SGD Quarterly Newsletter, Winter 2013

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About this newsletter:

This is the Winter 2013 issue of the quarterly SGD newsletter. The goal of this newsletter is to inform our users about new features in SGD and to foster communication within the yeast community. You can also subscribe to SGD's RSS feed to receive updates on SGD news: http://www.yeastgenome.org/feed

Contents

Regulation Data and Redesigned Tab Pages Now Available

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 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.

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.

New Data Tracks Added to GBrowse

SGD has added new data tracks to the GBrowse genome viewer covering differential expression RNA-seq data from Waern and Snyder, 2013 G3 3(2):343-352 and Transcript Leader RNA-seq data from Arribere and Gilbert, 2013 Genome Res. 23(6):977-987.

Download data tracks, metadata and supplementary data by clicking on the ‘?’ icon on each data track within GBrowse or directly from the SGD Downloads site. We welcome new data submissions pre- or post-publication and invite authors to work with us to integrate their data into our GBrowse and PBrowse viewers. Please contact us if you are interested in participating or have questions and comments. Happy browsing!

Links to LoQate

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.

Seminal Yeast Literature

SGD has compiled a selection of seminal yeast literature, comprising landmark papers in yeast biology. The list is available on the SGD Wiki and includes important publications on cell biology, early genetic maps and genome surveys, and the original S288C sequencing consortium. Also listed are key papers describing the genomes of other sequenced strains of S. cerevisiae.

Contribute Education Material/Tutorials

In a recent blog we highlighted an innovative hands-on class offered at Stanford where undergraduates study a mutation in p53 using the awesome power of yeast. The creators of the course, Tim Stearns and Martha Cyert have offered to share course materials and knowledge with others interested in replicating this class at their institutions.

SGD is currently developing an "Educational Resources" section for our site and the material from this class is exactly the kind of information we would like to add to this shared resource. If you are using SGD for classes, lectures or labs, please consider contributing your materials to this shared resource. Selected contributions will also be highlighted in our blog.

Upcoming Conferences and Meetings

Li Ka Shing Center for Learning and Knowledge, Stanford, CA
April 19, 2014
Sant Feliu de Guixols, Spain
June 14-19, 2014
Steamboat Springs, Colorado
July 13-18, 2014
University of Washington, Seattle WA
July 29 - August 3, 2014


*asterisks indicate attendance by SGD

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