New & Noteworthy
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.
June 23, 2012
SGD now provides links from both the Locus Summary and Interactions pages for each S. cerevisiae ORF to DRYGIN (Data Repository of Yeast Genetic Interactions), a database of quantitative genetic interactions of S. cerevisiae (Koh et al., 2010). These genetic interactions were determined from SGA double-mutant arrays conducted in Charles Boone’s laboratory at the University of Toronto, and include both published data (Costanzo et al., 2010) and new interactions released by the Boone laboratory as they become available. Clicking on a DRYGIN link in SGD from an ORF’s Locus Summary or Interactions page goes directly to the DRYGIN search results page for that ORF, which lists both positive and negative genetic interactions as well as any genetic correlations for the given ORF.
April 23, 2012
SGD has added a new mix of data tracks to our GBrowse genome viewer from seven publications covering transcriptome exploration via tiling microarrays (David et al. 2006), genomic occupancy of RNA polymerase II and III and associated factors (Kim et al. 2010; Ghavi-Helm 2008), 3′ end processing (Johnson et al. 2011), histone H2BK123 monoubiquitination (Schulze et al. 2011) and high-resolution ChIP by a novel method called ChIP-exo (Rhee et al. 2011; Rhee et al. 2012). Download data tracks, metadata and supplementary data by clicking on the ‘?’ icon on each data track within GBrowse or directly from the SGD downloads page. 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!
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.