Developing Genome-Scale Prediction System for Transcription Factors and Their Targets

Complete genome sequences of many organisms have become available and the functional analysisof genomes is a target of intensive research. Gene regulation in higher organisms is one of the mostimportant biological functions, and it is achieved by a complex system of transcription factors. Thegenome analyses show that in most species about a half of the genes is of function unknown. Manyof the genes may turn out to code for transcription factors. Subsequent functional analyses of tran-scription factors involve identi cation of their target genes. Transcription factors usually bind tomultiple target sequences and regulate multiple genes in a complex manner. Thus, identifying tran-scription factors and nding their target genes at the genome level will lay a basis for the analysisof the gene regulatory network. We have been developing methods for predicting transcription fac-tors and their targets based on various kinds of information ranging from sequence to structure. Weare developing an integrated genome-scale prediction system by combining those methods together.Figure 1: Strategy for genome-scale prediction oftranscription factors and their targets.