Expression differences of donor-PDX tumor pairs and impact on transcriptome pair similarity. RNASeq for nine pairs of donor/PDX tumors were processed with patient and PDX pipelines respectively. XDGs indicate differentially expressed genes between paired donor/PDX tumors after excluding previously identified genes that are sensitive to pipeline differences. (a) MA plot with XDGs in red; (b) Box plot of correlation coefficients of paired PDX-donor tumors before and after removing XDGs; (c) Hierarchical clustering of donor/PDX tumor pairs before removing XDGs; (d) Hierarchical clustering of donor/PDX tumor pairs after removing XDGs. Patient hetrotransplant (PH) numbers represent a single tumor line and the suffix indicates either the patient donor (P) or corresponding xenograft (PDX).