cis element/transcription factor analysis (cis/TF): a method for discovering transcription factor/cis element relationships.

Journal Article (Journal Article)

We report a simple new algorithm, cis/TF, that uses genomewide expression data and the full genomic sequence to match transcription factors to their binding sites. Most previous computational methods discovered binding sites by clustering genes having similar expression patterns and then identifying over-represented subsequences in the promoter regions of those genes. By contrast, cis/TF asserts that B is a likely binding site of a transcription factor T if the expression pattern of T is correlated to the composite expression patterns of all genes containing B, even when those genes are not mutually correlated. Thus, our method focuses on binding sites rather than genes. The algorithm has successfully identified experimentally-supported transcription factor binding relationships in tests on several data sets from Saccharomyces cerevisiae.

Full Text

Duke Authors

Cited Authors

  • Birnbaum, K; Benfey, PN; Shasha, DE

Published Date

  • September 2001

Published In

Volume / Issue

  • 11 / 9

Start / End Page

  • 1567 - 1573

PubMed ID

  • 11544201

Pubmed Central ID

  • PMC311103

Electronic International Standard Serial Number (EISSN)

  • 1549-5469

International Standard Serial Number (ISSN)

  • 1088-9051

Digital Object Identifier (DOI)

  • 10.1101/gr.158301


  • eng