New & Noteworthy
August 20, 2013
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!
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.
May 28, 2013
YeastMine, SGD’s powerful search and retrieval tool, has been upgraded to use InterMine version 1.1 software. Highlights of this release include a new format for the template results page, the addition of PantherDB and Homologene homolog data, an improved representation of Gene Ontology (GO) information, the ability to set background population within the GO enrichment widget, and an option to share lists with other users. In addition to the existing video tutorials, a new Help document describes some common queries. See an overview of these new features in the video below, New, Fun YeastMine 1.1!:
March 5, 2013
Sixty new datasets have been added to our expression analysis tool at SGD, facilitating the rapid identification of co-expressed genes based on patterns of expression shared with query gene(s) across the entire collection. Expression data are now available at SGD from a comprehensive collection of 430 datasets representing 9190 microarrays from a total of 286 publications. The expression analysis tool can be accessed via the Expression tab and Expression Summary histogram located on Locus Summary pages, or using the ‘Expression’ option in the Function pulldown in the menu bar at the top of SGD pages. The new data will by default be included with the previous data when using the ‘New Search’, ‘Show Expression Levels’, or ‘Dataset Listing’ options. Alternatively, the new datasets can be specifically filtered using the dataset tag ‘not yet curated’. All of the RNA expression data are available for download in expression directory. Datasets are grouped by publication and are in PCL format.