抄録
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.
| 元の言語 | 英語 |
|---|---|
| ページ（範囲） | 273-288 |
| ページ数 | 16 |
| ジャーナル | Journal of bioinformatics and computational biology |
| 巻 | 2 |
| 発行部数 | 2 |
| DOI | |
| 出版物ステータス | 出版済み - 6 1 2004 |
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All Science Journal Classification (ASJC) codes
- Biochemistry
- Molecular Biology
- Computer Science Applications
これを引用
Efficiently finding regulatory elements using correlation with gene expression. / Bannai, Hideo; Inenaga, Shunsuke; Shinohara, Ayumi; Takeda, Masayuki; Miyano, Satoru.
：: Journal of bioinformatics and computational biology, 巻 2, 番号 2, 01.06.2004, p. 273-288.研究成果: ジャーナルへの寄稿 › 記事
}
TY - JOUR
T1 - Efficiently finding regulatory elements using correlation with gene expression
AU - Bannai, Hideo
AU - Inenaga, Shunsuke
AU - Shinohara, Ayumi
AU - Takeda, Masayuki
AU - Miyano, Satoru
PY - 2004/6/1
Y1 - 2004/6/1
N2 - 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.
AB - 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.
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UR - http://www.scopus.com/inward/citedby.url?scp=4043181443&partnerID=8YFLogxK
U2 - 10.1142/S0219720004000612
DO - 10.1142/S0219720004000612
M3 - Article
VL - 2
SP - 273
EP - 288
JO - Journal of Bioinformatics and Computational Biology
JF - Journal of Bioinformatics and Computational Biology
SN - 0219-7200
IS - 2
ER -