title: CYCLoPs: A Comprehensive Database Constructed from Automated Analysis of Protein Abundance and Subcellular Localization Patterns in Saccharomyces cerevisiae.
abstract: Changes in protein subcellular localization and abundance are central to biological regulation in eukaryotic cells. Quantitative measures of protein dynamics in vivo are therefore highly useful for elucidating specific regulatory pathways. Using a combinatorial approach of yeast synthetic genetic array technology, high-content screening, and machine learning classifiers, we developed an automated platform to characterize protein localization and abundance patterns from images of log phase cells from the open-reading frame-green fluorescent protein collection in the budding yeast, Saccharomyces cerevisiae. For each protein, we produced quantitative profiles of localization scores for 16 subcellular compartments at single-cell resolution to trace proteome-wide relocalization in conditions over time. We generated a collection of ∼300,000 micrographs, comprising more than 20 million cells and ∼9 billion quantitative measurements. The images depict the localization and abundance dynamics of more than 4000 proteins under two chemical treatments and in a selected mutant background. Here, we describe CYCLoPs (Collection of Yeast Cells Localization Patterns), a web database resource that provides a central platform for housing and analyzing our yeast proteome dynamics datasets at the single cell level. CYCLoPs version 1.0 is available at http://cyclops.ccbr.utoronto.ca. CYCLoPs will provide a valuable resource for the yeast and eukaryotic cell biology communities and will be updated as new experiments become available.
authors.affiliation: The Donnelly Centre, University of Toronto, Toronto, Ontario, Canada, M5S3E1.
authors.forename: Judice L Y
authors.initials: JL
authors.lastname: Koh
authors.affiliation: The Donnelly Centre, University of Toronto, Toronto, Ontario, Canada, M5S3E1.
authors.forename: Yolanda T
authors.initials: YT
authors.lastname: Chong
authors.affiliation: The Donnelly Centre, University of Toronto, Toronto, Ontario, Canada, M5S3E1.
authors.forename: Helena
authors.initials: H
authors.lastname: Friesen
authors.affiliation: Department of Cell & Systems Biology, University of Toronto, Toronto, Ontario, Canada, M5S3E1.
authors.forename: Alan
authors.initials: A
authors.lastname: Moses
authors.affiliation: The Donnelly Centre, University of Toronto, Toronto, Ontario, Canada, M5S3E1 Department of Molecular Genetics, University of Toronto, Toronto, Ontario, Canada, M5S3E1 j.moffat@utoronto.ca brenda.andrews@utoronto.ca charlie.boone@utoronto.ca.
authors.forename: Charles
authors.initials: C
authors.lastname: Boone
authors.affiliation: The Donnelly Centre, University of Toronto, Toronto, Ontario, Canada, M5S3E1 Department of Molecular Genetics, University of Toronto, Toronto, Ontario, Canada, M5S3E1 j.moffat@utoronto.ca brenda.andrews@utoronto.ca charlie.boone@utoronto.ca.
authors.forename: Brenda J
authors.initials: BJ
authors.lastname: Andrews
authors.affiliation: The Donnelly Centre, University of Toronto, Toronto, Ontario, Canada, M5S3E1 Department of Molecular Genetics, University of Toronto, Toronto, Ontario, Canada, M5S3E1 j.moffat@utoronto.ca brenda.andrews@utoronto.ca charlie.boone@utoronto.ca.
authors.forename: Jason
authors.initials: J
authors.lastname: Moffat
mesh_terms: D000465:Algorithms; D001331:Automation; D030562:Databases, Protein; D008853:Microscopy; D021381:Protein Transport; D012441:Saccharomyces cerevisiae / Q000378:metabolism*; D029701:Saccharomyces cerevisiae Proteins / Q000378:metabolism*; D059010:Single-Cell Analysis; D013347:Subcellular Fractions / Q000378:metabolism
chemical_list: D029701:Saccharomyces cerevisiae Proteins
keywords: GFP; abundance; images; microscopy; subcellular localization