New & Noteworthy
New SGD Help Video: What is GO?
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
SGD Help: Interaction Overview and Network
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
SGD Help Video: Genome Snapshot
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
SGD Help Videos: Working with Lists in YeastMine
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!
Saving Search Results as a List
Creating and Using Gene Lists
Adding Objects to a Saved List
Feeding Lists into Templates
List Operations
Categories: Tutorial
SGD Help Video: Gene Name Reservation
July 13, 2015
The eminent Drosophila geneticist Michael Ashburner famously said: “Biologists would rather share their toothbrush than share a gene name.” It’s true that assigning names to genes is often a sticky subject.
In the Saccharomyces cerevisiae community we’re very lucky to have well-defined guidelines for genetic nomenclature, an established system for reserving gene names, and criteria for making them “standard,” or official, names. This system was agreed upon by yeast researchers nearly two decades ago and has served the community well.
Take a look at this video to get an overview of how the gene naming system works. And as always, please contact us with any questions or suggestions.
Categories: Tutorial
Tags: gene nomenclature, Saccharomyces cerevisiae, video
SGD Help Video: YeastMine is Awesome!
July 07, 2015
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!
This versatile tool lets you slice and dice data from SGD in any way you choose. You can ask questions like “How many proteins between 25 and 35 kDa in size are integral to the nuclear membrane?” or “Which genes can mutate to confer oxidative stress resistance, and what biological processes are they involved in?”
Start with this video to see a quick sample of three cool features in YeastMine.
Categories: Tutorial
New SGD Help Video: Yeast-Human Functional Complementation Data
June 30, 2015
Yeast and humans diverged about a billion years ago, but there’s still enough functional conservation between some pairs of yeast and human genes that they can be substituted for each other. How cool is that?! Which genes are they? What do they do?
This two-minute video explains how to find, search, and download the yeast-human functional complementation data in SGD. You can find help with many other aspects of SGD in the tutorial videos on our YouTube channel. And as always, please be sure to contact us with any questions or suggestions.
Categories: Homologs, New Data, Tutorial
Tags: video, yeast model for human disease
New fungal homolog data at SGD
September 15, 2014
Have you ever wondered about the role played by the homolog of a particular yeast gene in other fungal species? SGD’s advanced search tool, YeastMine, can now be used to find homologs of your favorite Saccharomyces cerevisiae genes in the pathogenic yeast, Candida glabrata. There are now 25 species of pathogenic and non-pathogenic fungi in YeastMine, including S. cerevisiae.
The fungal homologs of a given S. cerevisiae gene can be found using the template called “Gene –> Fungal Homologs.” Fungal homology data comes from various sources including FungiDB, the Candida Gene Order Browser (CGOB), the Yeast Gene Order Browser (YGOB), the Candida Genome Database (CGD), the Aspergillus Genome Database (AspGD) and PomBase, and the results link directly to the corresponding homolog gene pages in the relevant databases.
A results table is generated after each query and the identifiers and standard names for the fungal homologs are listed in the table. As with other YeastMine templates, results can be saved as lists for further analysis. You can also create a list of yeast gene names and/or identifiers using the updated Create Lists feature that allows you to specify the organism representing the genes in your list. The query for homologs can then be made against the custom gene list.
All of the new templates that query fungal homolog data can be found on the YeastMine Home page under the “Homology” tab. This template complements the template “Gene → Non-Fungal and S. cerevisiae Homologs” that retrieves homologs of S. cerevisiae genes in humans, rats, mice, worms, flies, mosquitos, and zebrafish.
We invite you to watch SGD’s YeastMine Fungal Homologs video tutorial (also available below) for tips on accessing Fungal Homolog data at SGD. You can view all Video Tutorials for YeastMine here.
Categories: Homologs, New Data, Tutorial
Create, Analyze, Save: the Power of Gene Lists in YeastMine
May 30, 2014
If you love to make and analyze lists of genes, you will love YeastMine – you can use it to create all kinds of lists! For instance, use a YeastMine template to search for all genes associated with a given GO term or phenotype observable and save these genes as a list. Or, search for all genes that interact with your gene of interest and save that as a gene list.
What’s even more fun is that you can make lists from your lists! For instance, take the list of genes you found to be associated with a given GO term and plug it into a YeastMine query template to find all the genes that interact with your list of genes – then save those genes as a list. The possibilities are endless given the different types of queries you can perform using YeastMine! Who knows what biological connections you will uncover?
Lastly, save your lists for future use by creating a MyMine account – all you need to sign up is an email and a password.
You can find a link to YeastMine in the top right corner of most SGD pages (“YeastMine: Batch Analysis or Advanced Search”) or go to SGD’s purple main menu bar, click on “Analyze” and select “Gene Lists” to go straight to creating a List in YeastMine.
To see how simple it is to save your search results as a List in YeastMine, view this brief tutorial – YeastMine: Saving Search Results as a List. To view other great SGD tutorials, YeastMine and otherwise, visit and “Subscribe” to the Saccharomyces Genome Database Channel on YouTube.
Categories: Tutorial
SGD: New look, new features!
January 26, 2012
SGD has added more than just a new look, we’ve added some great new features!
View the short video “We’ve added more than just a new look…” on Vimeo to learn about our enhanced Search Box and our new navigational menu bar.
Categories: Tutorial, Website changes