ArticleBMC genomics2010
FUNGIpath: a tool to assess fungal metabolic pathways predicted by orthology.
Article in BMC genomics, 2010. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 17 papers.
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Who cites it
17 citing papers in PubMed, 47 citations in OpenAlex.
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- A RID-like putative cytosine methyltransferase homologue controls sexual development in the fungus Podospora anserina.PLoS genetics · 2019Article
- Gearing up to handle the mosaic nature of life in the quest for orthologs.Bioinformatics (Oxford, England) · 2018Article
- Mitochondrial impairment and oxidative stress mediated apoptosis induced by α-FeToxicology research · 2017Article
- Toxicological effects of graphene oxide onToxicology research · 2017Article
- Proximity ligation scaffolding and comparison of twoBiotechnology for biofuels · 2017Article
- Differential gene retention as an evolutionary mechanism to generate biodiversity and adaptation in yeasts.Scientific reports · 2015Article
- Homocitrate synthase expression and lysine content in fruiting body of different developmental stages in Flammulina velutipes.Current microbiology · 2015Article
- Maintenance of sex-related genes and the co-occurrence of both mating types in Verticillium dahliae.PloS one · 2014Article
- The transcriptional response to nonself in the fungus Podospora anserina.G3 (Bethesda, Md.) · 2013Article
- A network of HMG-box transcription factors regulates sexual cycle in the fungus Podospora anserina.PLoS genetics · 2013Article
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Corrections and comments
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Authors and funding
3 authors at 2 institutions in 1 country.
Funding
No grant is acknowledged in the PubMed record.
Abstract
backgroundMore and more completely sequenced fungal genomes are becoming available and many more sequencing projects are in progress. This deluge of data should improve our knowledge of the various primary and secondary metabolisms of Fungi, including their synthesis of useful compounds such as antibiotics or toxic molecules such as mycotoxins. Functional annotation of many fungal genomes is imperfect, especially of genes encoding enzymes, so we need dedicated tools to analyze their metabolic pathways in depth. DESCRIPTION: FUNGIpath is a new tool built using a two-stage approach. Groups of orthologous proteins predicted using complementary methods of detection were collected in a relational database. Each group was further mapped on to steps in the metabolic pathways published in the public databases KEGG and MetaCyc. As a result, FUNGIpath allows the primary and secondary metabolisms of the different fungal species represented in the database to be compared easily, making it possible to assess the level of specificity of various pathways at different taxonomic distances. It is freely accessible at http://www.fungipath.u-psud.fr.
conclusionsAs more and more fungal genomes are expected to be sequenced during the coming years, FUNGIpath should help progressively to reconstruct the ancestral primary and secondary metabolisms of the main branches of the fungal tree of life and to elucidate the evolution of these ancestral fungal metabolisms to various specific derived metabolisms.
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Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.