tan2009: LOPIT data from Tan et al. (2009)

tan2009R Documentation

LOPIT data from Tan et al. (2009)

Description

This is the data from Tan et al., Mapping organelle proteins and protein complexes in Drosophila melanogaster, J Proteome Res. 2009 Jun;8(6):2667-78. See below for more details.

Usage

data(tan2009r1)
data(tan2009r2)
data(tan2009r3)
data(tan2009r1goCC)

Format

The data is 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 partial least square discriminant analysis results from the paper are available as PLSDA feature meta-data and the markers used in analysis are available as markers feature meta-data (Note: the ER and Golgi organelle markers were combined in original PLSDA analysis).

Replicate 1 was also used in testing the phenotype discovery algorithm from Breckels et al., The Effect of Organelle Discovery upon Sub-Cellular Protein Localisation, J Proteomics, In Press., see phenoDisco. New phenotype clusters identified from algorithm application are available as pd.2013 feature meta-data.

The tan2009r1goCC 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

Supporting Information on http://pubs.acs.org/doi/full/10.1021/pr800866n

References

Mapping organelle proteins and protein complexes in Drosophila melanogaster. Tan DJ, Dvinge H, Christoforou A, Bertone P, Martinez Arias A, Lilley KS. J Proteome Res. 2009 Jun;8(6):2667-78. PMID: 19317464

Breckels LM, Gatto L, Christoforou A, Groen AJ, Lilley KS and Trotter MWB. The Effect of Organelle Discovery upon Sub-Cellular Protein Localisation J Proteomics. In Press.

Examples

data(tan2009r1)
tan2009r1
pData(tan2009r1)
head(exprs(tan2009r1))
# Organelle markers
table(fData(tan2009r1)$markers)
# PLSDA assignment results
table(fData(tan2009r1)$PLSDA)

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