Saccharomyces genome database provides new regulation data
The Saccharomyces Genome Database (SGD; http://www.yeastgenome.org) is the community resource for genomic, gene and protein information about the budding yeast Saccharomyces cerevisiae, containing a variety of functional information about each yeast gene and gene product. We have recently added regu...
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| Format: | Online |
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Oxford University Press
2014
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| Online Access: | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3965049/ |
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pubmed-39650492014-03-25 Saccharomyces genome database provides new regulation data Costanzo, Maria C. Engel, Stacia R. Wong, Edith D. Lloyd, Paul Karra, Kalpana Chan, Esther T. Weng, Shuai Paskov, Kelley M. Roe, Greg R. Binkley, Gail Hitz, Benjamin C. Cherry, J. Michael IV. Viruses, bacteria, protozoa and fungi The Saccharomyces Genome Database (SGD; http://www.yeastgenome.org) is the community resource for genomic, gene and protein information about the budding yeast Saccharomyces cerevisiae, containing a variety of functional information about each yeast gene and gene product. We have recently added regulatory information to SGD and present it on a new tabbed section of the Locus Summary entitled ‘Regulation’. We are compiling transcriptional regulator–target gene relationships, which are curated from the literature at SGD or imported, with permission, from the YEASTRACT database. For nearly every S. cerevisiae gene, the Regulation page displays a table of annotations showing the regulators of that gene, and a graphical visualization of its regulatory network. For genes whose products act as transcription factors, the Regulation page also shows a table of their target genes, accompanied by a Gene Ontology enrichment analysis of the biological processes in which those genes participate. We additionally synthesize information from the literature for each transcription factor in a free-text Regulation Summary, and provide other information relevant to its regulatory function, such as DNA binding site motifs and protein domains. All of the regulation data are available for querying, analysis and download via YeastMine, the InterMine-based data warehouse system in use at SGD. Oxford University Press 2014-01-01 2013-11-20 /pmc/articles/PMC3965049/ /pubmed/24265222 http://dx.doi.org/10.1093/nar/gkt1158 Text en © The Author(s) 2013. Published by Oxford University Press. http://creativecommons.org/licenses/by/3.0/ This is an Open Access article distributed under the terms of the Creative Commons Attribution Non-Commercial License (http://creativecommons.org/licenses/by/3.0/), which permits non-commercial reuse, distribution, and reproduction in any medium, provided the original work is properly cited. For commercial re-use, please contact journals.permissions@oup.com |
| repository_type |
Open Access Journal |
| institution_category |
Foreign Institution |
| institution |
US National Center for Biotechnology Information |
| building |
NCBI PubMed |
| collection |
Online Access |
| language |
English |
| format |
Online |
| author |
Costanzo, Maria C. Engel, Stacia R. Wong, Edith D. Lloyd, Paul Karra, Kalpana Chan, Esther T. Weng, Shuai Paskov, Kelley M. Roe, Greg R. Binkley, Gail Hitz, Benjamin C. Cherry, J. Michael |
| spellingShingle |
Costanzo, Maria C. Engel, Stacia R. Wong, Edith D. Lloyd, Paul Karra, Kalpana Chan, Esther T. Weng, Shuai Paskov, Kelley M. Roe, Greg R. Binkley, Gail Hitz, Benjamin C. Cherry, J. Michael Saccharomyces genome database provides new regulation data |
| author_facet |
Costanzo, Maria C. Engel, Stacia R. Wong, Edith D. Lloyd, Paul Karra, Kalpana Chan, Esther T. Weng, Shuai Paskov, Kelley M. Roe, Greg R. Binkley, Gail Hitz, Benjamin C. Cherry, J. Michael |
| author_sort |
Costanzo, Maria C. |
| title |
Saccharomyces genome database provides new regulation data |
| title_short |
Saccharomyces genome database provides new regulation data |
| title_full |
Saccharomyces genome database provides new regulation data |
| title_fullStr |
Saccharomyces genome database provides new regulation data |
| title_full_unstemmed |
Saccharomyces genome database provides new regulation data |
| title_sort |
saccharomyces genome database provides new regulation data |
| description |
The Saccharomyces Genome Database (SGD; http://www.yeastgenome.org) is the community resource for genomic, gene and protein information about the budding yeast Saccharomyces cerevisiae, containing a variety of functional information about each yeast gene and gene product. We have recently added regulatory information to SGD and present it on a new tabbed section of the Locus Summary entitled ‘Regulation’. We are compiling transcriptional regulator–target gene relationships, which are curated from the literature at SGD or imported, with permission, from the YEASTRACT database. For nearly every S. cerevisiae gene, the Regulation page displays a table of annotations showing the regulators of that gene, and a graphical visualization of its regulatory network. For genes whose products act as transcription factors, the Regulation page also shows a table of their target genes, accompanied by a Gene Ontology enrichment analysis of the biological processes in which those genes participate. We additionally synthesize information from the literature for each transcription factor in a free-text Regulation Summary, and provide other information relevant to its regulatory function, such as DNA binding site motifs and protein domains. All of the regulation data are available for querying, analysis and download via YeastMine, the InterMine-based data warehouse system in use at SGD. |
| publisher |
Oxford University Press |
| publishDate |
2014 |
| url |
https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3965049/ |
| _version_ |
1612071038210801664 |