Prediction of AP-1 Target Genes based on Genome-wide Motif Search and GO Annotation
Prediction in silico of the target genes is a very important and challenging problem for the study of biological function and molecular network of a transcription factor. Inspired from the experiment in vitro of the binding affinity measurement between the human protein AP-1 (Activator Protein 1) and its DNA binding sites and variants, genome-wide search of some DNA motifs of AP-1 are performed and the distribution of these motifs are analyzed. The results from the analysis of know targets imply that the characteristics of motif distribution in the promoter regions will give some clues for target prediction. In addition, Gene ontology annotation information is introduced in the determining of the candidate target genes following the hypothesis that AP-1 is involved in the same biological pathways with its target genes. The results indicate that integrating genomic data and gene ontology information can provide more information for the prediction of target genes. A novel approach combining consensus and PSFM based-method for motif search and the tool for gene acquiring based on GO terms are developed and the program is available upon request from the authors.
Transcription factor binding site genome-wide motif search GO ontology, AP-1 target genes prediction
Jianming Xie Minli Li Xiao Sun Zuhong Lu
State Key Laboratory of Bioelectronics, Southeast University, Nanjing, Jiangsu 210096, China
国际会议
The 5th International Forum on Post-genome Technologies(5IFPT)(第五届国际后基因组生命科学技术学术论坛)
苏州
英文
2007-09-10（万方平台首次上网日期，不代表论文的发表时间）