TNMplot

TNMplot: differential gene expression analysis in Tumor, Normal, and Metastatic tissues.

The pan-cancer analysis page displays the expression range for a selected gene across all tissues using RNA Seq data from normal and cancer tissues.

Select a gene

Select tissue types

red*: Mann-Whitney p<0.05 and
expression >10 in tumor or normal

Display sample numbers

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Database setup:
TNMplot includes 56,938 unique samples:
from GEO, GTex, TCGA, and TARGET databases.
This includes 15,648 normal, 40,442 tumor, and 848 metastasis samples.

Gene summary:

Please kindly cite our paper:
A. Bartha, B. Gyorffy, TNMplot.com: A Web Tool for the Comparison of Gene Expression in Normal, Tumor and Metastatic Tissues Int. J. Mol. Sci. 2021, 22(5), 2622.

Copyright ©: TNMplot.com, 2021-2025
Check our other webtools: http://www.kmplot.com ; http://www.rocplot.com ; https://www.cancerhallmarks.com/

The pan-cancer heatmap analysis page displays log2 FC values of tumor/normal RNA-Seq data, red color represents higher expression in tumor, while the blue color indicates higher expression in normal tissues. The sizes of the circles are inversely proportional to the adjusted P values.

Select genes

Please select at least 2 genes, the maximal number of genes allowed simultaneously is is 100. To paste multiple gene names please use capital names separated with space (e.g.: TOP2A MKI67 PIK3CA).

Select tissue types

Boxplot
Violinplot

Boxplot
Violinplot

Boxplot
Violinplot

Boxplot
Violinplot

Density Plot
Box Plot

Density Plot
Box Plot

Boxplot
Violinplot

Boxplot
Violinplot

Dotplot
Barplot

Dotplot
Barplot

Dotplot
Barplot

1. Overview

TNMplot v2 is an advanced web-based platform designed for transcriptomic analysis, integrating RNA-Seq and gene-chip data from 57 thousand samples. It facilitates differential gene expression analysis across normal, primary tumor, and metastatic tissues, supporting over 20 tumor types with publication-ready visualizations. The new TNMplot v2 introduces stage-specific analysis, multi-gene analysis, correlation analysis tools, and expanded visualization features.

2. Features

- The pan-cancer analysis page displays the expression range for a selected gene across all tissues using RNA Seq data from normal and cancer tissues.

- The pan-cancer dot matrix analysis page displays log2 FC values of tumor/normal RNA-Seq data, red color represents higher expression in tumor, while the blue color indicates higher expression in normal tissues. The sizes of the circles are inversely proportional to the adjusted P values.

- TN-plot: the Normal and Tumor analysis page provides detailed analysis for a selected gene in a selected tissue type using RNA-seq and gene chip based data.

- TNM-plot: The Normal, Tumor and Metastatic analysis page provides detailed analysis for a selected gene in a selected tissue type using RNA-Seq and gene chip based data.

- Multi-Gene Analysis: Compare multiple genes simultaneously using density plots and box plots in both RNA-seq and gene chip datasets.

- Targetgram analysis: provides an overview of the selected gene set in the selected tissue using gene chip and RNA-Seq based data, the size of the segments represent the mean values, length of the dashed lines represent the median values of each types.

- Gene Signature Analysis: Analyze predefined gene signatures and their expression patterns. This papge page calculates the means of the selected gene signature across each patient one by one and provides a summary plot.

- Gene vs. Gene Correlation: Compare the correlation of two selected genes using multiple correlation methods in the selected tissue type.

- Correlation Matrix: Analyze relationships between multiple genes, and explore the correlation matrix of a selected gene set in the selected tissue type

- Correlation Profile Analysis: Explore correlation network for a selected gene by browsing all the genes showing correlation with the input gene in the selected tissue type.

- Stage-Specific Analysis: Investigate gene expression across different tumor stages.

- Functional analysis: perform GO or KEGG enrichment analysis

3. Data Sources

TNMplot v2 integrates transcriptomic data from multiple reputable sources:
- Genomic Data Commons (GDC): RNA-seq data from TCGA (adult tumors) and TARGET (pediatric tumors).
- Genotype-Tissue Expression (GTEx): Normal reference tissues.
- NCBI Gene Expression Omnibus (GEO): Manually curated gene chip datasets (>33,000 samples).

4. Performing an Analysis

Choose the dataset type (RNA-seq or gene-chip).

Select a gene from the input field.