Build a Promoter Motif Database for System Biology Research

摘要

The system biology research is trying to systematically study complex interaction in the biological systems, and has been a very active research area in the post-genome era. One of the key tasks in system biology is to understand the genome-wide functionality of transcription factors. This however can be done by analyzing the corresponding transcription factor bind sites within promoter region. Most current existing information related to promoter region is partial and scatter across several sources. This makes difficult for the biologists to access and analyze information about transcription factor binding sites (motif), and thus a unified promoter motif database is necessary. In this paper we describe how a genome-wide mouse promoter motif database is built. We followed three steps to reach the goal. The first step is to consolidate the position weight matrix information gathered from TRANSFAC and JASPAR into a single database. In the second step, we implement a C program to search motif patterns in the promoter region based on the existing position weight matrix, and then loaded them into the database. In the final step, we describe the development of a JSP application as the user interface to database. This database will provide biologist an easy way to access the transcription factor binding sites as well as the promoter information. We believe it will play a major role in system biology research.