RNA-Seq Heatmap: How to Create & Interpret Expression Heatmaps
📖 RNA-Seq Data Analysis Workflow — check it out for an overview.
In RNA-Seq analysis, heatmaps are one of the most important tools for visualizing gene expression patterns.
What is a Heatmap?
A heatmap is a graphical representation that uses color gradients to display the magnitude of values in a data matrix.
Heatmaps are used across many fields beyond molecular biology. For instance, web analytics teams use heatmaps to show which areas of a webpage attract the most user attention.
Reading a Heatmap in RNA-Seq Analysis
An RNA-Seq analysis produces a gene expression table like the one below. (The image shows only 10 genes, but a real dataset typically contains tens of thousands of rows.)
When this data is visualized as a heatmap, it looks like this:
In an RNA-Seq heatmap, columns typically represent samples and rows represent genes.
In the figure above, red indicates high expression, white indicates moderate expression, and blue indicates low expression.
You can see that genes in the lower half of the heatmap are more highly expressed in sample1, sample2, and sample3, while genes in the upper half show higher expression in sample4, sample5, and sample6.
An alternative color scheme using red, black, and green is also common in RNA-Seq heatmaps.
RNA-Seq heatmaps are typically drawn after hierarchical clustering, which is why genes with similar expression patterns appear near each other in the figure above.
In this example, only gene-level clustering is shown, but sample-level clustering can also be applied before generating the heatmap.
RNA-Seq Data Analysis Software
This is an RNA-Seq Data Analysis Software recommended for those who:
✔︎ Seeking to avoid outsourcing or collaboration for RNA-Seq data analysis.
✔︎ Lacking time to learn RNA-Seq data analysis.
✔︎ Frustrated by the complexity of existing tools.
Users can perform gene expression quantification, identification of differentially expressed genes, gene ontology(GO) analysis, pathway analysis, as well as drawing volcano plots, MA plots, and heatmaps.
About the Author
BxINFO LLC
A research support company specializing in bioinformatics.
We provide tools and information to support life science research, with a focus on RNA-Seq analysis.