Show simple item record

dc.contributor.authorBrazma, Alviseng
dc.contributor.authorJonassen, Ingeeng
dc.contributor.authorVilo, Jaakeng
dc.contributor.authorUkkonen, Eskoeng
dc.date.accessioned2008-08-04T08:20:13Z
dc.date.available2008-08-04T08:20:13Z
dc.date.issued1998-05-18eng
dc.identifier.citationGenome Research 8: 1202-1215en
dc.identifier.issn1088-9051eng
dc.identifier.urihttp://hdl.handle.net/1956/2745
dc.description.abstractWe performed a systematic analysis of gene upstream regions in the yeast genome for occurrences of regular expression-type patterns with the goal of identifying potential regulatory elements. To achieve this goal, we have developed a new sequence pattern discovery algorithm that searches exhaustively for a priori unknown regular expression-type patterns that are over-represented in a given set of sequences. We applied the algorithm in two cases, (1) discovery of patterns in the complete set of >6000 sequences taken upstream of the putative yeast genes and (2) discovery of patterns in the regions upstream of the genes with similar expression profiles. In the first case, we looked for patterns that occur more frequently in the gene upstream regions than in the genome overall. In the second case, first we clustered the upstream regions of all the genes by similarity of their expression profiles on the basis of publicly available gene expression data and then looked for sequence patterns that are over-represented in each cluster. In both cases we considered each pattern that occurred at least in some minimum number of sequences, and rated them on the basis of their over-representation. Among the highest rating patterns, most have matches to substrings in known yeast transcription factor-binding sites. Moreover, several of them are known to be relevant to the expression of the genes from the respective clusters. Experiments on simulated data show that the majority of the discovered patterns are not expected to occur by chance.en
dc.language.isoengeng
dc.publisherCold Spring Harbor Laboratory Presseng
dc.titlePredicting Gene Regulatory Elements in Silico on a Genomic Scaleeng
dc.typeJournal articleeng
bibo.doihttp://dx.doi.org/10.1101/gr.8.11.1202eng
dc.identifier.doihttp://dx.doi.org/10.1101/gr.8.11.1202


Files in this item

Thumbnail

This item appears in the following Collection(s)

Show simple item record