New tools at the Candida Genome Database: biochemical pathways and full-text literature search
Open accessAbstract
The Candida Genome Database (CGD, http://www.candidagenome.org/) provides online access to genomic sequence data and manually curated functional information about genes and proteins of the human pathogen Candida albicans. Herein, we describe two recently added features, Candida Biochemical Pathways and the Textpresso full-text literature search tool. The Biochemical Pathways tool provides visualization of metabolic pathways and analysis tools that facilitate interpretation of experimental data, including results of large-scale experiments, in the context of Candida metabolism. Textpresso for Candida allows searching through the full-text of Candida-specific literature, including clinical and epidemiological studies.
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Growth ability and virulence factor production of C. albicans in the host determine the infection trend, and growth ability affects virulence factor production to some extent, but virulence factor production is not always affected by growth ability.
“The growth ability30–32 and virulence factor production31 of C. albicans in the host determine the infection trend, and the former affects the latter to some extent, but the latter is not always affected by the former31.”
From The δ subunit of F1Fo-ATP synthase is required for pathogenicity of Candida albicans (2021) · cites this paper as [32]
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- [1]Butler G Rasmussen MD Lin MF Santos MA Sakthikumar S Munro CA Rheinbay E Grabherr M Forche A Reedy JL Evolution of pathogenicity and sexual reproduction in eight Candida genomes Nature 2009 459 657 662 19465905 PMC2834264
- [2]Karp PD Paley S Romero P The Pathway Tools software Bioinformatics 2002 18 S225 S232 12169551
- [3]Krieger CJ Zhang P Mueller LA Wang A Paley S Arnaud M Pick J Rhee SY Karp PD MetaCyc: a multiorganism database of metabolic pathways and enzymes Nucleic Acids Res. 2004 32 D438 D442 14681452 PMC308834
- [4]Hong EL Balakrishnan R Dong Q Christie KR Park J Binkley G Costanzo MC Dwight SS Engel SR Fisk DG Gene Ontology annotations at SGD: new data sources and annotation methods Nucleic Acids Res. 2008 36 D577 D581 17982175 PMC2238894
- [5]Green ML Karp PD A Bayesian method for identifying missing enzymes in predicted metabolic pathway databases BMC Bioinformatics 2004 5 76 15189570 PMC446185
- [6]Muller HM Kenny EE Sternberg PW Textpresso: an ontology-based information retrieval and extraction system for biological literature PLoS Biol. 2004 2 e309 15383839 PMC517822
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- Authors
- Skrzypek, M. S., Arnaud, M. B., Costanzo, M. C., Inglis, D. O., Shah, P., Binkley, G., Miyasato, S. R., & Sherlock, G.
- Affiliations
- Stanford Medicine (US)
- Corresponding author
- Arnaud, Martha B.
- ORCID
- Venue
- Nucleic Acids Research
- Publisher
- Oxford University Press (OUP)
- Published
- 2009-10-06
- Volume
- 38
- Issue
- suppl_1
- Pages
- D428-D432
- ISSN
- 0305-1048 (ISSN-L)
- 1362-4962
- PMC
- PMC2808937
- OpenAlex
- W2034837383
- Cited by
- 67
- References
- 0
- Citations by year
- 2025: 1 · 2024: 1 · 2023: 1 · 2021: 1 · 2020: 4 · 2018: 2 · 2017: 2 · 2016: 2 · 2015: 2 · 2014: 7 · 2013: 6 · 2012: 9
- FWCI
- 5.11
- Type
- journal article
- Language
- en
- Open access
- gold
- doi.org
- Licence
- Locations
- Nucleic Acids Research (publishedVersion, cc-by-nc)
- PubMed Central (publishedVersion, cc-by-nc)
- PubMed (publishedVersion)
- HighWire Press Open Archive (submittedVersion)
- Funders
- National Institute of Dental and Craniofacial Research (R01DE015873)
- Topics
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Fungal and yeast genetics research
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Bioinformatics and Genomic Networks
- Health Sciences › Medicine › Infectious Diseases › Antifungal resistance and susceptibility
- Keywords
- Candida albicans, metabolic pathways, gene function annotation, fungal genomics
- MeSH terms
- Candida albicans, DNA, Fungal, Genes, Fungal, Software, User-Computer Interface, Information Storage and Retrieval, Open Reading Frames, Genome, Fungal, Protein Structure, Tertiary, Computational Biology, Internet, Databases, Genetic, Databases, Nucleic Acid, Databases, Protein
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