Bioinformatic solution for the restriction analysis of gene expression

• Main Authors: Hsih-Ho Chung, 鍾希和
• Other Authors: Geen-Dong Chang
• Format: Others
• Language: en_US
• Published: 2004
• Online Access: http://ndltd.ncl.edu.tw/handle/45072766117680603241

碩士 === 國立臺灣大學 === 生化科學研究所 === 92 === Many gene families play important roles in medical studies. For example, most of the protein tyrosine kinase (PTK) genes are proto-oncogenes. They are involved in the cell growth, differentiation, development, apoptosis and signal transduction pathways. There are more than ninety different tyrosine kinase genes that have been identified, and cross-talks between different PTKs have been reported. Therefore, it is essential to examine the overall expression profile of PTK family, as well as other gene families. In performing the experiment of restriction analysis of gene expression (RAGE), researchers should design the degenerate primers to amplify the genes of interest. Previously in our laboratory, the genes of interest are the tyrosine kinase family. The previous method for finding the suitable degenerate primers is based on translating the conserved motif of DFG and DVW into their degenerate genetic codons. Then researchers can use them as the PCR primer to amplify the tyrosine kinase family. With the release of Conserved Domain Database (CDD) from NCBI and newly developed tools in bioinformatics, we can now automate this procedure. And for the efficacy and reproducibility of computer program, researchers can choose any family of interest and follow the simple steps in our program to do the degenerate primer design and fragments matching after PCR products being cut by restriction enzymes in RAGE experiment. The program is valuable for the automatic process of primer design and restriction analysis. By running this program, researchers can avoid the possible errors resulted from manual design and analysis.