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ooTFD


NAR Molecular Biology Database Collection entry number 185
Ghosh D.
Institute for Transcriptional Informatics, PO Box 2556, Pittsburgh, PA 15230, USA
Contact dghosh@ifti.org

Database Description

ooTFD (1) is a database of transcription factors maintained in object-oriented and object-relational database systems. There are, at the time of this writing, about 7500 TF binding sites entries in this database, from both prokaryotic and eukaryotic sources, as well as roughly 500 TF binding site matrices. A number of tools and services are available for commonly performed sequence analyses against these datasets, as well as for the performing of ooTfd database queries are provided at the IFTI-MIRAGE web site. Matrix entries in this database are given a quality score according to the statistical methodology described by Rahmann et.al. (2), which may be utilized in the interpretation of matrix-based TF binding site searches. Entries in this database resource are linked, either through hard links based on published experimental results, or through precomputed datasets, to entries in EPD (3), PKR (4), and PDB (5). ooTFD and associated utilities can be accessed at http://www.ifti.org/ootfd/ .

Acknowledgements

Portions of this work were made possible through computational resources of the Pittsburgh Supercomputer Center (MCB980021P).

References

1. Ghosh D (2000) Object-oriented transcription factors database (ooTFD). Nucleic Acids Res 28: 308-10.
2. Rahmann S, T Muller, M Vingron (2003) On the Power of Profiles for Transcription Factor Binding Site Detection. Statistical Applications in Genetics and Molecular Biology 2.1: art7.
3. Praz V, R Perier, C Bonnard, P Bucher (2002) The Eukaryotic Promoter Databbase, EPD: new entry types and links to gene expression data. Nucleic Acids Res 30: 322-4.
4. Smith CM, IN Shindyalov, S Veretnik, M Gribskov, SS Taylor, LF TenEyck, P Bourne (1997) The Protein Kinase Resource. Trends Biochem Sci 22: 444-6.
5. Berman HM, J Westbrook, Z Fend, G Gilliland, TN Bhat, H Weissig, IN Shindyalov, P Bourne (2000) Nucleic Acids Res 28: 235-42.


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