hpar (version 1.14.2)

hpar: Human Protein Atlas in R

Description

This package provides a simple interface to the Human Protein Atlas. From the Human Protein Atlas Project page: The Swedish Human Protein Atlas project, funded by the Knut and Alice Wallenberg Foundation, has been set up to allow for a systematic exploration of the human proteome using Antibody-Based Proteomics. This is accomplished by combining high-throughput generation of affinity-purified antibodies with protein profiling in a multitude of tissues and cells assembled in tissue microarrays. Confocal microscopy analysis using human cell lines is performed for more detailed protein localization. The program hosts the Human Protein Atlas portal with expression profiles of human proteins in tissues and cells.

Usage

hpaRna
hpaNormalTissue
hpaSubcellularLoc

Details

Three data tables are distributed by the HPA project and available within the package as dataframes. The description below is adapted from the HPA site:

1. Normal tissue data(hpaNormalTissue) Expression profiles for proteins in human tissues based on immunohistochemisty using tissue micro arrays. Thedataframeincludes Ensembl gene identifier ("Gene"), tissue name ("Tissue"), annotated cell type ("Cell.type"), expression value ("Level"), the type of annotation (annotated protein expression (APE), based on more than one antibody, or staining, based on one antibody only) ("Expression.type"), and the reliability or validation of the expression value ("Reliability").
2. Subcellular location data(hpaSubcellularLoc) Subcellular localisation of proteins based on immunofluorescently stained cells. Thedataframeincludes Ensembl gene identifier ("Gene"), main subcellular location of the protein ("Main.location"), other locations ("Other.location"), the type of annotation (annotated protein expression (APE), based on more than one antibody, or staining, based on one antibody only) ("Expression.type"), and the reliability or validation of the expression value ("Reliability"). Note that the Gene Ontology and UniProt are both importing part of this data into their respective databases. UniProt cite the source withsource:HPA.
3. RNA data(hpaRna) RNA levels in three different cell lines, based on RNAseq. Thedataframeincludes Ensembl gene identifier ("Gene"), analysed cell line ("Cell.line"), number of reads per kilobase gene model and million reads ("RPKM"), and abundance class ("Abundance").

Detailed description for gene entries and images and not included in the package but can be accessed from within the Renvironment through a web browser while on-line. The full data sets can be individually loaded using the data function (see example below). Data about individual genes of interest can retrived with the getHpa function.

HPA data usage policy: The use of data and images from this site in publications and presentations is permitted provided that the following conditions are met:

1. The publication and/or presentation are solely for informational and non-commercial purposes.
2. The source of the data and/or image is referred to this site (www.proteinatlas.org) and/or one or more of our publications are cited.

References

See the Human Protein Atlas Project page http://www.proteinatlas.org/ for more details and documentation.

Uhlen et al (2010). Towards a knowledge-based Human Protein Atlas. Nat Biotechnol. 28(12):1248-50. Berglund et al (2008). A gene-centric Human Protein Atlas for expression profiles based on antibodies. Mol Cell Proteomics. 7(10):2019-27. Uhlen et al (2005). A human protein atlas for normal and cancer tissues based on antibody proteomics. Mol Cell Proteomics. 4(12):1920-1932. Ponten et al (2008). The Human Protein Atlas - a tool for pathology. J Pathology. 216(4):387-93.

See Also

getHpaDate for release information. Gene-specific information should be accessed using the getHpa function.

The package vignette can be accessed with vignette("hpar").

Examples

data(hpaRna)
head(hpaRna)
dim(hpaRna)
data(hpaNormalTissue)
head(hpaNormalTissue)
dim(hpaNormalTissue)
data(hpaSubcellularLoc)
head(hpaSubcellularLoc)
dim(hpaSubcellularLoc)