Fig. 3
Gene expression recapitulating the copy-number signature of MAD+ PanNETs. a, b The copy-number signature was inferred from RNA-seq data from the Sadanandam (nMAD+ = 28, nMAD− = 47) and Chan (nMAD+ = 30, nMAD− = 17) datasets by calculating the z-score on a per-gene basis using MAD+ PANETs compared to MAD−. These plots visualize data from the a Sadanandam dataset and the b Chan dataset. c, d Regions of a chromosome arm that have elevated or repressed gene expression in MAD+ samples for the LOH chromosomes (red) relative to genes on heterozygous chromosomes (blue) are plotted against the fractional distance to the centromere (0 = at centromere boundary, 1 = chromosomal arm end). Three datasets are illustrated here: the Tang et al. dataset composed of 77 normal pancreatic islets (top), the Sadanandam PANET dataset (middle), and the Chan PANET dataset (bottom). d Distances between loess regression lines of LOH to heterozygous chromosomes where all 3 aforementioned datasets are overlapped on each other to better visualize overlapping and discordant regions relative to normal islet cells