ATTED-II in 2018: A Plant Coexpression Database Based on Investigation of the Statistical Property of the Mutual Rank Index

• DOI: 10.1093/pcp/pcx191
• Publication Date: 2017-12-01T07:29:39Z
• Authors: Takeshi Obayashi; Yuichi Aoki; Shu Tadaka; Yuki Kagaya; Kengo Kinoshita
• Keywords: Jaccard index; Rank (graph theory); False Discovery Rate

ATTED-II (http://atted.jp) is a coexpression database for plant species to aid in the discovery of relationships unknown genes within species. As an advanced analysis method, multispecies comparisons have potential detect alterations gene evolutionary context. However, determining validity comparative studies difficult without quantitative assessments quality data. (version 9) provides 16 platforms nine species, including seven supported by both microarray- and RNA sequencing (RNAseq)-based Two independent sources data enable assessment reproducibility coexpression. The latest Arabidopsis (Ath-m.c7-1 Ath-r.c3-0) showed highest (Jaccard coefficient = 0.13) among previous ATTED-II. We also investigated statistical basis mutual rank (MR) index as measure bootstrap sampling experimental units. found that error distribution logit-transformed MR normality with equal variances each platform. Because was strongly correlated number samples data, typical confidence intervals can be estimated any These new, high-quality analyzed tool combined external resources obtain insight into biology.