Bergen Open Research Archive

Predicting Gene Regulatory Elements in Silico on a Genomic Scale

Bergen Open Research Archive

Show simple item record Brazma, Alvis eng Jonassen, Inge eng Vilo, Jaak eng Ukkonen, Esko eng 2008-08-04T08:20:13Z 2008-08-04T08:20:13Z 1998-05-18 eng
dc.identifier.citation Genome Research 8: 1202-1215 en
dc.identifier.issn 1088-9051 eng
dc.description.abstract We 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.iso eng eng
dc.publisher Cold Spring Harbor Laboratory Press eng
dc.title Predicting Gene Regulatory Elements in Silico on a Genomic Scale eng
dc.type Journal article eng
bibo.doi eng

Files in this item


This item appears in the following Collection(s)

Show simple item record

Search BORA


My Account