andy2011 | R Documentation |
This is a LOPIT dataset from a standard LOPIT experimental design on Human Embryonic Kidney (HEK293T) fibroblast cells. See below for more details.
Note: this data was originally called andy2011
. It is still
available under that name but might be deprecated in the future and
hence it is advised to use HEK293T2011
.
data(HEK293T2011)
data(HEK293T2011hpa)
data(HEK293T2011goCC)
The data is an instance of class MSnSet
from package MSnbase
.
This is a LOPIT experiment. Normalised intensities for 1371 proteins
for eight iTRAQ 8-plex labelled fractions.
This dataset was used in testing the phenotype discovery algorithm from
Breckels et al., The Effect of Organelle Discovery upon Sub-Cellular
Protein Localisation, J Proteomics, 2013, 88:129-40, see phenoDisco
.
New phenotype clusters identified from algorithm application are available as
pd.2013
feature meta-data and the markers used as input for the analysis
are available as markers
feature meta-data.
The HEK293T2011goCC
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.
The HEK293T2011hpa
instance contains binary assay data. Its
columns represent subcellular locations that have been observed from
microscopy images from the Human Protein Atlas, for each protein. A 1
indicates that a subcellular term has been associated to a given
feature (protein); a 0 means not such association was found. This
matrix of terms was generated from version 13, released on 11/06/2014
of the Human Protein Atlas.
The data was generated by A. Christoforou at the Cambridge Centre for Proteomics.
http://www.bio.cam.ac.uk/proteomics/.
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. 2013 Aug 2;88:129-40. doi: 10.1016/j.jprot.2013.02.019. Epub 2013 Mar 21. PubMed PMID: 23523639
data(HEK293T2011)
HEK293T2011
pData(HEK293T2011)
head(exprs(HEK293T2011))
## Organelle marker proteins
table(fData(HEK293T2011)$markers)
## PhenoDisco assignment results
table(fData(HEK293T2011)$pd.2013)
data(HEK293T2011goCC)
dim(HEK293T2011goCC)
head(featureNames(HEK293T2011goCC))
exprs(HEK293T2011goCC)[1:10, 1:5]
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