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Protocols

CGD specifications

Information


Unique identifier OMICS_03098
Name CGD
Alternative name Candida Genome Database
Restrictions to use None
Community driven Yes
Data access File download, Browse
User data submission Not allowed
Maintained Yes

Taxon


  • Plants and Fungi
    • Candida albicans

Documentation


Maintainers


  • person_outline Martha B. Arud
  • person_outline Gavin Sherlock

Publications for Candida Genome Database

CGD citations

 (65)
library_books

Redox Regulation, Rather than Stress Induced Phosphorylation, of a Hog1 Mitogen Activated Protein Kinase Modulates Its Nitrosative Stress Specific Outputs

2018
MBio
PMCID: 5874921
PMID: 29588408
DOI: 10.1128/mBio.02229-17

[…] ), Trim Galore (v. 3.1), Samtools (v. 1.19), STAR aligner (v. 2.4), and HTSeq (v. 5.4). Genome alignments were generated against the C_albicans_SC5314_version_A21-s02-m09-r08 chromosome file from the Candida Genome Database (http://www.candidagenome.org) (). Gene expression analysis was performed using Partek Genomics Suite software, v. 6.6, using a log2 data transformation. Gene ontology (GO) ter […]

library_books

Aspartyl proteases in Candida glabrata are required for suppression of the host innate immune response

2018
PMCID: 5925793
PMID: 29491142
DOI: 10.1074/jbc.M117.813741

[…] DNA molecules, the library was amplified using eight cycles of PCR for enrichment of adapter-ligated fragments, and 76-base pair paired-end reads were produced with the Illumina NextSeq500. Using the Candida genome database as the reference genome (http://www.candidagenome.org),3 differentially expressed genes (>1.5-fold change and a false discovery rate–adjusted p value of ≤0.05) were identified […]

call_split

Investigation of Candida parapsilosis virulence regulatory factors during host pathogen interaction

2018
Sci Rep
PMCID: 5777994
PMID: 29358719
DOI: 10.1038/s41598-018-19453-4
call_split See protocol

[…] mics facility. We sequenced paired-end 50bp-long reads RNAseq data for the above-mentioned time-points. The reference genomes for the reference strain CDC317 and the human hg19 were obtained from the Candida Genome Database (CGD) and UCSC (UCSC Genome Browser), respectively. Gene annotations were obtained from the gencode project, version 18 and from CGD. Read mapping and alignment were carried ou […]

library_books

Put3 Positively Regulates Proline Utilization in Candida albicans

2017
PMCID: 5729217
PMID: 29242833
DOI: 10.1128/mSphere.00354-17

[…] , and then target genes with log of ratio values of at least 1.4 that were also upregulated in the SCPUT3GAD1A strain expressing a hyperactive Put3 () () were further annotated for function using the Candida Genome Database Gene Ontology tool. Consistent with transcription profiling data for the SCPUT3GAD1A strain, Put3 targets identified by ChIP-chip include the promoters of PUT1 and orf19.1584, […]

library_books

The Candida albicans TOR Activating GTPases Gtr1 and Rhb1 Coregulate Starvation Responses and Biofilm Formation

2017
PMCID: 5687921
PMID: 29152581
DOI: 10.1128/mSphere.00477-17

[…] This analysis required the use of a database of publicly available genome-wide data sets (constructed by Andre Nantel, National Research Council of Canada, Montreal), that can be downloaded from the Candida Genome Database. To visualize these enrichments and to identify related gene sets, the data were export to Cytoscape 3.2.1. Once the data were exported to Cytoscape, enrichment maps were gener […]

library_books

Eukaryotic transporters for hydroxyderivatives of benzoic acid

2017
Sci Rep
PMCID: 5566891
PMID: 28827635
DOI: 10.1038/s41598-017-09408-6

[…] The following databases were used to identify and analyze the gene and protein sequences: Candida Genome Database (http://www.candidagenome.org/), Candida Gene Order Browser (http://cgob3.ucd.ie/), ; Pfam database (http://pfam.xfam.org/), SMART (http://smart.embl-heidelberg.de/), UniProt ( […]

Citations

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CGD institution(s)
Department of Genetics, Stanford University Medical School, Stanford, CA, USA
CGD funding source(s)
This work was funded by the National Institute of Dental and Craniofacial Research at the US National Institutes of Health [R01 DE015873].

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