orre2019: SubCellBarCode: Proteome-wide Mapping of Protein Localization...

In lgatto/pRolocdata: Data accompanying the pRoloc package

SubCellBarCode: Proteome-wide Mapping of Protein Localization and Relocalization

Description

Data from 'SubCellBarCode: Proteome-wide Mapping of Protein Localization and Relocalization' Molecular cell.

Subcellular localization is a main determinant of protein function; however, a global view of cellular proteome organization remains relatively unexplored. We have developed a robust mass spectrometry-based analysis pipeline to generate a proteome-wide view of subcellular localization for proteins mapping to 12,418 individual genes across five cell lines. Based on more than 83,000 unique classifications and correlation profiling, we investigate the effect of alternative splicing and protein domains on localization, complex member co-localization, cell-type-specific localization, as well as protein relocalization after growth factor inhibition. Our analysis provides information about the cellular architecture and complexity of the spatial organization of the proteome; we show that the majority of proteins have a single main subcellular location, that alternative splicing rarely affects subcellular location, and that cell types are best distinguished by expression of proteins exposed to the surrounding environment. The resource is freely accessible via www.subcellbarcode.org.

Usage

  data("orre2019a431")
  data("orre2019h322")
  data("orre2019hcc827")
  data("orre2019hcc827gef")
  data("orre2019hcc827rep1")
  data("orre2019hcc827rep2")
  data("orre2019hcc827rep3")
  data("orre2019mcf7")
  data("orre2019u251")

Format

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

References

SubCellBarCode: Proteome-wide Mapping of Protein Localization and Relocalization Lukas Minus Orre, Mattias Vesterlund, Yanbo Pan, Taner Arslan, Yafeng Zhu, Alejandro Fernandez Woodbridge, Oliver Frings, Erik Fredlund, and Janne Lehtio https://doi.org/10.1016/j.molcel.2018.11.035

Examples

  data(orre2019a431)
  orre2019a431
  pData(orre2019a431)
  exprs(orre2019a431)[1:3,1:3]
  
  library("pRoloc")
  plot2D(orre2019a431,, main = "Orre 2019 A431")

lgatto/pRolocdata documentation built on Oct. 17, 2024, 10:16 p.m.