Hi. I have been able to download differentially expressed genes within a particular location of the tumor from the Ivy Atlas by downloading the list of genes to the left of the heatmap. However, all of the genes have a fold change of >1. I was wondering if there is a way to obtain a list of genes that are downregulated (i.e. <1 fold change or negative log fold change) as well for each location?
Thank you.
There was a recent post addressing normalization that touched on this topic for a different atlas. In short, it as a matter of website design. The website only shows genes the are overexpressed in the target vs the contrast structure. To see genes higher in the contrast structure, you need to click the double circle arrow icon to the right of the target structure, which switches the target and contrast and is equivalent to finding downregulated genes.