title: Predicting polymerase II core promoters by cooperating transcription factor binding sites in eukaryotic genes.
abstract: Several discriminate functions for predicting core promoters that based on the potential cooperation between transcription factor binding sites (TFBSs) are discussed. It is demonstrated that the promoter predicting accuracy is improved when the cooperation among TFBSs is taken into consideration. The core promoter region of a newly discovered gene CKLFSF1 is predicted to locate more than 1.5 kb far away from the 5' end of the transcript and in the last intron of its upstream gene, which is experimentally confirmed later. The core promoters of 3402 human RefSeq sequences, obtained by extending the mRNAs in human genome sequences, are predicted by our algorithm, and there are about 60% of the predicted core promoters locating within the +/- 500 bp region relative to the annotated transcription start site.
authors.affiliation: School of Mathematical Sciences, Peking University and Center for Theoretical Biology, Beijing, China.
authors.forename: Xiao-Tu
authors.initials: XT
authors.lastname: Ma
authors.forename: Min-Ping
authors.initials: MP
authors.lastname: Qian
authors.forename: Hai-Xu
authors.initials: HX
authors.lastname: Tang
mesh_terms: D000465:Algorithms; D001665:Binding Sites; D018899:CpG Islands; D004257:DNA Polymerase II / Q000235:genetics*; D016208:Databases, Factual; D005057:Eukaryotic Cells; D006801:Humans; D007438:Introns; D011401:Promoter Regions, Genetic; D012333:RNA, Messenger / Q000235:genetics; D015203:Reproducibility of Results; D014157:Transcription Factors / Q000235:genetics / Q000378:metabolism*; D024363:Transcription Initiation Site
chemical_list: D012333:RNA, Messenger; D014157:Transcription Factors; D004257:DNA Polymerase II