Finding transcription regulatory elements, using transcription factor data base and genome comparison.
Hiroshi Mizushima1, Kozo Kawahara2, Mitsuru Takatsu, Teruhiko Yoshida
1hmizushi@ncc.go.jp, National Cancer Center Research Institute; 2kkawahara@w-fusion.co.jp, World Fusion Co.
As the human genome sequence has been almost sequenced, it is a key issue to analyze the transcription regulation system of the genome information. Regulatory mechanisms of some genes have been analyzed precisely by experiments, however, there is little knowledge of the regulation system in genome wide range, and no consensus algorithm has been developed for unknown gene regulation. For this purpose, we have been maintaining Transcription Factor Database (TFDB) with binding site sequence information. Using this database, we tried to make a website for finding transcriptional regulatory elements.
Using TFDB as a source for the binding site analysis, the initial program raised so many fault positive binding sites all around the gene. To decrease these candidates, we have compared the orthologus genes from human and mouse. We developed a web server which shows the binding site along with the homology and the CpG islands, which are suggested to be related to gene regulation.
Using the recent Microarray technology, the expression levels of many genes are easily measured. So, we also tried to search for the common sequence near the gene with similar expression patterns.