itzhak2017dynamic: Global, quantitative and dynamic mapping of protein...

In lgatto/pRolocdata: Data accompanying the pRoloc package

Global, quantitative and dynamic mapping of protein subcellular localization

Description

Data from 'Global, quantitative and dynamic mapping of protein subcellular localization.

Subcellular localization critically influences protein function, and cells control protein localization to regulate biological processes. We have developed and applied Dynamic Organellar Maps, a proteomic method that allows global mapping of protein translocation events. We initially used maps statically to generate a database with localization and absolute copy number information for over 8700 proteins from HeLa cells, approaching comprehensive coverage. All major organelles were resolved, with exceptional prediction accuracy (estimated at >92%). Combining spatial and abundance information yielded an unprecedented quantitative view of HeLa cell anatomy and organellar composition, at the protein level. We subsequently demonstrated the dynamic capabilities of the approach by capturing translocation events following EGF stimulation, which we integrated into a quantitative model. Dynamic Organellar Maps enable the proteome-wide analysis of physiological protein movements, without requiring any reagents specific to the investigated process, and will thus be widely applicable in cell biology.

Usage

  data("itzhak2016helaCtrl")
  data("itzhak2016helaEgf")

Format

The data is an instance of class MSnSet from package MSnbase.

References

Itzhak DN, Tyanova S, Cox J, Borner GH. Global, quantitative and dynamic mapping of protein subcellular localization. Elife. 2016 Jun 9;5:e16950.

Examples

  data("itzhak2016helaCtrl")
  helaCtrl <- itzhak2016helaCtrl
  pData(helaCtrl)
  exprs(helaCtrl)[1:3,1:3]
  
  library("pRoloc")
  plot2D(helaCtrl, main = "HeLa Ctrl", dims = c(1, 3))

lgatto/pRolocdata documentation built on April 7, 2023, 1:56 a.m.