4.8. Marker gene analysis

For the marker gene comparison in Section 2.3, we derived a ranking of domain specific marker genes from the GASTON inferred 1-D expression functions hg by ranking genes by the standard deviation of the mean of each expression function. Specifically, for each gene g, we compute the mean mg,p of the 1-D expression function hg(w) in spatial domain Rp, i.e. mg,p=αp+βp⋅bp-1+bp2, and we rank genes by the standard deviation of the values mg,pp=1,…,P. Intuitively, a marker gene should have high expression in one spatial domain and low expression in other domains, leading to a large standard deviation, while a non-marker gene will have similar expression in all domains, leading to a small standard deviation.