New & Noteworthy

Redesigned Expression pages

October 6, 2014

The Expression pages have been redesigned and now include a clickable histogram depicting conditions and datasets in which the gene of interest is up- or down-regulated. Expression data are derived from records contained in the Gene Expression Omnibus, and datasets are assigned one or more categories to facilitate grouping, filtering and browsing. Short descriptions of the focus of each experiment are also provided. The PCL files generated for each dataset are used to populate the expression analysis tool SPELL. Also included on the pages are network diagrams which display genes that share expression profiles. The Expression pages provide seamless access to the SPELL tool at SGD, as well as external resources such as Cyclebase, GermOnline, YMGV and FuncBase.

Please explore these new pages, accessible via the Expression tab on your favorite Locus Summary page, and send us your feedback.

New fungal homolog data at SGD

September 15, 2014

Have you ever wondered about the role played by the homolog of a particular yeast gene in other fungal species? SGD’s advanced search tool, YeastMine, can now be used to find homologs of your favorite Saccharomyces cerevisiae genes in the pathogenic yeast, Candida glabrata. There are now 25 species of pathogenic and non-pathogenic fungi in YeastMine, including S. cerevisiae.

The fungal homologs of a given S. cerevisiae gene can be found using the template called “Gene –> Fungal Homologs.” Fungal homology data comes from various sources including FungiDB, the Candida Gene Order Browser (CGOB), the Yeast Gene Order Browser (YGOB), the Candida Genome Database (CGD), the Aspergillus Genome Database (AspGD) and PomBase, and the results link directly to the corresponding homolog gene pages in the relevant databases.

A results table is generated after each query and the identifiers and standard names for the fungal homologs are listed in the table. As with other YeastMine templates, results can be saved as lists for further analysis. You can also create a list of yeast gene names and/or identifiers using the updated Create Lists feature that allows you to specify the organism representing the genes in your list. The query for homologs can then be made against the custom gene list.

All of the new templates that query fungal homolog data can be found on the YeastMine Home page under the “Homology” tab. This template complements the template “Gene → Non-Fungal and S. cerevisiae Homologs” that retrieves homologs of S. cerevisiae genes in humans, rats, mice, worms, flies, mosquitos, and zebrafish.

We invite you to watch SGD’s YeastMine Fungal Homologs video tutorial (also available below) for tips on accessing Fungal Homolog data at SGD. You can view all Video Tutorials for YeastMine here.

New Sequence, Chromosome, and Contig pages

August 25, 2014

New Sequence pages are now available in SGD for virtually every yeast gene (e.g., HMRA1 Sequence page), and include genomic sequence annotations for the Reference Strain S288C, as well as several Alternative Reference Genomes from strains such as CEN.PK, RM11-1a, Sigma1278b, and W303 (more Alternative References coming soon). Each page includes an Overview section containing descriptive information, maps depicting genomic context in Reference Strain S288C (as shown below) and Alternative Reference strains, as well as chromosomal and relative coordinates in S288C.

The sequence itself includes display options for genomic DNA, coding DNA, or translated protein.

Also available on each Sequence page are links to redesigned S288C Chromosome pages, links to new Contig pages for Alternative Reference Genomes, and a Downloads menu for easy access to DNA sequences of several other industrial strains and environmental isolates. The new Sequence, Chromosome, and Contig pages make use of many of the features you enjoy on other new or redesigned pages at SGD, including graphical display of data, sortable tables, and responsive visualizations. The Sequence pages also provide seamless access to other tools at SGD such as BLAST and Web Primer. Please explore these new pages, accessible via the Sequence tab on your favorite Locus Summary page, and send us your feedback.

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.

« Previous Page
Next Page »