New & Noteworthy
New at SGD: GO Annotation Extension Data, Redesigned GO and Phenotype Pages
February 12, 2014
Annotation Extension data for select GO annotations are now available at SGD. The Annotation Extension field (also referred to as column 16 after its position in the gene_association file of GO annotations) was introduced by the Gene Ontology Consortium (GOC) to capture details such as substrates of a protein kinase, targets of regulators, or spatial/temporal aspects of processes. The information in this field serves to provide more biological context to the GO annotation. At SGD, these data are accessible for select GO annotations via the small blue ‘i’ icon on the newly redesigned GO Details pages. See, for example, the substrate information for MEK1 kinase (image below). Currently, a limited number of GO annotations contain data in this field because we have only recently begun to capture this information; more will be added in the future.
We have also redesigned the GO Details and Phenotype Details tab pages to make it easier to understand and make connections within the data. In addition to all of the annotations that were previously displayed, these pages now include graphical summaries, interactive network diagrams displaying relationships between genes and tables that can be sorted, filtered, or downloaded. In addition, SGD Paper pages, each focusing on a particular reference that has been curated in SGD, now show all of the various types of data that are derived from that paper in addition to the list of genes covered in the paper (example). These pages provide seamless access to other tools at SGD such as GO Term Finder, GO Slim Mapper, and YeastMine. Please explore all of these new features from your favorite Locus Summary page and send us your feedback.
Categories: New Data, Website changes
Links to S. pombe Orthologs
December 20, 2013
SGD now provides links from individual S. cerevisiae genes to their Schizosaccharomyces pombe orthologs at PomBase. These links are labeled “PomBase”, and can be found on the Locus Summary Pages, within the Homologs section.
Categories: Website changes
More Regulation Data and Redesigned Tab Pages Now Available
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.
Categories: New Data, Website changes
Regulation Information Integrated into SGD
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.
New Regulation Data at SGD from yeastgenome on Vimeo.
Categories: New Data, Website changes
Links to LoQate
July 09, 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.
Categories: New Data, Website changes
Yeast, More Interesting than your Parents Think
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!
Categories: Website changes
Community Wiki Updated
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.
Categories: Website changes
SGD Server Move Successfully Completed
December 05, 2012
Thank you for your patience during our move to the new data center last week.
Systems Administrator Stuart Miyasato with the SGD servers in their new location
This move is very significant for us, as we are now in a professionally managed computing facility with all the necessary backup cooling and power contingencies available. This move also allows us to continue expanding our services.
The computer room is critical for the stability of SGD and other resources. Our previous location was created when SGD was young, and did not accommodate the amount of growth we have enjoyed. We are very happy to have the opportunity to be located in this brand new facility designed for research computing.
-Mike Cherry
The new Stanford Data Center housing SGD’s and other servers
Categories: Website changes
SGD Hardware Update
October 09, 2012
We are in the process of migrating SGD servers to new faster hardware! You may have already noticed an increase in performance. There could be some teething issues in the next couple days – so please bear with us!
Categories: Website changes
Expression Data and LiftOver Files Available for Download
February 14, 2012
RNA expression data that are included in SGD’s SPELL expression analysis tool are now available for download in the expression directory. Datasets have been grouped by publication and are in PCL format.
LiftOver files that allow conversion of chromosomal coordinates between different S. cerevisiae genome versions are also now available for download via the genome_releases link in the sequence directory.
Categories: New Data, Website changes