andy2011: LOPIT experiment on Human Embryonic Kidney fibroblast HEK293T...

In lgatto/pRolocdata: Data accompanying the pRoloc package

LOPIT experiment on Human Embryonic Kidney fibroblast HEK293T cells from Breckels et al. (2013)

Description

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.

Usage

data(HEK293T2011)
data(HEK293T2011hpa)
data(HEK293T2011goCC)

Format

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

Details

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.

Source

The data was generated by A. Christoforou at the Cambridge Centre for Proteomics.

http://www.bio.cam.ac.uk/proteomics/.

References

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

Examples

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]

lgatto/pRolocdata documentation built on April 7, 2023, 1:56 a.m.