Differential expression analysis of human genes in parental tumors and derivative xenografts.

<p>(A) Conceptual model illustrating the bipartite classification of CRC xenografts as either Carcinoma Xenografts (CXs) or Stromal Xenografts (SXs). (B)Differential expression of all genes between the D61540.T1, D61540.T2, P2726.Om, and P2726.Ov parental human tumors (PHTs) and their derivative CXs D61540.T2.X1, D61540.T2.X2, P2726.Ov.X1, P2726.Ov.X2 (left Venn diagram), or between the P2726.Om, P2726.Ov, and P2750 PHTs and their derivative SXs P2726.As.X1 and P2750.Tu.X1 (right Venn diagram). The number following the “X” in each xenograft name indicates its passage generation. The number of genes with a Benjamini-Hochberg false discovery rate (FDR) of 0.05 or higher, which were interpreted as being “shared,” is indicated in the area of intersection in each Venn diagram. The number of genes with FDR <0.05, which are candidates for differentially expressed genes, are indicated under the labels PHT, CX, or SX. Listed in each Venn diagram are the 20 human genes with the lowest FDR. (C) Relative expression of orthologous human/murine genes in a representative xenograft. The symbols indicate the normalized human (<i>x</i> axis) and murine (<i>y</i> axis) transcript counts for genes with human and murine orthologues in the first generation xenograft from the P2726 ovarian CRC metastasis (P2726.Ov.X1). In the left plot, green ‘X’s indicates the read counts for genes that were preferentially expressed in SXs over PHTs (SX >PHT), and in the right plot yellow ‘+’s indicate the read counts for genes that were preferentially expressed in PHTs over CXs (PHT>CX). The read counts for all other orthologous human/murine gene pairs are indicated by blue circles for genes expressed in both and red triangles for genes expressed in one but not the other. The gray diagonal line represents 1∶1 correlation.