#Human protein atlas software#
HPAanalyze is an R software package with GPL-3 license that is designed for easy retrieval and exploratory analysis of data from HPA. Here, we introduce HPAanalyze, an R package that aims to simplify exploratory data analysis from those data, as well as provide other functions complementary to hpar. Previously, the R package hpar has been created for fast and easy programmatic access of HPA data. Together, these data provide a detailed picture of protein expression in human cells and tissues, facilitating tissue-based diagnostic and research.ĭata from the HPA are freely available via, allowing scientists to access and incorporate the data into their research. Starting from version 4.0, the HPA includes subcellular localization profiles based on confocal images of immunofluorescent, stained cells. The database also includes classification of proteins into both functional classes (such as transcription factors or kinases) and project-related classes (such as candidate genes for cancer). These profiles are accompanied by a large collection of high-quality histological staining images that are annotated with clinical data and quantification. The program has generated protein expression profiles in human non-malignant tissues, cancers, and cell lines with cell type-specific expression patterns via an innovative immunohistochemistry-based approach. The Human Protein Atlas (HPA) is a comprehensive resource for exploration of the human proteome which contains a vast amount of proteomics and transcriptomics data generated from antibody-based tissue micro-array profiling and RNA deep-sequencing. HPAanalyze integrates into the R workflow with the tidyverse framework, and it can be used in combination with Bioconductor packages for easy analysis of HPA data. Additionally, we provide an interactive website for non-programmers to explore and visualize data without the use of R. For example, we confirm Epidermal Growth Factor Receptor elevation and Phosphatase and Tensin Homolog loss and suggest the importance of the GTP Cyclohydrolase I/Tetrahydrobiopterin pathway. We provide examples of the use of HPAanalyze to investigate proteins altered in the deadly brain tumor glioblastoma. The package is free, open source, and available via Bioconductor and GitHub. HPAanalyze provides functionality for importing data tables and xml files from HPA, exporting and visualizing data, as well as downloading all staining images of interest. HPAanalyze is an R package for retrieving and performing exploratory analysis of data from HPA. Access of the HPA data is mainly via web-based interface allowing views of individual proteins, which may not be optimal for data analysis of a gene set, or automatic retrieval of original images.
The Human Protein Atlas (HPA) aims to map human proteins via multiple technologies including imaging, proteomics and transcriptomics.
0 kommentar(er)
