Please use this identifier to cite or link to this item: http://dx.doi.org/10.14279/depositonce-4614
Main Title: New resources for functional analysis of omics data for the genus Aspergillus
Author(s): Nitsche, Benjamin M.
Crabtree, Jonathan
Cerqueira, Gustavo C.
Meyer, Vera
Ram, Arthur F.J.
Wortman, Jennifer R.
Type: Article
Language: English
Language Code: en
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.
URI: urn:nbn:de:kobv:83-opus4-70178
http://depositonce.tu-berlin.de/handle/11303/4911
http://dx.doi.org/10.14279/depositonce-4614
Issue Date: 2011
Date Available: 7-Aug-2015
DDC Class: 570 Biowissenschaften; Biologie
610 Medizin und Gesundheit
Subject(s): Aspergillus species
Gene ontology
Genom annotation
GO annotation
Creative Commons License: https://creativecommons.org/licenses/by/2.0/
Journal Title: BMC Genomics
Publisher: BioMed Central
Publisher Place: London
Volume: 12
Article Number: 486
Publisher DOI: 10.1186/1471-2164-12-486
Notes: Published By BioMed Central Nitsche, Benjamin M. ; Crabtree, Jonathan ; Cerqueira, Gustavo C. ; Meyer, Vera ; Ram, Arthur F.J. ; Wortman, Jennifer R. : New resources for functional analysis of omics data for the genus Aspergillus. - In: BMC Genomics. - ISSN 1471-2164 (online). - 12 (2011), art. 486. - doi:10.1186/1471-2164-12-486.
Appears in Collections:Technische Universität Berlin » Fakultäten & Zentralinstitute » Fakultät 3 Prozesswissenschaften » Institut für Biotechnologie » Publications

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