dunkley2006: LOPIT data from Dunkley et al. (2006)

In lgatto/pRolocdata: Data accompanying the pRoloc package

LOPIT data from Dunkley et al. (2006)

Description

This is the data from Dunkley et al., Mapping the Arabidopsis organelle proteome, PNAS 2006 (PMID 16618929). See below for more details.

Usage

data(dunkley2006)
data(dunkley2006goCC)

Format

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

Details

This is a LOPIT experiment. Normalised intensities for 689 proteins for four iTRAQ 4-plex labelled fraction and 2 membrane preparation in duplicate (16 samples, see phenoData(dunkley2006) for more details) are provided.

Partial least square discriminant analysis (PLSDA) has originally been applied to the test data fData(dunkley)$markers); assignment results are available with fData(dunkley)$assigned) for 5 organelles.

This dataset 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 dunkley2006goCC 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://www.pnas.org/content/103/17/6518.abstract.

References

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.

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(dunkley2006)
dunkley2006 
phenoData(dunkley2006)
## Input training data (organelle markers)
table(fData(dunkley2006)$markers)
## PLSDA assignment results
table(fData(dunkley2006)$assigned)
## PhenoDisco results
table(fData(dunkley2006)$pd.2013)

lgatto/pRolocdata documentation built on Nov. 27, 2024, 12:12 a.m.