title: PAP: a comprehensive workbench for mammalian transcriptional regulatory sequence analysis.
abstract: Given the recent explosion of publications that employ microarray technology to monitor genome-wide expression and that correlate these expression changes to biological processes or to disease states, the determination of the transcriptional regulation of these co-expressed genes is the next major step toward deciphering the genetic network governing the pathway or disease under study. Although computational approaches have been proposed for this purpose, there is no integrated and user-friendly software application that allows experimental biologists to tackle this problem in higher eukaryotes. We have previously reported a systematic, statistical model of mammalian transcriptional regulatory sequence analysis. We have now made crucial extensions to this model and have developed a comprehensive, user-friendly web application suite termed the Promoter Analysis Pipeline (PAP). PAP is available at: http://bioinformatics.wustl.edu/webTools/portalModule/PromoterSearch.do.
authors.affiliation: Department of Biomedical Engineering, Washington University, St. Louis, MO 63130, USA.
authors.forename: Li-Wei
authors.initials: LW
authors.lastname: Chang
authors.forename: Burr R
authors.initials: BR
authors.lastname: Fontaine
authors.forename: Gary D
authors.initials: GD
authors.lastname: Stormo
authors.forename: Rakesh
authors.initials: R
authors.lastname: Nagarajan
mesh_terms: D000465:Algorithms; D000818:Animals; D019295:Computational Biology / Q000379:methods*; D030541:Databases, Genetic; D020869:Gene Expression Profiling / Q000379:methods*; D005786:Gene Expression Regulation; D006801:Humans; D020407:Internet; D008957:Models, Genetic; D011401:Promoter Regions, Genetic; D011485:Protein Binding / Q000235:genetics*; D014157:Transcription Factors / Q000235:genetics / Q000378:metabolism*; D014158:Transcription, Genetic; D014584:User-Computer Interface
chemical_list: D014157:Transcription Factors