A computation to integrate the analysis of genetic variations occurring within regulatory elements and their possible effects.
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.
Wu
Li-Ching
LC
Institute of System Biology and Bioinformatics, National Central University Jhongli City, Taoyuan County 32001, Taiwan.
Horng
Jorng-Tzong
JT
Chen
Yong-An
YA
D000818:Animals; D001483:Base Sequence; D001665:Binding Sites; D002877:Chromosomes, Human / Q000235:genetics; D019295:Computational Biology / Q000379:methods*; D018899:CpG Islands / Q000235:genetics; D019175:DNA Methylation / Q000235:genetics; D030541:Databases, Genetic; D014644:Genetic Variation; D006801:Humans; D020407:Internet / Q000295:instrumentation*; D051379:Mice; D035683:MicroRNAs / Q000235:genetics; D020641:Polymorphism, Single Nucleotide / Q000235:genetics; D051381:Rats; D012045:Regulatory Sequences, Nucleic Acid / Q000235:genetics*; D014157:Transcription Factors / Q000378:metabolism
D035683:MicroRNAs; D014157:Transcription Factors