ArticleBMC genomics2011
New resources for functional analysis of omics data for the genus Aspergillus.
Article in BMC genomics, 2011. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 16 papers.
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16 citing papers in PubMed, 33 citations in OpenAlex.
- Succession of physiological stages hallmarks the transcriptomic response of the fungusBiotechnology for biofuels · 2020Article
- Antifungal Peptides of the AFP Family Revisited: Are These Cannibal Toxins?Microorganisms · 2018Review
- Inducer-independent production of pectinases in Aspergillus niger by overexpression of the D-galacturonic acid-responsive transcription factor gaaR.Applied microbiology and biotechnology · 2018Article
- Expression ofBiotechnology for biofuels · 2017Article
- Metabolic activity in dormant conidia of Aspergillus niger and developmental changes during conidial outgrowth.Fungal genetics and biology : FG & B · 2016Article
- A Transcriptome Meta-Analysis Proposes Novel Biological Roles for the Antifungal Protein AnAFP in Aspergillus niger.PloS one · 2016Article
- RNAseq reveals hydrophobins that are involved in the adaptation of Aspergillus nidulans to lignocellulose.Biotechnology for biofuels · 2016Article
- The role of carbon starvation in the induction of enzymes that degrade plant-derived carbohydrates in Aspergillus niger.Fungal genetics and biology : FG & B · 2014Article
- Recent advances in genome mining of secondary metabolite biosynthetic gene clusters and the development of heterologous expression systems in Aspergillus nidulans.Journal of industrial microbiology & biotechnology · 2014Review
- Transcriptional changes in the transition from vegetative cells to asexual development in the model fungus Aspergillus nidulans.Eukaryotic cell · 2013Article
- The function and evolution of the Aspergillus genome.Trends in microbiology · 2013Review
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- The transcriptomic fingerprint of glucoamylase over-expression in Aspergillus niger.BMC genomics · 2012Article
- The carbon starvation response of Aspergillus niger during submerged cultivation: insights from the transcriptome and secretome.BMC genomics · 2012Article
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Authors and funding
6 authors at 4 institutions in 3 countries.
Funding
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.
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