New & Noteworthy

Sign Up Now! Next SGD Webinar: December 14, 2016

December 12, 2016


Looking for human disease-related information in SGD? There is so much to find! Active areas of curation at SGD include yeast-human homology, disease associations, alleles and phenotype variants, and functional complementation relationships.

Join our upcoming webinar on December 14th, 9:30 AM PST to learn about homology and disease data in SGD. In this quick 15 minute session, we will demonstrate the best ways to research this information on our website and provide a helpful tutorial on related SGD tools and features. Our webinars are always an excellent opportunity to connect with the SGD team–be sure to bring questions if you have them!

All are welcome to this event. If you are interested attending, please register herehttp://bit.ly/SGDwebinar6

This is the sixth episode in the SGD Webinar Series. For more information on the SGD Webinar Series, please visit our wiki page: SGD Webinar Series.

Categories: Announcements Homologs Yeast and Human Disease Tutorial

New SGD Help Video: Finding Human Homology & Disease Information

October 24, 2016


Looking for human disease-related information in SGD? There is so much to find! Active areas of curation at SGD include yeast-human homology, alleles and phenotype variants, functional complementation relationships, and disease associations. There are plenty of ways to find this information on our website, and it takes just 90 seconds to learn how – what are you waiting for?

For more SGD Help Videos, visit our YouTube channel, and be sure to subscribe so you don’t miss anything!

Categories: Announcements Homologs Yeast and Human Disease Tutorial

Sign Up Now for the Next SGD Webinar: September 7, 2016

September 02, 2016


The SPELL expression analysis tool at SGD makes it easy to find expression datasets and coexpressed genes that are relevant to your genes of interest. Just plug in a set of genes and go! Once given a query, SGD’s instance of SPELL locates informative expression datasets from over 270 published studies and identifies additional genes with similar expression profiles.

Find out how to use SPELL in our upcoming webinar on September 7th, 9:30 AM PDT. This quick 10-minute tutorial will explain how to run a multi-gene query in SPELL, locate expression datasets relevant to your query, and find genes with similar expression profiles.

If you are interested in attending this event, please register using this online form: http://bit.ly/SGDwebinar5

This is the fifth episode in the SGD Webinar Series. For more information on the SGD Webinar Series, please visit our wiki page: SGD Webinar Series.

Categories: Announcements Tutorial

New SGD Help Video: Exploring Expression Datasets with SPELL

August 09, 2016


Trying to find relevant expression datasets or genes with similar expression profiles for your favorite genes? Look no further than SPELL – the Serial Pattern of Expression Levels Locator. Given a set of genes, SGD’s instance of SPELL locates informative expression datasets from over 270 published studies and pairs the genes in your query with additional coexpressed genes.

To learn the basics of SPELL and find out how to run a query, check out our help video:

For more SGD Help Videos, visit our YouTube channel, and be sure to subscribe so you don’t miss anything!

Categories: Tutorial

Sign Up Now for the Next SGD Webinar: August 3, 2016

July 28, 2016


SGD’s Variant Viewer is an easy-to-learn web application that allows visualization of differences in both gene and protein sequences. With Variant Viewer, you can compare the nucleotide and amino acid sequences of your favorite genes in twelve widely-used S. cerevisiae strains. Our upcoming webinar on August 3rd, 9:30 AM PDT will provide a quick 10 minute tutorial on how to use Variant Viewer. We will demonstrate how to compare nucleotide and amino acid sequences of different S. cerevisiae genomes, and how to visualize strain-specific single nucleotide polymorphisms, insertions, and deletions contained within a given open reading frame.

If you are interested in attending this event, please register using this online form: http://bit.ly/SGDwebinar4

This is the fourth episode in the SGD Webinar Series. For more information on the SGD Webinar Series, please visit our wiki page: SGD Webinar Series.

Categories: Announcements Tutorial Sequence

Next SGD Webinar: June 1, 2016

May 26, 2016


If you’re not already using JBrowse to view all your favorite S. cerevisiae genes…you should be! SGD’s JBrowse is a quick and easy way to browse through the information-rich yeast genome. Using JBrowse, you can visualize spatial relationships between genes, locate SGD annotations throughout the yeast genome, and align chromosomal features to hundreds of experimental data sets.

Our upcoming webinar on June 1st will provide a short 15-minute tutorial on the basics of JBrowse. We will demonstrate how to navigate the genome with JBrowse, locate your favorite genes or chromosomal features, and visualize experimental data with data tracks. Whether you’re an experienced GBrowse user looking to try JBrowse for the first time, or someone new to genome browsing as a whole, this webinar is sure to help you get started.

If you are interested in attending this event, please register using this online form: http://bit.ly/SGDwebinar3

This is the third episode of the SGD Webinar Series. For more information on the SGD Webinar Series, please visit our wiki page: SGD Webinar Series.

Categories: Announcements Tutorial

New SGD Help: Downloading and Uploading JBrowse Data Tracks

May 10, 2016


SGD’s new JBrowse genome browser allows quick and easy browsing of the information-rich yeast genome.

Take a look at our newest video tutorial to learn how to download or upload JBrowse data tracks. Let us know if you have any questions or suggestions.

For more SGD Help Videos, visit our YouTube channel, and be sure to subscribe so you don’t miss anything!

Categories: Tutorial

New SGD Help Video: YeastMine Scenario

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

New SGD Help Video: Variant Viewer

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: Tutorial Sequence

SGD Help Video: Mutant Phenotypes

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

SGD Help Video: Literature Page

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

New SGD Help Video: GO Term Finder

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 , video , GO Term Finder

New SGD Help Video: GO Slim Mapper

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: GO Slim Mapper , Gene Ontology , video

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: protein-protein interactions , genetic interactions , BioGRID

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: video , Genome Snapshot

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

Tags: video , YeastMine

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: Saccharomyces cerevisiae , video , gene nomenclature

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

Tags: video , YeastMine

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 Tutorial New Data

Tags: yeast model for human disease , video

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