New resources for functional analysis of omics data for the genus Aspergillus.
New resources for functional analysis of omics data for the genus Aspergillus.
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DOI：
10.1186/1471-2164-12-486
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发表时间：
2011-10-05
期刊：
影响因子：
4.4
通讯作者：
Wortman JR
中科院分区：
文献类型：
--
作者：
Nitsche BM;Crabtree J;Cerqueira GC;Meyer V;Ram AF;Wortman JR
详细而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先决条件。因此，基因本体（GO）注释已成为公认的功能注释框架。曲霉属包括作为重要模式生物、植物和人类病原体以及工业主力的真菌物种。然而，基于计算预测和扩展手动管理的 GO 注释迄今为止仅适用于其中一种物种，即构巢构巢菌。基于蛋白质同源性，我们将 3,498 个 GO 注释的构巢曲霉基因中的 97% 映射到其他七种曲霉属物种中的至少一种：黑曲霉、烟曲霉、黄曲霉、棒曲霉、土曲霉、米曲霉和 Neosartorya fischeri。与各种公开可用工具兼容的 GO 注释文件已生成并在线存储。为了进一步提高其可访问性，我们开发了一个名为 FetGOat 的 GO 富集分析网络应用程序，并集成了具有公共基因组序列的所有曲霉属物种的 GO 注释。注释文件和 Web 应用程序 FetGOat 都可以通过 Broad Institute 的网站 (http://www.broadinstitute.org/fetgoat/index.html) 访问。为了证明这些新资源对曲霉属组学数据功能分析的价值，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。我们将构巢曲霉 GO 注释映射到其他七个曲霉菌。通过在线存放新映射的 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、有价值的且易于访问的资源。此外，我们还给出了一个一般性示例，说明注释良好的基因组如何帮助改进相关物种的 GO 注释，从而促进组学数据的解释。
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. 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. 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.
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影响因子：
14.9
作者：
Du Z;Li L;Chen CF;Yu PS;Wang JZ
通讯作者：
Wang JZ
影响因子：
4.5
作者：
Dunning Hotopp JC;Lin M;Madupu R;Crabtree J;Angiuoli SV;Eisen JA;Seshadri R;Ren Q;Wu M;Utterback TR;Smith S;Lewis M;Khouri H;Zhang C;Niu H;Lin Q;Ohashi N;Zhi N;Nelson W;Brinkac LM;Dodson RJ;Rosovitz MJ;Sundaram J;Daugherty SC;Davidsen T;Durkin AS;Gwinn M;Haft DH;Selengut JD;Sullivan SA;Zafar N;Zhou L;Benahmed F;Forberger H;Halpin R;Mulligan S;Robinson J;White O;Rikihisa Y;Tettelin H
通讯作者：
Tettelin H
影响因子：
64.8
作者：
Carlton, Jane M.;Adams, John H.;Silva, Joana C.;Bidwell, Shelby L.;Lorenzi, Hernan;Caler, Elisabet;Crabtree, Jonathan;Angiuoli, Samuel V.;Merino, Emilio F.;Amedeo, Paolo;Cheng, Qin;Coulson, Richard M. R.;Crabb, Brendan S.;del Portillo, Hernando A.;Essien, Kobby;Feldblyum, Tamara V.;Fernandez-Becerra, Carmen;Gilson, Paul R.;Gueye, Amy H.;Guo, Xiang;Kang'a, Simon;Kooij, Taco W. A.;Korsinczky, Michael;Meyer, Esmeralda V. -S.;Nene, Vish;Paulsen, Ian;White, Owen;Ralph, Stuart A.;Ren, Qinghu;Sargeant, Tobias J.;Salzberg, Steven L.;Stoeckert, Christian J.;Sullivan, Steven A.;Yamamoto, Marcio M.;Hoffman, Stephen L.;Wortman, Jennifer R.;Gardner, Malcolm J.;Galinski, Mary R.;Barnwell, John W.;Fraser-Liggett, Claire M.
通讯作者：
Fraser-Liggett, Claire M.
影响因子：
4.3
作者：
Reference Genome Group of the Gene Ontology Consortium
通讯作者：
Reference Genome Group of the Gene Ontology Consortium
影响因子：
4.4
作者：
Jorgensen, Thomas R.;Nitsche, Benjamin M.;Ram, Arthur F.
通讯作者：
Ram, Arthur F.