A Study of SNPs in Transcription Factor Binding Sites and Gene Expression in Drug Response

• Main Authors: Chun Shen, 沈峻
• Other Authors: Yao-Ting Haung
• Format: Others
• Language: en_US
• Published: 2014
• Online Access: http://ndltd.ncl.edu.tw/handle/8ae6u3

碩士 === 國立中正大學 === 資訊工程研究所 === 102 === Massive parallel sequencing has become a popular platform for genome-wide association studies. A number of studies have used RNA-seq for comparing gene expression profiles between treatment and control groups and identifying differential expression gene (DEG). Gene expression is regulated by transcription factors (TFs) which bind on a specific sequence called Transcription Factor Binding Site (TFBS). The expression level may be up- or down-regulated due to SNPs in the TFBS. In this thesis, we integrate DNA-seq, RNA-seq, and chromatin sequencing to identify risk SNPs would may up-/down- regulate expression of genes between case and control groups. The potential regulatory SNPs within TFBS are identified via integration of TF database and computational methods. The experimental results indicate that many DEGs possessed risk SNPs in TFBS, whereas the genes without change of expression have less SNPS occurred in TFBS. Thus, these risk SNPs are worth of validation by subsequent wet-lab experiments.