Analysis on the relationship between DNase and DNA motif pairs through Data Mining

Abstract

This project is two-fold in field of bioinformatics and computer science. The impact of this project to the society is significantly greater comparing to other final year projects as the results are very biologically important, especially to the researches in human cells (the impact factor of Bioinformatics in 2016 is 7.307). Studies on transcription factor binding sites (TFBSs, also known as DNA motifs) are becoming more popular with the advancement of sequencing technology to genomes in Bioinformatics. DNA binding and proteins interaction plays an important role in gene transcription and thus, are involved in different mechanism, especially the cancer pathways. Techniques involved in this project not only include those in computer science, but also those in bioinformatics. Based on the background study in bioinformatics on DNA motif pairs, the relationship between newly discovered DNA motif pairs and DNase accessibility, evolutionary conservation (PhyloP hg19), genome ontology (GO) enrichment will be further investigated in this project. The findings can be used for future medical studies including cancer studies as the findings can be used to locate DNA-binding sites for cancer-related protein. A web server will be provided with a user-friendly interactive platform to visualize the bioinformatics data including DNase accessibility of DNA motif pairs, evolutionary conservation and genome ontology (GO) enrichment. It carried a large database storing bioinformatics information and analysis results. This report will also discuss the result on data mining on the relationship between DNA motif pair and DNase.