Curated protein information in the Saccharomyces genome database

Abstract

Due to recent advancements in the production of experimental proteomic data, the Saccharomyces genome database (SGD; www.yeastgenome.org ) has been expanding our protein curation activities to make new data types available to our users. Because of broad interest in post-translational modifications (PTM) and their importance to protein function and regulation, we have recently started incorporating expertly curated PTM information on individual protein pages. Here we also present the inclusion of new abundance and protein half-life data obtained from high-throughput proteome studies. These new data types have been included with the aim to facilitate cellular biology research.

Database url: : www.yeastgenome.org.

Figure 1.

Descriptive information is included in the Overview section of protein pages in the SGD.

Figure 2.

Integration of PTM information in the SGD is a multi-step process involving the identification of relevant papers, expert curation of PTM studies, and the visualization and display of PTM data.

Figure 3.

PTM information is integrated into the SGD and displayed on protein pages as highlighted residues overlaid on the protein sequence. The example shown here is from the MCD1 protein page.

Figure 4.

PTM information is integrated into the SGD and displayed on protein pages in a searchable, sortable table. The example shown here is from the MCD1 protein page.

Figure 5.

Experimental abundance and half-life data obtained from high-throughput proteome studies are integrated into the SGD and displayed on protein pages in a searchable, sortable table. The example shown here is from the STH1 protein page.

Figure 6.

PTM information can be queried and retrieved using the ‘Gene → PTM’ template in YeastMine (yeastmine.yeastgenome.org).