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

In lgatto/pRolocdata: Data accompanying the pRoloc package

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 April 7, 2023, 1:56 a.m.