David Peyruc; Chris P Ponting; Jeremy D Selengut; Florence Servant; Christian J A Sigrist; Robert Vaughan; Evgueni M Zdobnov
Journal: Nucleic Acids Res Date: 2003-01-01 Impact factor: 16.971

6. The phylogenetic diversity of eukaryotic transcription.

Authors: Richard M R Coulson; Christos A Ouzounis
Journal: Nucleic Acids Res Date: 2003-01-15 Impact factor: 16.971

7. The Bioperl toolkit: Perl modules for the life sciences.

Authors: Jason E Stajich; David Block; Kris Boulez; Steven E Brenner; Stephen A Chervitz; Chris Dagdigian; Georg Fuellen; James G R Gilbert; Ian Korf; Hilmar Lapp; Heikki Lehväslaiho; Chad Matsalla; Chris J Mungall; Brian I Osborne; Matthew R Pocock; Peter Schattner; Martin Senger; Lincoln D Stein; Elia Stupka; Mark D Wilkinson; Ewan Birney
Journal: Genome Res Date: 2002-10 Impact factor: 9.043

8. Basic local alignment search tool.

Authors: S F Altschul; W Gish; W Miller; E W Myers; D J Lipman
Journal: J Mol Biol Date: 1990-10-05 Impact factor: 5.469

9. The Proteome Analysis database: a tool for the in silico analysis of whole proteomes.

Authors: Manuela Pruess; Wolfgang Fleischmann; Alexander Kanapin; Youla Karavidopoulou; Paul Kersey; Evgenia Kriventseva; Virginie Mittard; Nicola Mulder; Isabelle Phan; Florence Servant; Rolf Apweiler
Journal: Nucleic Acids Res Date: 2003-01-01 Impact factor: 16.971

10. TRANSFAC: transcriptional regulation, from patterns to profiles.

Authors: V Matys; E Fricke; R Geffers; E Gössling; M Haubrock; R Hehl; K Hornischer; D Karas; A E Kel; O V Kel-Margoulis; D-U Kloos; S Land; B Lewicki-Potapov; H Michael; R Münch; I Reuter; S Rotert; H Saxel; M Scheer; S Thiele; E Wingender
Journal: Nucleic Acids Res Date: 2003-01-01 Impact factor: 16.971

5 in total

TrSDB: a proteome database of transcription factors.

1. Transcription factors: bound to activate or repress.

2. Transcription-associated protein families are primarily taxon-specific.

3. TranScout: prediction of gene expression regulatory proteins from their sequences.

4. The Gene Ontology Annotation (GOA) project: implementation of GO in SWISS-PROT, TrEMBL, and InterPro.

5. The InterPro Database, 2003 brings increased coverage and new features.

6. The phylogenetic diversity of eukaryotic transcription.

7. The Bioperl toolkit: Perl modules for the life sciences.

8. Basic local alignment search tool.

9. The Proteome Analysis database: a tool for the in silico analysis of whole proteomes.

10. TRANSFAC: transcriptional regulation, from patterns to profiles.

1. Semantic integration of data on transcriptional regulation.

2. wDBTF: an integrated database resource for studying wheat transcription factor families.

3. DBD: a transcription factor prediction database.

4. Malleable machines in transcription regulation: the mediator complex.

5. DBD--taxonomically broad transcription factor predictions: new content and functionality.