Efficiently finding regulatory elements using correlation with gene expression

Hideo Bannai, Shunsuke Inenaga, Ayumi Shinohara, Masayuki Takeda, Satoru Miyano

Research output: Contribution to journalArticlepeer-review

19 Citations (Scopus)


We present an efficient algorithm for detecting putative regulatory elements in the upstream DNA sequences of genes, using gene expression information obtained from microarray experiments. Based on a generalized suffix tree, our algorithm looks for motif patterns whose appearance in the upstream region is most correlated with the expression levels of the genes. We are able to find the optimal pattern, in time linear in the total length of the upstream sequences. We implement and apply our algorithm to publicly available microarray gene expression data, and show that our method is able to discover biologically significant motifs, including various motifs which have been reported previously using the same data set. We further discuss applications for which the efficiency of the method is essential, as well as possible extensions to our algorithm.

Original languageEnglish
Pages (from-to)273-288
Number of pages16
JournalJournal of bioinformatics and computational biology
Issue number2
Publication statusPublished - Jun 2004

All Science Journal Classification (ASJC) codes

  • Biochemistry
  • Molecular Biology
  • Computer Science Applications


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