WikiPathways for plants: a community pathway curation portal and a case study in rice and arabidopsis seed development networks.
WikiPathways for plants: a community pathway curation portal and a case study in rice and arabidopsis seed development networks.
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DOI：
10.1186/1939-8433-6-14
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发表时间：
2013-05-29
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影响因子：
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通讯作者：
Jaiswal P
中科院分区：
文献类型：
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作者：
Hanumappa M;Preece J;Elser J;Nemeth D;Bono G;Wu K;Jaiswal P
下一代测序和“组学”平台广泛用于植物生物学研究，以解开新基因组并研究它们与生长环境中非生物和生物因子的相互作用。尽管有大量且不断增长的基因组数据集可供使用，但为植物途径提供精心策划的最新代谢和调控网络的资源却有限。使用 PathVisio（与 WikiPathways 相关的途径编辑工具），我们通过整理已发表文献中报道的相互作用，创建了一个由参与种子发育过程的 430 个水稻 (Oryza sativa) 基因组成的基因相互作用网络。然后，我们对这些基因应用基于 InParanoid 的同源性搜索，并使用生成的基因簇来识别 351 个拟南芥基因。利用这个同源基因列表，我们通过我们开发的名为 Pathway GeneSWAPPER 的 Perl 实用软件处理基因列表和水稻网络，构建了拟南芥种子发育网络。为了证明这些网络在更深入的下游分析之前生成可检验的假设和初步分析的效用，我们使用 PathVisio 的表达查看器和统计分析功能来分析公开的和已发表的有关昼夜光周期响应和种子发育时间过程的微阵列基因表达数据集，以发现水稻和拟南芥种子发育网络中发现的共表达基因的模式。本文描述的这些种子发育网络以及其他植物途径和网络可以在 WikiPathways (http://plants.wikipathways.org) 的植物途径门户网站上免费获得。我们与 WikiPathways 项目合作，为植物生物学家提供了一个社区管理和分析平台，注册用户可以在其中自由创建、编辑、共享和监控已发表文献支持的路径。我们描述了水稻种子发育网络的管理和注释，以及拟南芥中类似的基于基因同源性的网络的预测。我们还展示了 Pathway GeneSWAPPER (PGS) 应用程序的实用性，当使用以 GPML 格式编译的一个物种中的参考网络基于基因同源性在另一物种中投影类似网络时，可以节省宝贵的时间和劳动力。本文的在线版本 (doi:10.1186/1939-8433-6-14) 包含补充材料，可供授权用户使用。
Next-generation sequencing and ‘omics’ platforms are used extensively in plant biology research to unravel new genomes and study their interactions with abiotic and biotic agents in the growth environment. Despite the availability of a large and growing number of genomic data sets, there are only limited resources providing highly-curated and up-to-date metabolic and regulatory networks for plant pathways. Using PathVisio, a pathway editor tool associated with WikiPathways, we created a gene interaction network of 430 rice (Oryza sativa) genes involved in the seed development process by curating interactions reported in the published literature. We then applied an InParanoid-based homology search to these genes and used the resulting gene clusters to identify 351 Arabidopsis thaliana genes. Using this list of homologous genes, we constructed a seed development network in Arabidopsis by processing the gene list and the rice network through a Perl utility software called Pathway GeneSWAPPER developed by us. In order to demonstrate the utility of these networks in generating testable hypotheses and preliminary analysis prior to more in-depth downstream analysis, we used the expression viewer and statistical analysis features of PathVisio to analyze publicly-available and published microarray gene expression data sets on diurnal photoperiod response and the seed development time course to discover patterns of coexpressed genes found in the rice and Arabidopsis seed development networks. These seed development networks described herein, along with other plant pathways and networks, are freely available on the plant pathways portal at WikiPathways (http://plants.wikipathways.org). In collaboration with the WikiPathways project we present a community curation and analysis platform for plant biologists where registered users can freely create, edit, share and monitor pathways supported by published literature. We describe the curation and annotation of a seed development network in rice, and the projection of a similar, gene homology-based network in Arabidopsis. We also demonstrate the utility of the Pathway GeneSWAPPER (PGS) application in saving valuable time and labor when a reference network in one species compiled in GPML format is used to project a similar network in another species based on gene homology. The online version of this article (doi:10.1186/1939-8433-6-14) contains supplementary material, which is available to authorized users.