New & Noteworthy
November 26, 2013
Transcriptional regulation data are now available on new “Regulation” tab pages for virtually every yeast gene. We are collaborating with the YEASTRACT database to display regulation annotations curated both by SGD and by YEASTRACT on these new pages. Regulation annotations are each derived from a published reference, and include a transcriptional regulator, a target gene, the experimental method used to determine the regulatory relationship, and additional data such as the strain background or experimental conditions. The relationships between regulators and the target gene are also depicted in an interactive Network Visualization diagram. The Regulation tab for DNA-binding transcription factors (TFs) includes these items and additionally contains a Regulation Summary paragraph summarizing the regulatory role of that TF, a table listing its protein domains and motifs, DNA binding site information, a table of its regulatory target genes, and an enrichment of the GO Process terms to which its target genes are annotated (view an example). In the coming months we will be adding this extra information to the Regulation pages of other classes of TFs, such as those that act by binding other TFs.
We have also completely redesigned the web display of the Interactions and Literature tab pages, which now include graphical display of data, sortable tables, interactive visualizations, and more navigation options. These pages provide seamless access to other tools at SGD such as GO tools and YeastMine. Please feel free to explore all of these new features from your favorite Locus Summary page and send us your feedback.
July 18, 2013
The Locus Summary pages of 147 DNA-binding transcription factors (TFs; retrieve the list) now include a new tabbed page, Regulation. This page contains information on the regulatory targets of the TF, its binding sites, and its domains and motifs, as well as a free-text paragraph summarizing its biological context. Take a look at a brief video, below, that explains the different kinds of data found on the Regulation tab. In addition to viewing these data page by page, you can download them all using SGD’s data search and retrieval tool, YeastMine. Click on “Regulation” in the YeastMine menu bar to view the predefined templates for regulation data searches.
July 9, 2013
SGD now provides links to LoQate (the localization and quantitation atlas of the yeast proteome) from the Protein Information section of the Locus Summary Pages. The LoQate database provides localization and abundance data for 5300 yeast proteins at single-cell resolution under three different stress conditions: DTT, H2O2, and nitrogen starvation (Breker et al, 2013, J Cell Biol. 200(6), 839-850). Thanks to Maya Schuldiner for helping us set up the links.
April 23, 2013
Are you tired of getting asked why you study yeast? And having your grandma’s eyes glaze over when you try to explain your latest research result to her? Well, we here at SGD have decided to help you out.
We have revamped our “What are yeast?” page to make it even better. We’ve stripped out a lot of the jargon making it much simpler for the nonscientist to read. Not only that, but we’ve consolidated the information onto a single page so you won’t have to link out so much to find what you are looking for.
So now when your mom asks why you’re wasting your time on yeast, you don’t have to tear your hair out and try to explain it to her. We’ve done the work for you.
You can send her to our reworked page where she can see what makes yeast such an ideal organism to study. She’ll learn that we share a whole lot with yeast even though they are single-celled. Our cells are set up similarly, we share lots of the same genes, and yeast are way easier to grow and manipulate than a person. She’ll see we’ve learned a lot about cancer, Alzheimer’s, Lou Gehrig’s Disease, and so on from our little friends. She’ll learn how useful they are for making existing medicines better and finding new ones. And that’s just a couple of the sections!
After reading this, your friends and family will realize there is much more to yeast than making bread or wine (although these are awesome as well). They will see how useful yeast is for understanding us and they will have a newfound respect for the work you do. At least we hope they will!
April 22, 2013
SGD’s Community Wiki now has a new look and a clearer organization, making it even easier for you to share important information with the yeast community. Use the wiki to record facts about your favorite gene, post a job opening or meeting announcement, or add links to yeast resources. Please contact the SGD help desk for an account that will allow you to log in and add to the wiki.