ATTED-II in 2018: A Plant Coexpression Database Based on Investigation of the Statistical Property of the Mutual Rank Index.
ATTED-II in 2018: A Plant Coexpression Database Based on Investigation of the Statistical Property of the Mutual Rank Index.
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DOI：
10.1093/pcp/pcx191
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发表时间：
2018-01-01
影响因子：
4.9
通讯作者：
Kinoshita K
中科院分区：
文献类型：
--
作者：
Obayashi T;Aoki Y;Tadaka S;Kagaya Y;Kinoshita K
ATTED-II（http：atted.jp）是植物物种的共表达数据库，以帮助发现物种内未知基因的关系。作为一种先进的共表达分析方法，多物种比较有可能在进化背景下检测基因关系的改变。然而，如果没有对共表达数据的质量进行定量评估，很难确定比较共表达研究的有效性。ATTED-II（第9版）为9种植物物种提供了16个共表达平台，其中包括7种由基于微阵列和RNA测序（RNAseq）的共表达数据支持的物种。两个独立来源的共表达数据，使评估的共表达的再现性。拟南芥（Ath-m.c7-1和Ath-r.c3-0）的最新共表达数据显示在ATTED-II的先前共表达数据中具有最高的再现性（Jaccard系数= 0.13）。我们还调查了统计基础的相互排名（MR）指数作为一个coexpression措施，通过自举抽样的实验单位。我们发现，logit转换的MR指数的误差分布显示出正态性，每个共表达平台的方差相等。由于MR误差与共表达数据的样本数量密切相关，因此可以估计任何共表达平台的MR指数的典型置信区间。这些新的高质量共表达数据可以使用ATTED-II中的任何工具进行分析，并与外部资源相结合，以深入了解植物生物学。
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.
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影响因子：
4.9
作者：
Aoki Y;Okamura Y;Ohta H;Kinoshita K;Obayashi T
通讯作者：
Obayashi T
影响因子：
14.9
作者：
Obayashi T;Kinoshita K
通讯作者：
Kinoshita K
影响因子：
3.7
作者：
Okamura Y;Obayashi T;Kinoshita K
通讯作者：
Kinoshita K
影响因子：
14.9
作者：
Ogasawara O;Mashima J;Kodama Y;Kaminuma E;Nakamura Y;Okubo K;Takagi T
通讯作者：
Takagi T
影响因子：
14.9
作者：
Kolesnikov N;Hastings E;Keays M;Melnichuk O;Tang YA;Williams E;Dylag M;Kurbatova N;Brandizi M;Burdett T;Megy K;Pilicheva E;Rustici G;Tikhonov A;Parkinson H;Petryszak R;Sarkans U;Brazma A
通讯作者：
Brazma A