A two-way predicting computational tool website for transcription factor binding site andvertebrate genomes

• Main Authors: Chih-Kai Hsu, 許智凱
• Other Authors: Wen-shyong Tzou
• Format: Others
• Language: zh-TW
• Published: 2009
• Online Access: http://ndltd.ncl.edu.tw/handle/60071928811643946109

碩士 === 國立臺灣海洋大學 === 生物科技研究所 === 97 === Transcriptional control by the transcription factors plays the central roles in the regulation of the gene expression. Given the gene lists involved in a biological phenomenon generated in a gene expression profiling experiment, the commonly asked question is what kind of and how the transcription factors control a battery of genes. eMOG (Extraction of Motif or Gene) is the web tool that we develop to analyze the upstream sequence given a gene list. eMOG scans the upstream sequences of genes and, by judging a probability score, discover the over-represented known transcription factor binding site (TFBS). Furthermore, eMOG allows the users to employ TF names to predict the genes that are potentially regulated by the given TFs. Finally, the user can visualize the TFBS patterns on the upstream sequence of genes using Scalable Vector Graphics (SVG). We use 115 human genes the upstream sequences of which are bound by E2F family, a TF family that regulates the entry of S phase in cell cycle. eMOG revealed four TFBS (E2F, CREB, NF-Y, Nrf-1) that are over-represented in the upstream sequences of those 115 genes. Moreover, we discover another 27 genes that are potentially under the transcriptional control of these four TF by reverse eMOG. Functional analysis of these 27 genes reveals that 14 genes are known to be directly related to cell cycle control and two genes associated with membrane receptor. Interestingly, using the same approach, 26 mouse genes are discovered to be potentially under the transcriptional control of the same four TF by reverse eMOG. The function of 11 out of these 26 mouse genes are known to be related to cell cycle control.