CYCLoPs Documentation


CYCLoPs is a comprehensive Web database of protein abundance and localization changes for budding yeast Saccharomyces cerevisiae. CYCLoPs contains high resolution images covering about 75% of the yeast proteome (~4144 proteins) under multiple chemical and genetic perturbations. These images and quantitative measurements of changes in protein levels and sub-cellular localization following treatments were generated from high-content screening of yeast cells conducted in Moffat Lab and Andrews Lab at Terrence Donnelly Centre for Cellular and Biochemical Research (CCBR), University of Toronto.

Current version of CYCLoPS is 1.0

Contact Judice Koh, Yolanda Chong or Jason Moffat for information on CYCLoPs database or suggestions.

For detail on the CYCLoPs project and data, contact Jason Moffat


About CYCLoPs

  • The data stored in CYCLoPs correspond to studies described in Judice L.Y. Koh, Yolanda Chong, Brenda Andrews, Jason Moffat. CYCLoPs - A database of protein fluxes in Yeast Cell (Manuscript in preparation).
  • 18 screens were conducted in the study, comprising of 2 chemical treatments and 1 genetic mutation, they include:
    ScreenConditionTime courseWild-typeScreenConditionTime courseWild-type
    WT1wild-type--WT2wild-type--
    WT3wild-type--RAP60rapamycin treatment60 minWT3
    RAP140rapamycin treatment140 minWT3RAP220rapamycin treatment220 minWT3
    RAP300rapamycin treatment300 minWT3RAP380rapamycin treatment380 minWT3
    RAP460rapamycin treatment460 minWT3RAP540rapamycin treatment540 minWT3
    RAP620rapamycin treatment620 minWT3RAP700rapamycin treatment700 minWT3
    HU80hydroxyurea treatment80 minWT3HU120hydroxyurea treatment120 minWT3
    HU160hydroxyurea treatment160 minWT3rpd3del_1rpd3 knockout-WT3
    rpd3del_2rpd3 knockout-WT3rpd3del_3rpd3 knockout-WT3
    AF100alpha factor treatment100 minWT1AF140alpha factor treatment140 minWT1
    AF180alpha factor treatment180 minWT1

Search by protein
  • Enables the retrieval of localization and abundance changes of a protein under different environmental cues at multiple time-points.
  • Enter the common name (e.g. DIS3, ski4), ORF (e.g. YOL021C, ynl232w), or general descriptions (e.g. exosome, protease) of the protein of interest.
  • The quick protein search function is similar, but enables the retrieval of localization and abundance changes of a protein under all screens at different time-points using the common name, ORF, or alias of the protein of interest e.g. "DIS3", "rrp44", "YOL021c".
  • If more than one protein is found, a list of matching proteins is displayed.
  • The protein search result page comprises 4 sections detailed as follows:

  • Micrographs from wild-type screen
    * 3 wild-type screens were conducted over a period of a year, namely WT1, WT2 and WT3.
    * 4 RFP and 4 GFP images were acquired from each screen.
    * Toggle visualization between the GFP, RFP and GFP/RFP overlaid images using "RFP <-> RFP <-> GFP/RFP overlay".
      
    * Click on the image to zoom in and extract the cell-images using Cell viewer.
    * Use the Image Viewer to select visualization of micrographs from all screens.

  • Sub-cellular Localization
    * Display LOC-score (quantitative measurement of localization) of the protein in each screen
    * The LOC-score is calculated from the proportion of cells that exhibit morphology specific to a localization class.
    * The localization matrix can be downloaded as a flat file.
    * The following example of GLN3 shows a distribution of cells from cytoplasm i.e. LOC-score WT3/Cytoplasm-0.6 -> RAP60/Nucleus-0.8 in the presence of rapamycin treatment.
    * "Yeast GFP localization" shows the localization assignment determined manually by 2 annotators in previous study - W.-K. Huh, J.V. Falvo, L.C. Gerke, A.S. Carroll, R.W. Howson, J.S. Weissman & E.K. O'Shea, Global Analysis of Protein Localization in Budding Yeast, Nature, 425, 686-691 (2003).
    * If the column is left blank, it means that insufficient cells were obtained in the screen to make a definitive measurement of localization changes.

    * Toggle between LOC-score and cell-count using "Cell count <-> LOC-score"

  • Protein Abundance
    * Display the GFP intensity measures of the protein in each screen as a proxy of protein abundance.
    * The following example of COX4 shows that abundance of COX4 progressively increases in response to rapamycin treatment.

    * The intensity levels across time-points of each treatment can be plotted:


  • Localization change
    * The z-LOC scores quantify changes in sub-cellular compartments w.r.t wildtype LOC-scores
    * A negative z-LOC value denotes the exit of a protein from a particular compartment while a positive z-LOC value represents movement towards a specific location.
    * The localization change matrix can be downloaded as a flat file.
    For example, the rpd3del z-LOC scores for the nuclear classifier indicate that Pct1 moves into the nucleus following deletion of rpd3.


Image Viewer
  • Enables toggling of pairs of images of the selected protein from any screen.
  • Select image type (GFP, RFP, or GFP/RFP overlay), the image number (4 micrographs from each scren), and screen.
  • Useful for comparison of cell morphology between wild-type and treatment/knockout screens.
  • Frame may be resized to display bigger micrographs.

Cell Viewer

  • Segregates the micrographs into images of each cell. Display the localization assignment of each cell.

Localization

  • Retrieves top proteins (order by LOC-score) exhibiting significant localization in specified sub-cellular compartment.
  • The "Also localizes to" column indicates if the protein also localizes to other sub-cellular compartments and the corresponding LOC-scores in brackets.
  • Following example shows the top 10 proteins that localizes to Cell Periphery in the rpd3 screen

Flux

  • Retrieves top proteins exhibiting significant localization change (order by zLOC-score) from or towards a specified sub-cellular compartment.
  • A negative z-LOC value ("from") denotes the exit of a protein from a particular compartment while a positive ("towards") z-LOC value represents movement towards a specific location.

Abundance

  • Retrieves top proteins exhibiting significant intensity changes (order by δPL) in a specified screen.
  • A negative δPL denotes a down-regulated protein while a positive δPL denotes an up-regulated protein.

Download

  • Enables download of Intensity measurements, LOC-scores, ALMs and Thematic maps obtained from all screens.
  • Retrieves cell images for a protein and download abundance measurement and localization assignment of each cell obtained from the selected image.

Database Schema

  • CYCLoPs utilizes mySQL as the relational database management system (RDBMS).
  • It comprised of 3 general tables and 7 screen-specific tables for each screen to store micrographs, localization and abundance profiles of all genes across all screens.

Copyright © Andrews lab and Moffat Lab at CCBR, University of Toronto, 2014