ORegAnno: An open access database and curation system for literature-derived promoters, transcription factor binding sites and regulatory variation

Bioinformatics

Volumn 22, Issue 5, 2006, Pages 637-640

  Montgomery, S B ^a   Griffith, O L ^a   Sleumer, M C ^a   Bergman, C M ^b   Bilenky, M ^a   Pleasance, E D ^a   Prychyna, Y ^a   Zhang, X ^a   Jones, S J M ^a  

^a BRITISH COLUMBIA CANCER AGENCY   (Canada)

^b UNIVERSITY OF MANCHESTER   (United Kingdom)

Author keywords

[No Author keywords available]

Indexed keywords

TRANSCRIPTION FACTOR;

ACCESS TO INFORMATION; ARTICLE; BINDING SITE; COMPUTER PROGRAM; FACTUAL DATABASE; GENE MUTATION; GENETIC DATABASE; GENETIC POLYMORPHISM; GENETIC REGULATION; GENETIC VARIABILITY; HAPLOTYPE; INFORMATION PROCESSING; INFORMATION SYSTEM; MEDLINE; ONLINE SYSTEM; OPEN REGULATORY ANNOTATION DATABASE; PRIORITY JOURNAL; PROMOTER REGION; SCIENTIFIC LITERATURE; VALIDATION PROCESS;

EID: 33644861212     PISSN: 13674803     EISSN: 13674811     Source Type: Journal    
DOI: 10.1093/bioinformatics/btk027     Document Type: Article

References (30)

1. Altschul,S.F. et al. (1990) Basic local alignment search tool. J. Mol. Biol., 215, 403-410.
2. Bergman,C.M. et al. (2005) Drosophila DNase I footprint database: A systematic genome annotation of transcription factor binding sites in the fruitfly, Drosophila melanogaster. Bioinformatics, 21, 1747-1749.
3. Booth,D., Haas,H., McCabe,F., Newcomer,E., Champion,M., Ferris,C. and Orchard,D. (2004) Web Services architecture, W3C working group note, W3C.
4. Dowell,R.D. et al. (2001) The distributed annotation system. BMC Bioinformatics, 2, 7.
5. Frith,M.C. et al. (2004) Site2genome: Locating short DNA sequences in whole genomes. Bioinformatics, 20, 1468-1469.
6. Grienberg,I. and Benayahu,D. (2005) Osteo-Promoter Database (OPD) - promoter analysis in skeletal cells. BMC Genomics, 6, 46.
7. Ho Sui,S.J. et al. (2005) oPOSSUM: Identification of over-represented transcription factor binding sites in co-expressed genes. Nucleic Acids Res., 33, 3154-3164.
8. Hubbard,T. et al. (2005) Ensembl 2005. Nucleic Acids Res., 33, D447-D453.
9. Kanamori,M. et al. (2004) A genome-wide and nonredundant mouse transcription factor database. Biochem. Biophys. Res. Commun., 322, 787-793.
10. Kelso,J. et al. (2003) eVOC: A controlled vocabulary for unifying gene expression data. Genome Res., 13, 1222-1230.
11. Kent,W.J. et al. (2002) The human genome browser at UCSC. Genome Res., 12, 996-1006.
12. Kolchanov,N.A. et al. (2002) Transcription Regulatory Regions Database (TRRD): Its status in 2002. Nucleic Acids Res., 30, 312-317.
13. Lescot,M. et al. (2002) PlantCARE, a database of plant cis-acting regulatory elements and a portal to tools for in silico analysis of promoter sequences. Nucleic Acids Res., 30, 325-327.
14. Maglott,D. et al. (2005) Entrez Gene: Gene-centered information at NCBI. Nucleic Acids Res., 33, D54-D58.
15. Matys,V. et al. (2003) TRANSFAC: Transcriptional regulation, from patterns to profiles, Nucleic Acids Res., 31, 374-378.
16. Pohar,T.T. et al. (2004) HemoPDB: Hematopoiesis Promoter Database, an information resource of transcriptional regulation in blood cell development. Nucleic Acids Res., 32, D86-D90.
17. Ponomarenko,J.V. et al. (2001) rSNP_Guide, a database system for analysis of transcription factor binding to target sequences: application to SNPs and site-directed mutations. Nucleic Acids Res., 29, 312-316.
18. Robertson,A.G. et al. (2006) cisRED: A database system for genome-scale computational discovery of regulatory elements. Nucleic Acids Res., 34, D68-D73.
19. Schmid,C.D. et al. (2004) The Eukaryotic Promoter Database EPD: The impact of in silico primer extension. Nucleic Acids Res., 32, D82-D85.
20. Shahmuradov,I.A. et al. (2003) PlantProm: A database of plant promoter sequences. Nucleic Acids Res., 31, 114-117.
21. Sherry,S.T. et al. (2001) dbSNP: The NCBI database of genetic variation. Nucleic Acids Res., 29, 308-311.
22. Stenson,P.D. et al. (2003) Human Gene Mutation Database (HGMD): 2003 update. Hum. Mutat., 21, 577-581.
23. Tahira,T. et al. (2005) dbQSNP: A database of SNPs in human promoter regions with allele frequency information determined by single-strand conformation polymorphism-based methods. Hum. Mutat., 26, 69-77.
24. Tompa,M. et al. (2005) Assessing computational tools for the discovery of transcription factor binding sites. Nat. Biotechnol., 23, 137-144.
25. Wasserman,W.W. and Fickett,J.W. (1998) Identification of regulatory regions which confer muscle-specific gene expression. J. Mol. Biol., 278, 167-181.
26. Wasserman,W.W. and Sandelin,A. (2004) Applied bioinformatics for the identification of regulatory elements. Nat. Rev. Genet., 5, 276-287.
27. Wheeler,D.L. et al. (2005) Database resources of the National Center for Biotechnology Information. Nucleic Acids Res., 33, D39-D45.
28. Xie,X. et al. (2005) Systematic discovery of regulatory motifs in human promoters and 3′ UTRs by comparison of several mammals. Nature, 434, 338-345.
29. Zhao,T. et al. (2004) PromoLign: A database for upstream region analysis and SNPs. Hum. Mutat., 23, 534-539.
30. Zhu,J. and Zhang,M.Q. (1999) SCPD: A promoter database of the yeast Saccharomyces cerevisiae. Bioinformatics, 15, 607-611.