| Summary: | 碩士 === 中山醫學大學 === 生物醫學科學學系碩士班 === 97 === Gene expression is a very important process in cell development and cell function. Cell diversity was constituted by differential gene expression. The promoter of RNA polymerase II transcribed gene is a DNA region just 5'' upstream to the transcription start site (TSS) and there are many regulatory elements within this region which can be recognized by various transcription factors. Through the binding of transcription factors to these sites, it regulates the expression of gene. Therefore, via TSS identification is the most reliable method for promoter finding.
Most of current methods used to find promoter region were working in a prediction way. But the results were not as ideal as we thought because the promoter pattern was not entirely known. Public promoter database obtained from experimental data, such as EPD (Eukaryotic Promoter Database, http://www.epd.isb-sib.ch/), contain more authentic promoter sequences, but the number was far less than estimated, and the update speed is quite slow, too.
Here, we use human EST (Expression Sequence Tags) to against human mRNA by using miBLAST, an extended development tool of NCBI BLAST, to obtain full length cDNA (FL-cDNA). Simultaneously, according to the content of GenBank format of hit ESTs, we construct the gene expression profile database. On the other hand, we BLAST the FL-cDNA to human genomic DNA to find the TSS and the promoter region of each gene (mRNA). According to the TSS, we collect the sequence of −1000 ~ +50 nt region to establish the promoter candidate region database. Finally, we construct a relational database among promoter sequences, cDNA sequences and gene expression profiles and design a simple web service to search expression profile and promoter sequences of certain human mRNA. The web service is available at http://140.128.139.59:50124/vpbs/index.php.
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