ATTED-II in 2016: A Plant Coexpression Database Towards Lineage-Specific Coexpression

Plant Cell Physiol. 2016 Jan;57(1):e5. doi: 10.1093/pcp/pcv165. Epub 2015 Nov 6.

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.

Keywords: Arabidopsis; Comparative transcriptomics; Database; Evolution; Gene coexpression; Gene network.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Arabidopsis / genetics*
  • Cluster Analysis
  • Databases, Genetic*
  • Gene Expression Profiling
  • Gene Expression Regulation, Plant
  • Gene Regulatory Networks
  • Lycopersicon esculentum / genetics*
  • Oligonucleotide Array Sequence Analysis
  • Oryza / genetics*
  • Reproducibility of Results
  • Sequence Analysis, RNA
  • Soybeans / genetics*
  • Species Specificity
  • Zea mays / genetics*