Dataset Information

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

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.

SUBMITTER: Obayashi T

PROVIDER: S-EPMC5914358 | biostudies-literature | 2018 Jan

REPOSITORIES: biostudies-literature

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Publications

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

Obayashi Takeshi T Aoki Yuichi Y Tadaka Shu S Kagaya Yuki Y Kinoshita Kengo K

Plant & cell physiology 20180101 1

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 c ...[more]

PMID: 29216398

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Project description:The rapid assignment of genotypes to phenotypes has been a historically challenging process. The discovery of genes encoding biosynthetic pathway enzymes for defined plant specialized metabolites has been informed and accelerated by the detection of gene clusters. Unfortunately, biosynthetic pathway genes are commonly dispersed across chromosomes or reside in genes clusters that provide little predictive value. More reliably, transcript abundance of genes underlying biochemical pathways for plant specialized metabolites display significant coregulation. By rapidly identifying highly coexpressed transcripts, it is possible to efficiently narrow candidate genes encoding pathway enzymes and more easily predict both functions and functional associations. Mutual Rank (MR)-based coexpression analyses in plants accurately demonstrate functional associations for many specialized metabolic pathways; however, despite the clear predictive value of MR analyses, the application is uncommonly used to drive new pathway discoveries. Moreover, many coexpression databases aid in the prediction of both functional associations and gene functions, but lack customizability for refined hypothesis testing. To facilitate and speed flexible MR-based hypothesis testing, we developed MutRank, an R Shiny web-application for coexpression analyses. MutRank provides an intuitive graphical user interface with multiple customizable features that integrates user-provided data and supporting information suitable for personal computers. Tabular and graphical outputs facilitate the rapid analyses of both unbiased and user-defined coexpression results that accelerate gene function predictions. We highlight the recent utility of MR analyses for functional predictions and discoveries in defining two maize terpenoid antibiotic pathways. Beyond applications in biosynthetic pathway discovery, MutRank provides a simple, customizable and user-friendly interface to enable coexpression analyses relating to a breadth of plant biology inquiries. Data and code are available at GitHub: https://github.com/eporetsky/MutRank.

Dataset Information

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

Publications

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

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