HPAStainR

HPAStainR enables simultaneous analysis of multiple proteins or genes against Human Protein Atlas scored staining data to identify and rank associated cell types.

Key Features:

• Multi-Protein Query Capability: Accepts lists of multiple proteins or genes for simultaneous analysis, including large lists such as differential expression results from single-cell studies.
• R and Bioconductor Integration: Implemented as an R package integrated with Bioconductor to support R-based analysis workflows.
• Scored-staining-based Ranking: Uses Human Protein Atlas scored staining data to compute confidence scores and produce ranked tables of cell types with the strongest staining associations.
• Validation and Accuracy: Validated using the Panglao Database for cell type marker genes and a GTEx tissue deconvolution dataset, identifying 92% of Panglao cell types within the top quartile when limited to tissue types of origin and accurately recovering cell types in the GTEx dataset.

Scientific Applications:

• Cell Type Association Studies: Correlates experimentally generated protein or gene lists with known protein localization patterns to infer likely cellular origins.
• Exploratory Data Analysis: Highlights candidate cell type associations from ranked outputs to support hypothesis generation and downstream investigation.
• Ground Truth Establishment: Cross-references experimental lists with established protein localization data to validate cell type–specific expression patterns.

Methodology:

Queries Human Protein Atlas scored staining data for input proteins/genes, computes confidence scores from the scored staining values, and ranks cell types by those confidence scores.