title: ATTED-II in 2016: A Plant Coexpression Database Towards Lineage-Specific Coexpression.
abstract: ATTED-II (http://atted.jp) is a coexpression database for plant species with parallel views of multiple coexpression data sets and network analysis tools. The user can efficiently find functional gene relationships and design experiments to identify gene functions by reverse genetics and general molecular biology techniques. Here, we report updates to ATTED-II (version 8.0), including new and updated coexpression data and analysis tools. ATTED-II now includes eight microarray- and six RNA sequencing-based coexpression data sets for seven dicot species (Arabidopsis, field mustard, soybean, barrel medick, poplar, tomato and grape) and two monocot species (rice and maize). Stand-alone coexpression analyses tend to have low reliability. Therefore, examining evolutionarily conserved coexpression is a more effective approach from the viewpoints of reliability and evolutionary importance. In contrast, the reliability of species-specific coexpression data remains poor. Our assessment scores for individual coexpression data sets indicated that the quality of the new coexpression data sets in ATTED-II is higher than for any previous coexpression data set. In addition, five species (Arabidopsis, soybean, tomato, rice and maize) in ATTED-II are now supported by both microarray- and RNA sequencing-based coexpression data, which has increased the reliability. Consequently, ATTED-II can now provide lineage-specific coexpression information. As an example of the use of ATTED-II to explore lineage-specific coexpression, we demonstrate monocot- and dicot-specific coexpression of cell wall genes. With the expanded coexpression data for multilevel evaluation, ATTED-II provides new opportunities to investigate lineage-specific evolution in plants.
authors.affiliation: Graduate School of Information Sciences, Tohoku University, 6-3-09, Aramaki-Aza-Aoba, Aoba-ku, Sendai, 980-8679 Japan Core Research for Evolutional Science and Technology (CREST), Japan Science and Technology Agency, Kawaguchi, Saitama, Japan.
authors.forename: Yuichi
authors.initials: Y
authors.lastname: Aoki
authors.affiliation: Graduate School of Information Sciences, Tohoku University, 6-3-09, Aramaki-Aza-Aoba, Aoba-ku, Sendai, 980-8679 Japan.
authors.forename: Yasunobu
authors.initials: Y
authors.lastname: Okamura
authors.affiliation: Graduate School of Information Sciences, Tohoku University, 6-3-09, Aramaki-Aza-Aoba, Aoba-ku, Sendai, 980-8679 Japan.
authors.forename: Shu
authors.initials: S
authors.lastname: Tadaka
authors.affiliation: Graduate School of Information Sciences, Tohoku University, 6-3-09, Aramaki-Aza-Aoba, Aoba-ku, Sendai, 980-8679 Japan Institute of Development, Aging, and Cancer, Tohoku University, Sendai, 980-8575 Japan Tohoku Medical Megabank Organization, Tohoku University, Sendai, 980-8573 Japan.
authors.forename: Kengo
authors.initials: K
authors.lastname: Kinoshita
authors.affiliation: Graduate School of Information Sciences, Tohoku University, 6-3-09, Aramaki-Aza-Aoba, Aoba-ku, Sendai, 980-8679 Japan Core Research for Evolutional Science and Technology (CREST), Japan Science and Technology Agency, Kawaguchi, Saitama, Japan obayashi@ecei.tohoku.ac.jp.
authors.forename: Takeshi
authors.initials: T
authors.lastname: Obayashi
mesh_terms: D017360:Arabidopsis / Q000235:genetics*; D016000:Cluster Analysis; D030541:Databases, Genetic; D020869:Gene Expression Profiling; D018506:Gene Expression Regulation, Plant; D053263:Gene Regulatory Networks; D018551:Solanum lycopersicum / Q000235:genetics*; D020411:Oligonucleotide Array Sequence Analysis; D012275:Oryza / Q000235:genetics*; D015203:Reproducibility of Results; D017423:Sequence Analysis, RNA; D013025:Glycine max / Q000235:genetics*; D013045:Species Specificity; D003313:Zea mays / Q000235:genetics*
keywords: Arabidopsis; Comparative transcriptomics; Database; Evolution; Gene coexpression; Gene network