PromoterPlot: a graphical display of promoter similarities by pattern recognition.
PromoterPlot (http://promoterplot.fmi.ch) is a web-based tool for simplifying the display and processing of transcription factor searches using either the commercial or free TransFac distributions. The input sequence is a TransFac search (public version) or FASTA/Affymetrix IDs (local install). It uses an intuitive pattern recognition algorithm for finding similarities between groups of promoters by dividing transcription factor predictions into conserved triplet models. To minimize the number of false-positive models, it can optionally exclude factors that are known to be unexpressed or inactive in the cells being studied based on microarray or proteomic expression data. The program will also estimate the likelihood of finding a pattern by chance based on the frequency observed in a control set of mammalian promoters we obtained from Genomatix. The results are stored as an interactive SVG web page on our server.
Di Cara
Alessandro
A
Friedrich Miescher Institute for Biomedical Research, Maulbeerstrasse 66, CH-4058 Basel, Switzerland.
Schmidt
Karsten
K
Hemmings
Brian A
BA
Oakeley
Edward J
EJ
D000465:Algorithms; D000818:Animals; D001665:Binding Sites; D003196:Computer Graphics; D005786:Gene Expression Regulation; D023281:Genomics / Q000379:methods*; D006801:Humans; D020407:Internet; D051379:Mice; D011401:Promoter Regions, Genetic; D051381:Rats; D012984:Software; D014157:Transcription Factors / Q000378:metabolism*; D014584:User-Computer Interface
D014157:Transcription Factors