March 17, 2016
If you’re not already using YeastMine to answer all your questions about the Saccharomyces cerevisiae genome and the gene products it encodes…you should be! YeastMine enables slicing and dicing of data from SGD in any way you choose. Ask questions like “Which genes can mutate to confer oxidative stress resistance, and what biological processes are they involved in?” or “Are there any undiscovered subunits of the mitochondrial ribosome?”
Take a look at our newest video tutorial to dig into YeastMine, and let us know if you have any questions or suggestions.
For more SGD Help Videos, be sure to visit our YouTube channel!
Categories: Tutorial
November 05, 2015
Using SGD’s Variant Viewer, you can compare the nucleotide and protein sequences of your favorite genes in twelve widely-used S. cerevisiae genomes. This tool shows alignments, similarity scores, and sequence variants for open reading frames (ORFs) from the different strains relative to the S288C reference genome. Sequence data are derived from Song et al., 2015.
Take a look at our new video tutorial to get started with the Variant Viewer, and let us know if you have questions or suggestions.
Categories: Sequence, Tutorial
November 04, 2015
SGD’s Phenotype pages present detailed information about single mutant phenotypes for a particular gene, along with references for each observation. Phenotype pages are accessible from the ‘Phenotype’ tab of the Locus Summary and is also linked from the Mutant Phenotypes section of the Locus Summary, where the phenotype data are presented in summary form. Data are presented in tabular form on the Phenotype page.
This brief video will give you an overview of the contents and organization of SGD’s Phenotype pages.
Categories: Tutorial
October 29, 2015
If you’re interested in finding all the published literature about a gene or protein, there’s no need to wade through long lists of PubMed results. SGD curators have already done that for you! We review PubMed weekly for new papers about S. cerevisiae. You can find papers about a specific gene or protein on its Literature tab page (see an example).
Articles on the Literature page are categorized by several topics. The Primary Literature section lists papers in which the gene of interest is a primary focus of the study, while the Additional Literature section lists papers in which the gene is mentioned but is more peripheral to the research. There are other categories of references, and also a cool interactive graphic that shows the relationships between papers that are about the same set, or overlapping sets, of genes. You can get to the Literature page for a gene or protein via the Literature tab, located at the top of its Locus Summary page and all of its other tab pages.
Categories: Tutorial
Tags: video
October 26, 2015
Our GO Term Finder tool lets you start with a list of genes—perhaps a set of genes that are co-regulated, or a group of genes that can all mutate to the same phenotype—and analyze their Gene Ontology (GO) annotations to find out what else they might have in common. GO Term Finder searches for significantly shared terms within the GO annotations associated with the genes in your list. It takes advantage of the tree structure of GO to find terms that are related to each other within the ontology.
Finding shared terms within a gene set can bring meaning to experimental results and suggest new avenues to explore. For example, if the GO Term Finder results show that most of the genes in your co-regulated set mediate steps in a pathway, this might be a hint that the uncharacterized genes in the set also participate in that pathway. Or perhaps GO Term Finder will show that a group of genes that can mutate to confer resistance to a certain drug are all annotated to a certain cellular location, suggesting a mechanism for the effects of that drug. Give it a try and see what interesting results your gene list has in store!
Our new SGD Help video gives you a quick overview of how to use the GO Term Finder. You can find all the details on our GO Term Finder help page.
Categories: Tutorial
Tags: Gene Ontology, GO Term Finder, video
October 05, 2015
The GO Slim Mapper is a very useful tool that maps specific Gene Ontology (GO) annotations to more general GO terms. This allows you to take a group of genes and bin them into broad categories of function, process, or localization by mapping their GO annotations to broader terms.
Watch our new video to get an overview of how the GO Slim Mapper works:
Categories: Tutorial
Tags: Gene Ontology, GO Slim Mapper, video
September 14, 2015
The Gene Ontology (GO) is an integral part of modern biology. It provides a common language that unifies the description of gene products from all organisms, structured in a way that allows very detailed information to be captured while at the same time facilitating broad categorizations.
Watch our new video for a brief refresher course on GO: what it is, how it’s structured, and why it’s important.
Categories: Tutorial
Tags: Gene Ontology, Saccharomyces cerevisiae
August 24, 2015
SGD includes data on many thousands of genetic and physical interactions between the genes and proteins of Saccharomyces cerevisiae, as curated by our friends at the BioGRID database. We provide two different graphical displays that help you get a very quick and intuitive overview of known interactions for a particular gene or protein.
All interactions for a gene and its product are listed on its interactions page (see an example). At the top of the page, the Interactions Overview shows at a glance how many interactions have been curated and whether they are physical or genetic. This video explains the details of the Interactions Overview diagram:
Farther down on the Interactions page, the Interaction Network is a visual representation of genetic interactions for a particular gene and the protein-protein interactions for its gene product. The network is interactive, allowing you to choose to view either genetic or physical interactions or both. Using the slider, you can set a minimum number of experiments supporting the interactions displayed. Learn how to use the interactive features of the Interaction Network by watching this brief video:
Categories: Tutorial
Tags: BioGRID, genetic interactions, protein-protein interactions
August 10, 2015
Have you ever wondered just how many genes are found in the genome of the S. cerevisiae reference strain S288C, or how well characterized they are? SGD’s Genome Snapshot gives you a graphical overview of the annotation state of the genome, updated daily. This brief video gives you a tour of the page and explains the information shown in each section.
Categories: Tutorial
Tags: Genome Snapshot, video
July 28, 2015
Understanding lists and knowing how to work with them is crucial to getting the most out of YeastMine. This set of short videos explains everything you need to know.
YeastMine allows you to save objects in lists. Typically, these objects are genes, but you can also make lists of other objects such as Gene Ontology terms or PubMed IDs. One way to create a list in YeastMine is to run a query and save the results in a list. Another way is to type in or upload your own list.
Whenever you create a list in YeastMine, you’re immediately presented with information about the genes in the list, such as Gene Ontology and pathway enrichment, interactions, orthologs, and more. This can help you decide what kind of further analysis you’d like to do.
And what if you create a list but then realize that you forgot to include a gene? No worries. It’s easy to edit your saved lists.
Once you have a list of genes, you can feed it into any template query whose name begins with “Gene” to get results for all of the genes in the list. This powerful feature lets you run successive queries to narrow down your results. For example, you could make a list of all the proteins in a given size range, then query that list to see which ones are located in the nucleus, and finally ask how many of these nuclear proteins have human homologs.
And finally, once you’ve created and saved lists you can do a lot of different things with them: combine them, find their intersection, find genes that are not shared between two lists, or find genes that are in one list but not another. This provides a powerful way to combine or compare results from different YeastMine queries.
As always, please contact us if you have any questions about YeastMine. We’re happy to help!
Categories: Tutorial