A Computation to Integrate the Analysis of Genetic Variations Occurring within Regulatory Elements and Their Possible Effects

Abstract

Single nucleotide polymorphisms (SNPs) and short tandem repeats (STRs) are the most common genetic variations, are widespread within genomes, and form the diversity within species. These genetic variations affect many regulatory elements such as transcription factor binding sites (TFBSs), DNA methylation sites on CpG islands, and microRNA target sites; these elements have been found to play major as well as indirect roles in regulating gene expression. Currently, systems are available to display such genetic variation occurring within regulatory elements. To understand and display all the potential variation described above, we have developed a web-based system tool, the Regulatory Element and Genetic Variation Viewer (REGV Viewer [REGV]), which provides a friendly web interface for users and shows genetic variation information within regulatory elements by either inputting a gene list or selecting a chromosome by name. Moreover, our tool not only supports logic operation queries, but after a query is submitted, it also shows a high-throughput simulation, including combined data, statistical graphs, and graphical views of the genetic variants and regulatory elements. Additionally, when the SNP variation occurs within TFBSs and if the SNP allele frequency and TFBS position weight matrices (PWMs) are available, our system will show the new putative TFBSs resulting from the SNP variation.