• HCCDB v2.0 integrates bulk, single-cell, and spatial transcriptomic data, expanding bulk samples to 5,573 and adding 182,832 cells and 69,352 spatial spots.
• A novel sc-2D metric summarizes cell type-specific and dysregulated gene expression patterns, enhancing meta-analysis reliability.
• The database enables identification of prognosis-associated cells and tumor microenvironment, with applications in precision oncology.
• User-friendly online portal with graphical visualization facilitates data retrieval and navigation for researchers.