We present an updated version of TNMplot, a web-based platform integrating RNA-Seq and gene-chip data from 56,938 samples. TNMplot enables users to select a gene and tumor type for comprehensive gene expression analysis, supporting over 20 tumor types with publication-ready visualizations.

RNA sequencing data were sourced from the Genomic Data Commons (GDC), including adult tumor samples from TCGA, pediatric samples from the TARGET project, and normal reference data from the GTEx portal. Gene chip-based data, comprising over 33,000 manually curated samples, were obtained from the NCBI GEO database. TNMplot facilitates differential expression analysis across normal, primary tumor, and metastatic tissues, supported by an expanded clinical dataset for stage-specific tumor analysis.

The updated platform offers advanced tools, such as a pan-cancer dot matrix for simultaneous visualization of multiple tissue types and genes. It also includes correlation analysis between pairs of genes or multiple genes, along with correlation profile computation. The platform provides a unique feature for identifying progression-related genes through the recently added stage-based expression comparison. This analysis includes data from over 4,500 patient samples, encompassing breast (n = 2,331), colorectal (n = 648), skin (n = 82), prostate (n = 61), and lung (n = 1,399) cancer cases. The tool also has the ability to analyze gene expression using both RNA-seq and gene chip approaches, enabling internal validation across diverse patient populations. In addition to stage-specific expression estimation, this dual-platform capability is unique among comparable tools.

In conclusion, the updated TNMplot platform provides a comprehensive starting point for transcriptomic analysis for oncology-related basic, pharmacological, and translational research.