groen2014: LOPIT experiments on Arabidopsis thaliana roots, from Groen...

In lgatto/pRolocdata: Data accompanying the pRoloc package

LOPIT experiments on Arabidopsis thaliana roots, from Groen et al. (2014)

Description

This is the data from Groen et al. Identification of Trans Golgi Network proteins in Arabidopsis thaliana root tissue J. Proteome Res, 2014, Feb 7; 13(2):763-776. See below for more details.

Usage

data(groen2014r1)
data(groen2014r2)
data(groen2014r3)
data(groen2014cmb)
data(groen2014r1goCC)

Format

An instance of class MSnSet from package MSnbase.

Details

This is a LOPIT experiment. Normalised intensities for proteins for four iTRAQ 4-plex labelled fractions are available for 3 replicates (r1, r2 and r3 respectively). The 3 replicates have also been combined as described in Groen et al. and Trotter et al. (2010) to generate a fourth dataset (cmb), also shown in the example code below.

The groen2014r1goCC instance contains binary assay data. Its columns represent GO CC terms that have been observed for the object's features. A 1 indicates that a GO term has been associated to a given feature (protein); a 0 means not such association was found in the GO ontology.

Source

http://pubs.acs.org/doi/abs/10.1021/pr4008464

References

Groen AJ, Sancho-Andres G, Breckels LM, Gatto L, Aniento F, and Lilley KS. Identification of Trans Golgi Network proteins in Arabidopsis thaliana root tissue. J. Proteome Res, 2014, Feb 7; 13(2):763-776. DOI:10.1021/pr4008464, PMID: 24344820.

Trotter MWB, Sadowski PG, Dunkley TPJ, Groen AJ and Lilley KS. Improved sub-cellular resolution via simultaneous analysis of organelle proteomics data across varied experimental conditions. Proteomics 2010 10(23):4213-4219. PMID 21058340.

Sadowski PG, Groen AJ, Dupree P and Lilley KS. Sub-cellular localization of membrane proteins. Proteomics 2008 8(19):3991-4011. PMID 18780351.

Dunkley TP, Hester S, Shadforth IP, Runions J, Weimar T, Hanton SL, Griffin JL, Bessant C, Brandizzi F, Hawes C, Watson RB, Dupree P, Lilley KS. Mapping the Arabidopsis organelle proteome. Proc Natl Acad Sci U S A. 2006 Apr 25;103(17):6518-23. Epub 2006 Apr 17. PubMed PMID: 16618929; PubMed Central PMCID: PMC1458916.

Examples

data(groen2014r1)
data(groen2014r2)
data(groen2014r3)
data(groen2014cmb)

## The combine dataset can generated manually using 
cmb <- combine(groen2014r1, updateFvarLabels(groen2014r2))
cmb <- filterNA(cmb)
cmb <- combine(cmb, updateFvarLabels(groen2014r3))
cmb <- filterNA(cmb)
fData(cmb) <- fData(cmb)[, c(1,2,5)]
cmb

## or can simply be loaded directly
data(groen2014cmb)

## check datsets are the same
all.equal(cmb, groen2014cmb, check.attributes=FALSE)

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