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J Plant Res. 2010 May;123(3):311-9. doi: 10.1007/s10265-010-0333-6. Epub 2010 Apr 10.

Coexpression landscape in ATTED-II: usage of gene list and gene network for various types of pathways.

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1
Graduate School of Information Science, Tohoku University, 6-3-09 Aramaki-Aza-Aoba, Aoba-ku, Sendai 980-8679, Japan. obayashi@ecei.tohoku.ac.jp

Abstract

Gene coexpression analyses are a powerful method to predict the function of genes and/or to identify genes that are functionally related to query genes. The basic idea of gene coexpression analyses is that genes with similar functions should have similar expression patterns under many different conditions. This approach is now widely used by many experimental researchers, especially in the field of plant biology. In this review, we will summarize recent successful examples obtained by using our gene coexpression database, ATTED-II. Specifically, the examples will describe the identification of new genes, such as the subunits of a complex protein, the enzymes in a metabolic pathway and transporters. In addition, we will discuss the discovery of a new intercellular signaling factor and new regulatory relationships between transcription factors and their target genes. In ATTED-II, we provide two basic views of gene coexpression, a gene list view and a gene network view, which can be used as guide gene approach and narrow-down approach, respectively. In addition, we will discuss the coexpression effectiveness for various types of gene sets.

PMID:
20383554
DOI:
10.1007/s10265-010-0333-6
[Indexed for MEDLINE]
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