I would like use to move away from the projections onto the tSNEs for looking at cluster gene expression. We will still have one color coded tSNE, but I think I would rather highlight genes in a heatmap or rows of histograms where we can look at each of the genes where we will use an image and each of the genes that we discuss in the text in the next part of the figure. This gets around the problem with cells from one group looking like they belong to another. I think we could do expression in the group/average in all or a z-score. I would like to look for general tTAF signatures (translational control motif, altered core promoter sequence, any no-random distribution in clusters of expressed genes, or inactivation spreading). We still need to reparse genes for looking at X expression (including t=other ways of getting housekeeping functions, and looking at highly testis-biased expression as outlined at the end of the current text. We will also want to extend this comparative analysis to look at gene movement, especially using the species with neo-Xs.
jfear
commented
6 years ago
From Brian: