From manual curation to visualization of gene families and networks across Solanaceae plant species.
From manual curation to visualization of gene families and networks across Solanaceae plant species.
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DOI：
10.1093/database/bat028
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发表时间：
2013
期刊：
影响因子：
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通讯作者：
Mueller LA
中科院分区：
文献类型：
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作者：
Pujar A;Menda N;Bombarely A;Edwards JD;Strickler SR;Mueller LA
高质量的人工注释方法和实践需要扩展到基因组数据生产的增长速度。基于基因家族和基因网络的策展是一种可以显著提高策展效率和质量的方法。SolGenomics Network（SGN; http://solgenomics.net）是一个比较基因组学平台，提供茄科及其密切相关物种的遗传、基因组和表型信息，并结合了基于社区的基因和表型管理系统。在这篇文章中，我们描述了一个手动策展系统的基因家族，旨在促进策展，查询和可视化的基因相互作用模式的基础上复杂的生物过程，包括一个界面，有效地捕捉信息的实验与文献中报道的大数据集。注释良好的多基因家族对于进一步探索跨物种的基因组组织和基因进化是有用的。作为一个例子，我们说明了系统与多基因转录因子家族，WRKY和小生长素上调RNA（SAUR），这两个在响应非生物胁迫在植物中发挥重要作用。数据库URL：http://solgenomics.net/
High-quality manual annotation methods and practices need to be scaled to the increased rate of genomic data production. Curation based on gene families and gene networks is one approach that can significantly increase both curation efficiency and quality. The Sol Genomics Network (SGN; http://solgenomics.net) is a comparative genomics platform, with genetic, genomic and phenotypic information of the Solanaceae family and its closely related species that incorporates a community-based gene and phenotype curation system. In this article, we describe a manual curation system for gene families aimed at facilitating curation, querying and visualization of gene interaction patterns underlying complex biological processes, including an interface for efficiently capturing information from experiments with large data sets reported in the literature. Well-annotated multigene families are useful for further exploration of genome organization and gene evolution across species. As an example, we illustrate the system with the multigene transcription factor families, WRKY and Small Auxin Up-regulated RNA (SAUR), which both play important roles in responding to abiotic stresses in plants. Database URL: http://solgenomics.net/