HPAanalyze

HPAanalyze retrieves and analyzes Human Protein Atlas (HPA) data to support gene-set analyses, programmatic import of tables and XML, and automated retrieval of staining images from imaging, proteomics, and transcriptomics datasets.

Key Features:

• Data Retrieval and Import: Imports data tables and XML files directly from the Human Protein Atlas, including imaging, proteomics, and transcriptomics datasets.
• Gene-set Analysis: Performs gene-set analyses on HPA data to evaluate protein expression patterns across gene lists.
• Exploratory Data Analysis: Integrates with R and the tidyverse to enable programmatic exploratory data analysis and data manipulation.
• Data Export and Visualization: Provides programmatic data export and built-in visualization routines for representation of HPA-derived results.
• Image Downloading: Automates downloading of staining images related to specific proteins or gene sets for inspection and annotation.

Scientific Applications:

• Glioblastoma protein alteration analysis: Applied to investigate protein alterations in glioblastoma, confirming elevation of Epidermal Growth Factor Receptor (EGFR), loss of Phosphatase and Tensin Homolog (PTEN), and highlighting the potential role of the GTP Cyclohydrolase I/Tetrahydrobiopterin pathway.

Methodology:

Programmatic import of HPA tables and XML, gene-set analysis and automated staining-image retrieval, integration into R workflows leveraging Bioconductor packages, and programmatic data manipulation and visualization.