Fig. 2

Inferring clone-dependent gene expression in SA501 triple-negative breast cancer xenograft. a Clone-specific copy number for ground truth clones in scDNA-seq (bottom) and clone-specific z-score expression for clonealign inferred clones in scRNA-seq (top) for regions exhibiting inter-clone copy number aberrations. In every copy number segment except one, when the copy number for a given clone is higher than others, then on average the normalized gene expression is also higher. b The mean log expression as a function of copy number across all clones. c Clone assignment probabilities for 1152 single-cell RNA-seq profiles across three clones. clonealign confidently assigns cells to clone A, with some cells exhibiting high assignment uncertainty between clones B and C. d A PCA projection using only genes residing in copy number regions shows the cells clustering by clone along components 2 and 4. ez-score normalized gene expression and copy number profiles for held-out data on chromosomes 8 and 18 as a function of genomic position (gene index along chromosome). In all but one copy number segment, when the copy number profile of a clone is higher, the normalized gene expression in that chromosome is also higher on average. f Differential expression analysis for genes residing in regions whose copy number is identical between clones highlights downregulation of MHC class I proteins