PCTA

PCTA aggregates and curates RNA sequencing data from cancer cell lines into a pan-cancer transcriptome atlas to enable cross-cell-line comparison of gene expression.

Key Features:

• Data type: RNA sequencing (RNA-seq)–derived expression data.
• Expression matrix: Contains 24,965 genes organized into a matrix derived from 84,385 samples across 5,677 studies.
• Scope: Includes data for 535 cancer cell lines representing 114 distinct cancer types across 30 tissue origins.
• Visualization: Provides UMAP (Uniform Manifold Approximation and Projection) plots that illustrate clustering of cell lines by tissue similarity.
• Comparative analysis: Enables direct comparison of gene expression levels across diverse cell lines and samples.
• Gene-level exploration: Supports investigation of expression levels for specific genes across the compiled sample set.

Scientific Applications:

• Comparative oncology: Comparative analysis of gene expression patterns across cancer cell lines and tissue origins.
• Biomarker identification: Identification and comparison of candidate biomarkers across multiple cancer types and cell lines.
• Therapeutic target exploration: Exploration of gene expression signatures relevant to potential therapeutic targets.

Methodology:

Curated aggregation of RNA sequencing data into an expression matrix and visualization using UMAP (Uniform Manifold Approximation and Projection).