Each cell's expression landscape is described by the metagene expression values. They are arranged according to the underlying SOM grid and visualized by an appropriate color gradient (red and blue colors indicate over- and underexpressed metagenes, respectively; green and intermediate colors indicate no or low differential expression).
The color patterns emerge as smooth textures representing the fingerprint of transcriptional activity of each cell and are mutually comparable.
Spot module reports
Complementary approaches were applied to define expression modules using the metagene landscape. The reports comprise several visualizations and information of the modules obtained:
Overview about the landscape used to define modules (p.1, not available for k-means clusters)
Assignment of module labels and topmost enriched gene sets (p.2)
Supervised heatmap of module expression (p.3)
Module report sheets providing general information, expression profile across all cells, list of genes contained in the module, and enriched gene sets (p.4ff)
Group overexpression spot modules collect metagenes consistently overexpressed in the different groups, respectively.
k-means modules are defined by applying k-means clustering to the metagene expression data.
Transcriptome Analytics Browser - Tour (part 2 of 5)
Task I: Data portraying
High-dimensional expression data is transformed into so-called expression portraits serving as fingerprints of transcriptional activity of the samples. From these fingerprints, co-regulated gene modules are extracted and characterized.
Report PDF files are stored in LHA and can be downloaded or previewed using the browser.