Transcriptome visualization and data availability at the Saccharomyces Genome Database.

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

doi:10.1093/nar/gkz892

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.

Highlights

The annotation of >6000 genes in the reference genome of Saccharomyces cerevisiae is maintained by the Saccharomyces Genome Database (SGD; www.yeastgenome.org) [1], and is based on the common laboratory strain S288C [2]
As a model organism database, SGD maintains a record of the sequence and chromosomal location of these gene features and manually curates functional annotation of their protein products in accordance with the guidelines of the Gene Ontology consortium (GO; www.geneontology. org) [3]
Genome engineering projects seeking to alter or to vectorize the expression of S. cerevisiae genes [7] and transcript-based computational methods for measuring gene expression could benefit from categorization of full-length mRNA transcripts [8]

Summary

Introduction

The annotation of >6000 genes in the reference genome of Saccharomyces cerevisiae is maintained by the Saccharomyces Genome Database (SGD; www.yeastgenome.org) [1], and is based on the common laboratory strain S288C [2]. This track contains the longest transcript overlapping each individual ORF completely for WT cells grown in glucose (ypd) media. This track contains the longest transcript overlapping each individual ORF completely for WT cells grown in galactose (gal) media.

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Conclusion