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Plant Cell Physiol. 2018 Jan 1;59(1):e3. doi: 10.1093/pcp/pcx191.

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

Author information

1
Graduate School of Information Sciences, Tohoku University, 6-3-09, Aramaki-Aza-Aoba, Aoba-ku, Sendai, 980-8679 Japan.
2
Tohoku Medical Megabank Organization, Tohoku University, Sendai, 980-8573 Japan.
3
Graduate School of Medicine, Tohoku University, Sendai, 980-8573 Japan.
4
Institute of Development, Aging, and Cancer, Tohoku University, Sendai, 980-8575 Japan.

Abstract

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

KEYWORDS:

Arabidopsis; Comparative transcriptomics; Database; Gene coexpression; Gene network; Statistics

PMID:
29216398
PMCID:
PMC5914358
DOI:
10.1093/pcp/pcx191
[Indexed for MEDLINE]
Free PMC Article

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