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Iida K, Kawaguchi S, Kobayashi N, Yoshida Y, Ishii M, Harada E, Hanada K, Matsui A, Okamoto M, Ishida J, Tanaka M, Morosawa T, Seki M, Toyoda T. ARTADE2DB: improved statistical inferences for Arabidopsis gene functions and structure predictions by dynamic structure-based dynamic expression (DSDE) analyses. Plant Cell Physiol 2011; 52:254-64. [PMID: 21227933 PMCID: PMC3037080 DOI: 10.1093/pcp/pcq202] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/29/2010] [Accepted: 12/20/2010] [Indexed: 05/19/2023]
Abstract
Recent advances in technologies for observing high-resolution genomic activities, such as whole-genome tiling arrays and high-throughput sequencers, provide detailed information for understanding genome functions. However, the functions of 50% of known Arabidopsis thaliana genes remain unknown or are annotated only on the basis of static analyses such as protein motifs or similarities. In this paper, we describe dynamic structure-based dynamic expression (DSDE) analysis, which sequentially predicts both structural and functional features of transcripts. We show that DSDE analysis inferred gene functions 12% more precisely than static structure-based dynamic expression (SSDE) analysis or conventional co-expression analysis based on previously determined gene structures of A. thaliana. This result suggests that more precise structural information than the fixed conventional annotated structures is crucial for co-expression analysis in systems biology of transcriptional regulation and dynamics. Our DSDE method, ARabidopsis Tiling-Array-based Detection of Exons version 2 and over-representation analysis (ARTADE2-ORA), precisely predicts each gene structure by combining two statistical analyses: a probe-wise co-expression analysis of multiple transcriptome measurements and a Markov model analysis of genome sequences. ARTADE2-ORA successfully identified the true functions of about 90% of functionally annotated genes, inferred the functions of 98% of functionally unknown genes and predicted 1,489 new gene structures and functions. We developed a database ARTADE2DB that integrates not only the information predicted by ARTADE2-ORA but also annotations and other functional information, such as phenotypes and literature citations, and is expected to contribute to the study of the functional genomics of A. thaliana. URL: http://artade.org.
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Affiliation(s)
- Kei Iida
- RIKEN BASE (Bioinformatics And Systems Engineering) Division, Yokohama, Kanagawa, 230-0045 Japan
- These authors contributed equally to this work
| | - Shuji Kawaguchi
- RIKEN BASE (Bioinformatics And Systems Engineering) Division, Yokohama, Kanagawa, 230-0045 Japan
- These authors contributed equally to this work
| | - Norio Kobayashi
- RIKEN BASE (Bioinformatics And Systems Engineering) Division, Yokohama, Kanagawa, 230-0045 Japan
| | - Yuko Yoshida
- RIKEN BASE (Bioinformatics And Systems Engineering) Division, Yokohama, Kanagawa, 230-0045 Japan
| | - Manabu Ishii
- RIKEN BASE (Bioinformatics And Systems Engineering) Division, Yokohama, Kanagawa, 230-0045 Japan
| | - Erimi Harada
- RIKEN BASE (Bioinformatics And Systems Engineering) Division, Yokohama, Kanagawa, 230-0045 Japan
| | - Kousuke Hanada
- RIKEN BASE (Bioinformatics And Systems Engineering) Division, Yokohama, Kanagawa, 230-0045 Japan
- RIKEN Plant Science Center, Yokohama, Kanagawa, 230-0045 Japan
| | - Akihiro Matsui
- RIKEN Plant Science Center, Yokohama, Kanagawa, 230-0045 Japan
| | - Masanori Okamoto
- RIKEN Plant Science Center, Yokohama, Kanagawa, 230-0045 Japan
- Present address: Department of Botany and Plant Sciences, University of California, Riverside, CA 92521, USA
| | - Junko Ishida
- RIKEN Plant Science Center, Yokohama, Kanagawa, 230-0045 Japan
| | - Maho Tanaka
- RIKEN Plant Science Center, Yokohama, Kanagawa, 230-0045 Japan
| | - Taeko Morosawa
- RIKEN Plant Science Center, Yokohama, Kanagawa, 230-0045 Japan
| | - Motoaki Seki
- RIKEN Plant Science Center, Yokohama, Kanagawa, 230-0045 Japan
| | - Tetsuro Toyoda
- RIKEN BASE (Bioinformatics And Systems Engineering) Division, Yokohama, Kanagawa, 230-0045 Japan
- *Corresponding author: E-mail, ; Fax, +81-45-503-9553
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