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Open Access Research article

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

Benjamin M Nitsche1*, Jonathan Crabtree2, Gustavo C Cerqueira3, Vera Meyer145, Arthur FJ Ram14 and Jennifer R Wortman3

Author Affiliations

1 Institute of Biology Leiden, Leiden University, Sylviusweg 72, 2333 BE Leiden, The Netherlands

2 Institute for Genome Sciences, University of Maryland School of Medicine, Baltimore, MD 20850, USA

3 Microbial Informatics, Broad Institute, 320 Charles Street, MA 02141, USA

4 Kluyver Centre for Genomics of Industrial Fermentation, PO Box 5057, 2600 GA, Delft, The Netherlands

5 Institute of Biotechnology, Berlin University of Technology, Gustav-Meyer-Allee 25, 13355 Berlin, Germany

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BMC Genomics 2011, 12:486  doi:10.1186/1471-2164-12-486

Published: 5 October 2011

Abstract

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 webcite). 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.