--- title: "Human Protein Atlas in R" author: - name: Laurent Gatto affiliation: Computational Proteomics Unit, Cambridge, UK package: hpar abstract: > The Human Protein Atlas (HPA) is a systematic study oh the human proteome using antibody-based proteomics. Multiple tissues and cell lines are systematically assayed affinity-purified antibodies and confocal microscopy. The *hpar* package is an R interface to the HPA project. It distributes three data sets, provides functionality to query these and to access detailed information pages, including confocal microscopy images available on the HPA web page. bibliography: hpar.bib output: BiocStyle::html_document2: toc_float: true vignette: > %\VignetteIndexEntry{Human Protein Atlas in R} %\VignetteEngine{knitr::rmarkdown} %\VignetteKeywords{Infrastructure, Bioinformatics, Proteomics} %\VignetteEncoding{UTF-8} --- ```{r env, echo=FALSE} suppressPackageStartupMessages(library("BiocStyle")) suppressPackageStartupMessages(library("org.Hs.eg.db")) suppressPackageStartupMessages(library("GO.db")) ``` # Introduction ## The HPA project From the [Human Protein Atlas](http://www.proteinatlas.org/) [@Uhlen2005; @Uhlen2010] site: > 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 localisation. The program hosts > the Human Protein Atlas portal with expression profiles of human > proteins in tissues and cells. The `r Biocpkg("hpar")` package provides access to HPA data from the R interface. It also distributes the following data sets: - `hpaNormalTissue` *Normal tissue data*: Expression profiles for proteins in human tissues based on immunohistochemisty using tissue micro arrays. The comma-separated file includes 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").} - `hpaCancer` *Cancer tumor data*: Staining profiles for proteins in human tumor tissue based on immunohistochemisty using tissue micro arrays. The comma-separated file includes Ensembl gene identifier ("Gene"), tumor name ("Tumor"), staining value ("Level"), the number of patients that stain for this staining value ("Count patients"), the total amount of patients for this tumor type ("Total patients") and the type of annotation staining ("Expression type"). } - `rnaGeneTissue` *RNA gene data*: RNA levels in 45 cell lines and 32 tissues based on RNA-seq. The comma-separated file includes Ensembl gene identifier ("Gene"), analysed sample ("Sample"), fragments per kilobase of transcript per million fragments mapped ("Value" and "Unit"), and abundance class ("Abundance"). } - `rnaGeneCellLine` *RNA gene data*: RNA levels in 45 cell lines and 32 tissues based on RNA-seq. The comma-separated file includes Ensembl gene identifier ("Gene"), analysed sample ("Sample"), fragments per kilobase of transcript per million fragments mapped ("Value" and "Unit"), and abundance class ("Abundance"). } - `hpaSubcellularLoc` *Subcellular location data*: Subcellular localization of proteins based on immunofluorescently stained cells. The comma-separated file includes 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"). } - `hpaSubcellularLoc14`: Same as above, for version 14. ## HPA data usage policy The use of data and images from the HPA in publications and presentations is permitted provided that the following conditions are met: - The publication and/or presentation are solely for informational and non-commercial purposes. - The source of the data and/or image is referred to the HPA site^[www.proteinatlas.org] and/or one or more of our publications are cited. ## Installation `r Biocpkg("hpar")` is available through the Bioconductor project. Details about the package and the installation procedure can be found on its [landing page](http://bioconductor.org/packages/devel/bioc/html/hpar.html). To install using the dedicated Bioconductor infrastructure, run : ```{r install, eval = FALSE} source("http://bioconductor.org/biocLite.R") ## or, if you have already used the above before library("BiocInstaller") ## and to install the package biocLite("hpar") ``` After installation, `r Biocpkg("hpar")` will have to be explicitly loaded with ```{r load} library("hpar") ``` so that all the package's functionality and data is available to the user. # The `r Biocpkg("hpar")` package ## Data sets The data sets described above can be loaded with the `data` function, as illustrated below for `hpaNormalTissue` below. Each data set is a `data.frame` and can be easily manipulated using standard R functionality. The code chunk below illustrates some of its properties. ```{r hpaData} data(hpaNormalTissue) dim(hpaNormalTissue) names(hpaNormalTissue) ## Number of genes length(unique(hpaNormalTissue$Gene)) ## Number of cell types length(unique(hpaNormalTissue$Cell.type)) head(levels(hpaNormalTissue$Cell.type)) ## Number of tissues length(unique(hpaNormalTissue$Tissue)) head(levels(hpaNormalTissue$Tissue)) table(hpaNormalTissue$Expression.type) ``` ## HPA interface The package provides a interface to the HPA data. The `getHpa` allows to query the data sets described above. It takes three arguments, `id`, `hpadata` and `type`, that control the query, what data set to interrogate and how to report results respectively. The HPA data uses Ensembl gene identifiers and `id` must be a valid identifier. `hpadata` must be one of available dataset. `type` can be either `"data"` or `"details"`. The former is the default and returns a `data.frame` containing the information relevant to `id`. It is also possible to obtained detailed information, (including cell images) as web pages, directly from the HPA web page, using `"details"`. We will illustrate this functionality with using the TSPAN6 (tetraspanin 6) gene (ENSG00000000003) as example. ```{r getHpa} id <- "ENSG00000000003" head(getHpa(id, hpadata = "hpaNormalTissue")) getHpa(id, hpadata = "hpaSubcellularLoc") head(getHpa(id, hpadata = "rnaGeneCellLine")) ``` If we ask for `"detail"`, a browser page pointing to the relevant page is open (see figure below) ```{r getHpa2, eval=FALSE} getHpa(id, type = "details") ``` ![The HPA web page for the tetraspanin 6 gene (ENSG00000000003).](./hpa.png) If a user is interested specifically in one data set, it is possible to set `hpadata` globally and omit it in `getHpa`. This is done by setting the `hpar` options `hpardata` with the `setHparOptions` function. The current default data set can be tested with `getHparOptions`. ```{r opts} getHparOptions() setHparOptions(hpadata = "hpaSubcellularLoc") getHparOptions() getHpa(id) ``` ## HPA release information Information about the HPA release used to build the installed `r Biocpkg("hpar")` package can be accessed with `getHpaVersion`, `getHpaDate` and `getHpaEnsembl`. Full release details can be found on the [HPA release history](http://www.proteinatlas.org/about/releases) page. ```{r rel} getHpaVersion() getHpaDate() getHpaEnsembl() ``` # A small use case Let's compare the subcellular localisation annotation obtained from the HPA subcellular location data set and the information available in the Bioconductor annotation packages. ```{r uc-hpar} id <- "ENSG00000001460" getHpa(id, "hpaSubcellularLoc") ``` Below, we first extract all cellular component GO terms available for `id` from the `r Biocannopkg("org.Hs.eg.db")` human annotation and then retrieve their term definitions using the `r Biocannopkg("GO.db")` database. ```{r uc-db} library("org.Hs.eg.db") library("GO.db") ans <- select(org.Hs.eg.db, keys = id, columns = c("ENSEMBL", "GO", "ONTOLOGY"), keytype = "ENSEMBL") ans <- ans[ans$ONTOLOGY == "CC", ] ans sapply(as.list(GOTERM[ans$GO]), slot, "Term") ``` # Session information} ```{r sessioninfo, echo = FALSE} sessionInfo() ```