Prediction of AP-1 Target Genes based on Genome-wide Motif Search and GO Annotation

机译：基于全基因组主题搜索和GO注释的AP-1靶基因预测

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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.

机译：靶基因的计算机模拟预测对于研究转录因子的生物学功能和分子网络是非常重要且具有挑战性的问题。受人蛋白AP-1（激活蛋白1）与其DNA结合位点和变异体之间结合亲和力测量体外实验的启发，对AP-1的某些DNA图案进行了全基因组搜索，并对其分布进行了研究分析图案。对已知靶标的分析结果表明，启动子区域中基序分布的特征将为靶标预测提供一些线索。另外，根据AP-1与其靶基因参与相同生物学途径的假设，在确定候选靶基因时引入了基因本体注释信息。结果表明，整合基因组数据和基因本体信息可以为目标基因的预测提供更多信息。开发了一种将共识和基于PSFM的方法进行基序搜索相结合的新颖方法，并开发了基于GO术语的基因获取工具，该程序可应作者要求提供。

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来源
《International Forum on Progress on Post-Genome Technologies(5'IFPT); 20070910-11; Suzhou(CN)》|2007年|P.1-6|共6页
会议地点 Suzhou(CN)
作者
Jianming Xie; Minli Li; Xiao Sun; Zuhong Lu;
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作者单位

State Key Laboratory of Bioelectronics, Southeast University, Nanjing, Jiangsu 210096, China;

State Key Laboratory of Bioelectronics, Southeast University, Nanjing, Jiangsu 210096, China;

State Key Laboratory of Bioelectronics, Southeast University, Nanjin;

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原文格式 PDF
正文语种 eng
中图分类生物工程学（生物技术）;
关键词
Transcription factor binding site; genome-wide motif search; GO ontology, AP-1; target genes prediction;

机译：转录因子结合位点；全基因组搜索； GO本体，AP-1；目标基因预测;

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5. Prediction of regulatory network mechanisms in eukaryotic gene transcription based upon genome-wide expression and interaction studies. [D] . Harrison, Rhonda. 2004

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Prediction of AP-1 Target Genes based on Genome-wide Motif Search and GO Annotation

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