tan2009 | R Documentation |
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.
data(tan2009r1)
data(tan2009r2)
data(tan2009r3)
data(tan2009r1goCC)
The data is an instance of class MSnSet
from package MSnbase
.
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.
Supporting Information on http://pubs.acs.org/doi/full/10.1021/pr800866n
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.
data(tan2009r1)
tan2009r1
pData(tan2009r1)
head(exprs(tan2009r1))
# Organelle markers
table(fData(tan2009r1)$markers)
# PLSDA assignment results
table(fData(tan2009r1)$PLSDA)
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