New resources for functional analysis of omics data for the genus Aspergillus

BMC Genomics

Research Article

Jonathan Crabtree¹  Benjamin M Nitsche²  Arthur FJ Ram³  Vera Meyer⁴  Gustavo C Cerqueira⁵  Jennifer R Wortman⁵ 

[1] Institute for Genome Sciences, University of Maryland School of Medicine, 20850, Baltimore, MD, USA;Institute of Biology Leiden, Leiden University, Sylviusweg 72, 2333 BE, Leiden, The Netherlands;Institute of Biology Leiden, Leiden University, Sylviusweg 72, 2333 BE, Leiden, The Netherlands;Kluyver Centre for Genomics of Industrial Fermentation, PO Box 5057, 2600 GA, Delft, The Netherlands;Institute of Biology Leiden, Leiden University, Sylviusweg 72, 2333 BE, Leiden, The Netherlands;Kluyver Centre for Genomics of Industrial Fermentation, PO Box 5057, 2600 GA, Delft, The Netherlands;Institute of Biotechnology, Berlin University of Technology, Gustav-Meyer-Allee 25, 13355, Berlin, Germany;Microbial Informatics, Broad Institute, 320 Charles Street, 02141, MA, USA;

关键词: Gene Ontology;    Enrichment Analysis;    Aspergillus Species;    Omics Data;    Annotation File;   

DOI  :  10.1186/1471-2164-12-486

 received in 2011-07-04, accepted in 2011-10-05,  发布年份 2011

来源: Springer

【 摘 要 】

BackgroundDetailed 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.ResultsBased 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.ConclusionsWe 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.

【 授权许可】

CC BY   
© Nitsche et al; licensee BioMed Central Ltd. 2011