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Identification of Conserved Regulatory Elements in Mammalian Promoter Regions:A Case Study Using the PCK1 Promoter 被引量:1
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作者 George E. Liui Matthew T. Weirauch +6 位作者 Curtis P. Van Tassell Robert W. Li Tad S. Sonstegard LakshmiK. Matukumal Erin E. Connor Richard W. Hanson Jianqi Yang 《Genomics, Proteomics & Bioinformatics》 SCIE CAS CSCD 2008年第3期129-143,共15页
A systematic phylogenetic footprinting approach was performed to identify conserved transcription factor binding sites (TFBSs) in mammalian promoter regions using human, mouse and rat sequence alignments. We found t... A systematic phylogenetic footprinting approach was performed to identify conserved transcription factor binding sites (TFBSs) in mammalian promoter regions using human, mouse and rat sequence alignments. We found that the score distributions of most binding site models did not follow the Gaussian distribution required by many statistical methods. Therefore, we performed an empirical test to establish the optimal threshold for each model. We gauged our computational predictions by comparing with previously known TFBSs in the PCK1 gene promoter of the cytosolic isoform of phosphoenolpyruvate carboxykinase, and achieved a sensitivity of 75% and a specificity of approximately 32% Almost all known sites overlapped with predicted sites, and several new putative TFBSs were also identified. We validated a predicted SP1 binding site in the control of PCK1 transcription using gel shift and reporter assays. Finally, we applied our computational approach to the prediction of putative TFBSs within the promoter regions of all available RefSeq genes. Our full set of TFBS predictions is freely available at http://bfgl.anri.barc.usda.gov/tfbsConsSites. 展开更多
关键词 phylogenetic footprinting phosphoenolpyruvate carboxykinase transcription factor binding sites mammalian gene promoters
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