Abstract
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.
Highlights
Detailed and comprehensive genome annotation can be considered a prerequisite for effective analysis and interpretation of omics data
Mapping of Gene Ontology (GO) annotation A. nidulans is the only Aspergillus species for which comprehensive GO annotation based on both computational prediction and extended manual curation of genespecific literature is available [9]
It constitutes a valuable resource for GO enrichment analysis, which has proven to be a powerful tool for dissecting omics data, for example sets of differentially expressed genes
Summary
Detailed and comprehensive genome annotation can be considered a prerequisite for effective analysis and interpretation of omics data. Gene Ontology (GO) is a framework for functional annotation of gene products aiming to provide a unique vocabulary for living systems [1]. It comprises Biological Process (BP), Molecular Function (MF) and Cellular Component (CC) ontologies. Enrichment analysis of GO terms is a well accepted approach to dissecting omics data in a non-biased manner. It has been used in many studies to highlight major trends in genomic, transcriptomic or proteomic datasets and describe them with a controlled vocabulary [2,3,4,5]. If the frequency of specific GO terms in a list of genes or proteins is higher than expected by chance, it is likely that these enriched GO terms are related to the biological processes under investigation
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