YeastRGB: comparing the abundance and localization of yeast proteins across cells and libraries

• Published in: Nucleic acids research Vol. 47; no. D1; pp. D1245 - D1249
• Main Authors: Dubreuil, Benjamin, Sass, Ehud, Nadav, Yotam, Heidenreich, Meta, Georgeson, Joseph M, Weill, Uri, Duan, Yuanqiang, Meurer, Matthias, Schuldiner, Maya, Knop, Michael, Levy, Emmanuel D
• Format: Journal Article
• Language: English
• Published: England Oxford University Press 08.01.2019
• Subjects: Computational Biology - methods; Database Issue; Databases, Protein; Gene Library; Information Storage and Retrieval - methods; Internet; Luminescent Proteins - genetics; Luminescent Proteins - metabolism; Microscopy, Fluorescence; Open Reading Frames - genetics; Proteome - genetics; Proteome - metabolism; Saccharomyces cerevisiae - classification; Saccharomyces cerevisiae - genetics; Saccharomyces cerevisiae - metabolism; Saccharomyces cerevisiae Proteins - genetics; Saccharomyces cerevisiae Proteins - metabolism; User-Computer Interface
• ISSN: 0305-1048; 1362-4962
• DOI: 10.1093/nar/gky941

Abstract The ability to measure the abundance and visualize the localization of proteins across the yeast proteome has stimulated hypotheses on gene function and fueled discoveries. While the classic C’ tagged GFP yeast library has been the only resource for over a decade, the recent development of the SWAT technology has led to the creation of multiple novel yeast libraries where new-generation fluorescent reporters are fused at the N’ and C’ of open reading frames. Efficient access to these data requires a user interface to visualize and compare protein abundance, localization and co-localization across cells, strains, and libraries. YeastRGB (www.yeastRGB.org) was designed to address such a need, through a user-friendly interface that maximizes informative content. It employs a compact display where cells are cropped and tiled together into a ‘cell-grid.’ This representation enables viewing dozens of cells for a particular strain within a display unit, and up to 30 display units can be arrayed on a standard high-definition screen. Additionally, the display unit allows users to control zoom-level and overlay of images acquired using different color channels. Thus, YeastRGB makes comparing abundance and localization efficient, across thousands of cells from different strains and libraries.