rodriguez2012r1: Spatial proteomics of human inducible goblet-like LS174T...

In lgatto/pRolocdata: Data accompanying the pRoloc package

Spatial proteomics of human inducible goblet-like LS174T cells from Rodriguez-Pineiro et al. (2012)

Description

Data from Rodriguez-Pineiro AM, van der Post S, Johansson ME, Thomsson KA, Nesvizhskii AI, Hansson GC. Proteomic study of the mucin granulae in an intestinal goblet cell model. J Proteome Res. 2012 Mar 2;11(3):1879-90. doi: 10.1021/pr2010988. Epub 2012 Feb 2. PubMed PMID:22248381; PubMed Central PMCID:PMC3292267.

Usage

data("rodriguez2012r1")
data("rodriguez2012r2")
data("rodriguez2012r3")

Details

As no marker were provided with the data, we transferred markers from the hyperLOPIT2015 (mouse) data using gene names to match between experiments. To validate our marker annotations, we compared the relative distributions of our markers (see figure below) to the PCA plot provided by the authors (Figure 3). Both show a similar separation of mitochondion/ER vs the rest along PC1 and ribosomes/lysosome vs rest along PC2. The data do not match exactly as the different marker protein are used.

Source

The supplementary file is pr2010988_si_003.xls. See scripts/rodriguez-pineiro2012.R for data preparation.

Examples

data(rodriguez2012r1)
data(rodriguez2012r2)
data(rodriguez2012r3)

library("pRoloc")
par(mfrow = c(2, 2))
plot2D(rodriguez2012r1)
addLegend(rodriguez2012r1, cex = .7, where = "topleft")
plot2D(rodriguez2012r2)
plot2D(rodriguez2012r3)


## compare to figure 3
dev.new()
plot2D(markerMSnSet(rodriguez2012r1),
       mirrorX = TRUE, mirrorY = TRUE,
       main = "Our markers")
addLegend(markerMSnSet(rodriguez2012r1), where = "bottomright")

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