PMC

Expanded view of the gastric body-specific gene cluster (a), intestinal metabolism gene cluster (b), and intestinal differentiation gene cluster (c). Expression patterns of the same genes in small intestine and colon are depicted in the right panel for comparison. (d) Discovery of gastric cancer subtypes by expression of intestinal differentiation gene cluster. Hierarchical clustering of gastric cancer based on the genes of the intestinal differentiation signature shown in c. Two GC subgroups, “intestinal-like” (pink) and “gastric-like” (purple) were defined by this process. Associations with histological features or etiological agents are depicted by color-coded box below the dendrogram.

Features of the variation in gene expression patterns can be related to specific physiological and genotypic variations in the tumor and nontumor tissue samples. Data are the same as in . Selected gene clusters (a–d) illustrate coordinated variation in expression of genes in tumor samples, reflecting apparent variation in signaling pathways, chromosomal amplification, or cell proliferation. (a) Cyclin E cluster; (b) ErbB2 cluster; (c) proliferation cluster; (d) AXIN cluster. Genes depicted in the normal cluster (e and f) reflect loss of specialized gastric functional component as well as reduced expression of putative tumor suppressor gene or cell cycle inhibitor in the tumor samples.

Hierarchical clustering of the patterns of variation in expression of 5200 genes in 90 gastric tumors, 14 paired lymph node metastasis, and 22 nonneoplastic gastric mucosa. Each row represents a separate cDNA clone on the microarray and each column a separate mRNA sample. In each gastric tissue sample, the ratio of abundance of transcripts of each gene to its mean abundance across all tissue samples is depicted according to the color scale shown at the bottom. Gray indicates missing or excluded data. The dendrogram at the top provides a measure of the relatedness of gene expression in each sample and is color coded according to the category of mRNA sample studied. The dendrogram at the top of the figure represents the hierarchical clustering of the tumors based on similarity in their pattern of expression of these genes. See supplementary information for full data.