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. 2020 Jan 8;48(D1):D743-D748.
doi: 10.1093/nar/gkz892.

Transcriptome visualization and data availability at the Saccharomyces Genome Database

Patrick C Ng  1 , Edith D Wong  1 , Kevin A MacPherson  2 , Suzi Aleksander  1 , Joanna Argasinska  1 , Barbara Dunn  1 , Robert S Nash  1 , Marek S Skrzypek  1 , Felix Gondwe  1 , Sagar Jha  1 , Kalpana Karra  1 , Shuai Weng  1 , Stuart Miyasato  1 , Matt Simison  1 , Stacia R Engel  1 , J Michael Cherry  1
Affiliations

Transcriptome visualization and data availability at the Saccharomyces Genome Database

Patrick C Ng et al. Nucleic Acids Res. .

Abstract

The Saccharomyces Genome Database (SGD; www.yeastgenome.org) maintains the official annotation of all genes in the Saccharomyces cerevisiae reference genome and aims to elucidate the function of these genes and their products by integrating manually curated experimental data. Technological advances have allowed researchers to profile RNA expression and identify transcripts at high resolution. These data can be configured in web-based genome browser applications for display to the general public. Accordingly, SGD has incorporated published transcript isoform data in our instance of JBrowse, a genome visualization platform. This resource will help clarify S. cerevisiae biological processes by furthering studies of transcriptional regulation, untranslated regions, genome engineering, and expression quantification in S. cerevisiae.

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Figures

Figure 1.
Figure 1.
Unfiltered transcript isoforms that overlap ORFs displayed at various levels of zoom in JBrowse. (A) Individual glyphs representing each transcript isoform are visible at close zoom. (B) At lower magnification, the same region (outlined in the box) is displayed as a collapsed histogram.
Figure 2.
Figure 2.
Representative tracks for transcript isoforms and coverage in glucose containing media. (A) Plus-strand transcript coverage in blue. (B) Longest transcript isoform for each ORF. (C) Most abundant transcript isoform for each ORF. (D) Minus-strand transcript coverage in red.
Figure 3.
Figure 3.
Transcript isoform dialog popup. The ‘Ypd’ or ‘Gal’ attribute lists the raw abundance in the glucose- or galactose-media condition, respectively. ‘Region sequence’ displays the predicted sequence based on the S288C reference genome.
See this image and copyright information in PMC

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