G. Sanchita, Blessy M. Baby, Ashok Sharma
Abstract
The binding of transcription factors in transcription factor binding sites (TFBSs) play a key role in the regulation of different biological processes showing change in the expression of genes in presence of adverse conditions. In this study, an in silico analysis of the data of differentially expressed genes of seven plants of family solanaceae under different time periods of salt stress was performed to find out the TFBSs. The data used for the study was retrieved from the public domain. Our analysis revealed up and down expression of genes that might result due to binding of transcription factors in promoter region. The promoter regions of differentially expressed genes were utilized for the prediction of TFBSs. The prediction was done using position weight matrices (PWMs) constructed by taking the data of experimentally validated transcription factors and their respective binding sites. The PWMs were scanned over promoter sequences present in the upstream region of differentially expressed genes. The TFBSs with a threshold of similarity score ≥ 2.97 were selected to get highly up and down expressed genes. These predicted TFBSs would be of help to understand the role of turnover of TFBSs in the change of expression of genes under salt stress.
Keywords: Gene expression, Gene Expression Omnibus, Position Weight Matrix, Salt stress, Solanaceae, Transcription Factor
Download Full Article HERE
