New & Noteworthy

Shared Domains and Phosphorylation Sites on Protein Pages

June 24, 2014

We have redesigned the Protein page to include a new tabular display of protein domains. This table provides the identifier for each domain and illustrates the respective locations of the domains within the protein. In addition to this new table, the domains are displayed in an interactive network diagram that presents the proteins that share these domains with your protein of interest (see figure below, left).

Another new feature on the Protein page is the display of phosphorylation sites within the protein’s sequence (as curated by BioGRID). This feature is available for both the reference strain S288C and other commonly used S. cerevisae strains, using the pull-down to select the desired strain view (see figure below, right) .

Left: Proteins (gray circles) that share domains (colored squares) with Fas1p (yellow circle). Right: an example of some of the phosphorylation sites in Swe1p (red residues).

Proteins that share domains with Fas1p

Swe1p protein sequence and phophorylation sites highlighted in red.

Educational Resources on the SGD Community Wiki

February 21, 2014

Did you know you can find and contribute teaching and other educational resources to SGD? We have updated our Educational Resources page, found on the SGD Community Wiki. There are links to teaching resources such as classroom materials, courses, and fun sites, as well as pointers to books, dedicated learning sites, and tutorials that can help you learn more about basic genetics. Many thanks to Dr. Erin Strome and Dr. Bethany Bowling of Northern Kentucky University for being the first to contribute to this updated site by providing a series of Bioinformatics Project Modules designed to introduce undergraduates to using SGD and other bioinformatics resources.

We would like to encourage others to contribute additional teaching or general educational resources to this page. To do so, just request a wiki account by contacting us at the SGD Help desk – you will then be able to edit the SGD Community Wiki. If you prefer, we would also be happy to assist you directly with these edits.

Note that there are many other types of information you can add to the SGD Community Wiki, including information about your favorite genes, protocols, upcoming meetings, and job postings. The Community Wiki can be accessed from most SGD pages by clicking on “Community” on the main menu bar and selecting “Wiki.” The Educational Resources page is linked from the left menu bar under “Resources” from all the SGD Community Wiki pages. For more information on this newly updated page, please view the video below, “Educational Resources on the SGD Community Wiki.”

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.

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.

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