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To facilitate the application of gene function information to the study of natural variation in rice, we comprehensively searched for articles related to rice functional genomics and extracted information on functionally characterized genes.
In addition to sequence similarity approaches at the superfamily and family levels, the authors used information on functionally important residues to infer misannotations, making this one of the most reliable data sources suitable for our purposes.
Novel strategies using in silico methods that employ the knowledge of coevolved energetically coupled residues have also yielded valuable information on functionally important surfaces required for ligand binding in receptors of previously unknown function [53], [54].
The information on functionally characterized genes obtained in this study was compiled in a new database, the O verview of Functionally Characterized G enes in R ice O nline database (OGRO), which is located on the Q-TARO website (Yonemaru et al. 2010; http://qtaro.abr.affrc.go.jp/ogro).jp/ogro
Exome sequencing enables us to obtain information on functionally important coding regions.
Clearly, co-splicing clusters can provide complementary information on functionally related gene groups in addition to co-trancriptional clusters.
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This is largely due to lack of information on functionally-critical glomerular endothelium-restricted proteins and the unavailability of suitable mouse models that exhibit glomerular disease upon deletion of endothelial-expressed genes.
In this study, we comprehensively searched for articles related to rice functional genomics and extracted information on 702 functionally characterized genes (Figure 1).
Information on the functionally characterized genes compiled during this study is now available in the O verview of Functionally Characterized G enes in R ice O nline database (OGRO) on the Q-TARO website (http://qtaro.abr.affrc.go.jp/ogro).jp/ogro
Information on the functionally characterized genes compiled in this study is now available in OGRO on the Q-TARO Web site (Figure 4; http://qtaro.abr.affrc.go.jp/ogro).jp/ogro
Available reference brains, however, are restricted to the macroscopic scale and do not provide information on the functionally important microscopic dimension.
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