GSEA blue and pink o'gram - how are they plotted?

Question

[Genosa]

I notice GSEA automatically geneartes a heat-map like diagram for the pathways but does not include a 'scale' bar. I tried to get a better understand on how the heat map is plotted, but the explanation is not very clear on the tutorial site. Does anyone know how is the heat map generated? Are the colors based on fold change, or something else?

Thank you

Answer 1

[janders8]

Hi! My understanding is that expression levels are visualized by colors, with high expression shown in red and low expression shown in blue: "In a heat map, expression values are represented as colors, where the range of colors (red, pink, light blue, dark blue) shows the range of expression values (high, moderate, low, lowest)."

[Charles Warden]

Thank you very much for the question and answer.

I am not sure if this was the original question, but I am curious about the following (as asked by somebody else):

1) What is being plotted? For example, is this standardized expression (with mean of 0 and standard deviation of 1, for each gene) from the provided expression values?

2) What cutoffs correspond the color changes? Are values greater than some amount (such as |Z| > 2) set to some maximal color for all heatmaps? Or, does the darkest shade of red or blue mean something different in every heatmap?

I also posted that question here, and I can provide an update if additional details are provided.