GTEx Transcript Browser is for exploring expression of individual transcripts of a gene. The top tab bar in the browser provides view options for browsing expression data at the exon, junction or transcript level across multiple tissues summarized in a heatmap.

In the transcript expression view, the expressions of transcripts across tissues are summarized in a heatmap. The tissues (rows) and isoforms (columns) are hierarchically clustered using the Euclidean distance and average linkage method. The dendrogram scale shows the cluster distance. The individual transcript structures are illustrated below the heatmap--exons are represented as rectangles, and introns (the distance between two adjacent exons) are scaled by length up to 1 kilobases (kb) long. By clicking a tissue label on the heatmap, a lollipop plot of the transcript expression in the selected tissue will appear next to the transcript tracks.

Exon-level expression is calculated based on a collapsed gene model. To learn more about the collapsing transcript model, go to GTEx Portal Documentation: Analysis Methods. In the exon view, the heatmap summarizes expression of exons of the collapsed gene model across tissues. The tissues (rows) are hierarchically clustered based on the expression data. The exons (columns) are ordered by genomic location. Below the heatmap, the collapsed gene model is illustrated--exons are represented as rectangles, and introns are scaled by length up to 1 kb long. Additionally, the junctions between joined exons of all splice variants are mapped out on the model and shown as arcs. By clicking a tissue label on the heatmap, the gene model will change colors scaled by expression in the selected tissue. At times, an exon on the gene model may show dashed-line borders indicating that the exon or part of it has been filtered in the collapsed model.

In the junction view, the heatmap summarizes expression of junctions from all transcripts across tissues. The tissues (rows) are hierarchically clustered based on the junction expression data, and the junctions (columns) are sorted by genomic location.

All expression quantifications are described in the GTEx Portal Documentation: Analysis Methods -> Expression Quantification section of the portal.