用于曲霉属组学数据功能分析的新资源。
New resources for functional analysis of omics data for the genus Aspergillus.
机构信息
Institute of Biology Leiden, Leiden University, Sylviusweg 72, 2333 BE Leiden, The Netherlands.
出版信息
BMC Genomics. 2011 Oct 5;12:486. doi: 10.1186/1471-2164-12-486.
BACKGROUND
Detailed and comprehensive genome annotation can be considered a prerequisite for effective analysis and interpretation of omics data. As such, Gene Ontology (GO) annotation has become a well accepted framework for functional annotation. The genus Aspergillus comprises fungal species that are important model organisms, plant and human pathogens as well as industrial workhorses. However, GO annotation based on both computational predictions and extended manual curation has so far only been available for one of its species, namely A. nidulans.
RESULTS
Based on protein homology, we mapped 97% of the 3,498 GO annotated A. nidulans genes to at least one of seven other Aspergillus species: A. niger, A. fumigatus, A. flavus, A. clavatus, A. terreus, A. oryzae and Neosartorya fischeri. GO annotation files compatible with diverse publicly available tools have been generated and deposited online. To further improve their accessibility, we developed a web application for GO enrichment analysis named FetGOat and integrated GO annotations for all Aspergillus species with public genome sequences. Both the annotation files and the web application FetGOat are accessible via the Broad Institute's website (http://www.broadinstitute.org/fetgoat/index.html). To demonstrate the value of those new resources for functional analysis of omics data for the genus Aspergillus, we performed two case studies analyzing microarray data recently published for A. nidulans, A. niger and A. oryzae.
CONCLUSIONS
We mapped A. nidulans GO annotation to seven other Aspergilli. By depositing the newly mapped GO annotation online as well as integrating it into the web tool FetGOat, we provide new, valuable and easily accessible resources for omics data analysis and interpretation for the genus Aspergillus. Furthermore, we have given a general example of how a well annotated genome can help improving GO annotation of related species to subsequently facilitate the interpretation of omics data.
背景
详细全面的基因组注释可以被认为是有效分析和解释组学数据的前提。因此，基因本体论 (GO) 注释已成为功能注释的一个被广泛接受的框架。曲霉属包括重要的模式生物、植物和人类病原体以及工业用菌。然而，基于计算预测和扩展手动注释的 GO 注释，迄今为止仅可用于其一个种，即构巢曲霉。
结果
基于蛋白质同源性，我们将 3498 个 GO 注释的构巢曲霉基因中的 97%映射到了其他七个曲霉属物种中的至少一个：黑曲霉、烟曲霉、黄曲霉、棒曲霉、土曲霉、米曲霉和谢氏变种青霉。生成了与各种可用的公共工具兼容的 GO 注释文件，并在线存储。为了进一步提高它们的可访问性，我们开发了一个名为 FetGOat 的用于 GO 富集分析的网络应用程序，并将所有曲霉属物种的 GO 注释与公共基因组序列集成在一起。注释文件和网络应用程序 FetGOat 都可以通过 Broad 研究所的网站 (http://www.broadinstitute.org/fetgoat/index.html) 访问。为了展示这些新资源对于曲霉属组学数据的功能分析的价值，我们进行了两个案例研究，分析了最近发表的构巢曲霉、黑曲霉和米曲霉的微阵列数据。
结论
我们将构巢曲霉的 GO 注释映射到了其他七个曲霉属物种。通过在线存储新映射的 GO 注释并将其集成到网络工具 FetGOat 中，我们为曲霉属的组学数据分析和解释提供了新的、有价值且易于访问的资源。此外，我们提供了一个很好的示例，说明一个注释良好的基因组如何有助于提高相关物种的 GO 注释，从而有助于解释组学数据。
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