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Protocols

YeastMine specifications

Information


Unique identifier OMICS_03814
Name YeastMine
Restrictions to use None
Database management system PostgreSQL
Community driven No
Data access Browse, Application programming interface
User data submission Not allowed
Maintained Yes
Wikipedia https://wiki.yeastgenome.org/index.php/Main_Page

Taxon


  • Plants and Fungi
    • Saccharomyces cerevisiae

Documentation


Maintainers


  • person_outline YeastMine Team
  • person_outline J. Michael Cherry

Publication for YeastMine

YeastMine citations

 (30)
library_books

JAMI: a Java library for molecular interactions and data interoperability

2018
BMC Bioinformatics
PMCID: 5896107
PMID: 29642846
DOI: 10.1186/s12859-018-2119-0

[…] required by this specialist visualisation software. ComplexViewer is open source and hosted on GitHub under the Apache 2.0 licence and has been integrated into the Complex Portal [], HumanMine [] and YeastMine [] data resources.Fig. 2Fig. 3 […]

library_books

Updated regulation curation model at the Saccharomyces Genome Database

2018
PMCID: 5829562
PMID: 29688362
DOI: 10.1093/database/bay007

[…] uttons beneath each data table. The gene lists in each table can also be easily ported to other analysis tools within SGD via the ‘Analyze’ button. These tools include GO Term Finder (), SPELL () and YeastMine ().Regulation pages also include a visualization of regulatory relationships in order to reflect the complexity of local regulatory networks. These displays distinguish between regulators an […]

call_split

Different Non Saccharomyces Yeast Species Stimulate Nutrient Consumption in S. cerevisiae Mixed Cultures

2017
Front Microbiol
PMCID: 5671574
PMID: 29163412
DOI: 10.3389/fmicb.2017.02121
call_split See protocol

[…] ata transcripts per million (TPM). The remaining statistical analyses were done using STATA-SE. Venn diagram was done by using Venny 2.1 on-line tool software (). GO term analysis was performed using YeastMine (). The p-values were corrected for multiple testing by the Bonferroni test for functional associations and GO analyses. The statistical level of significance was set at p-value ≤ 0.05. Then […]

library_books

Complete genome sequence and comparative genomics of the probiotic yeast Saccharomyces boulardii

2017
Sci Rep
PMCID: 5428479
PMID: 28336969
DOI: 10.1038/s41598-017-00414-2

[…] The mapping studies to Sc genes of yeastmine database revealed that 50 genes had no reads mapped onto them. Also, we found that 94 genes apart from these 50 genes had read coverage <20 reads. The absence of these genes was confirmed by […]

library_books

Curated protein information in the Saccharomyces genome database

2017
PMCID: 5467551
PMID: 28365727
DOI: 10.1093/database/bax011

[…] eference. The data in the table are also available for download as a text (.txt) file. Curated data for the entire proteome can be retrieved and downloaded as a tab-separated values (.tsv) file using YeastMine (yeastmine.yeastgenome.org; ), SGD’s instance of the InterMine search and retrieval tool (see below). […]

library_books

Bdf1 Bromodomains Are Essential for Meiosis and the Expression of Meiotic Specific Genes

2017
PLoS Genet
PMCID: 5261807
PMID: 28068333
DOI: 10.1371/journal.pgen.1006541

[…] re then aligned to S. cerevisiae S288c genome build R64-1-1.82 using Bowtie2 []. The attribute file was downloaded from Ensembl website and modified to include yeast intronic sequences, obtained from Yeastmine. Raw read counts for each gene were calculated using HTSeqCount using defaults parameters []. Read count data was normalised using the DESeq2 R-package (, []). DESeq2 normalised read counts […]

Citations

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YeastMine institution(s)
Department of Genetics, Stanford University, Stanford, CA, USA; Department of Genetics, University of Cambridge, Genetics, Cambridge, UK
YeastMine funding source(s)
Supported by National Human Genome Research Institute: Saccharomyces Genome Database project (grant number P41 HG001315); YeastMine development (grant number R01 HG004834, PI).

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