The gene expression patterns of desmoplasia are becoming exposed through the application of global gene expression technologies such as cDNA microarrays or serial analysis of gene expression (SAGE). These patterns represent the sum of the many cellular components of the host stromal response to an infiltrating carcinoma. In studies of human neoplasms, it would be useful to identify those prototypical genes that characteristically indicate the recognizable forms of the responses to individual tumor types. Such genes may offer clues to better understand the process of invasion itself, the interactions between tumor and host cells, and tumor-specific differences in invasion. We used SAGE-defined genes and in situ transcript labeling to characterize the desmoplastic stroma induced by infiltrating ductal carcinomas of the breast. Principal component analysis identified 103 SAGE tags as specific for invasive breast carcinomas, in comparison with in situ duct carcinomas or normal breast epithelium. Of these, 68 tags corresponded to known genes. Six of the 68 genes from this breast cancer "invasion-specific" cluster were further characterized by in situ hybridization to breast cancer tissues. Results of in situ hybridization demonstrated that each gene was expressed within one of five distinct regions of the invasive tumors (neoplastic epithelium; angioendothelium; inflammatory, panstromal, and juxtatumoral stroma), reflecting a defined architectural structure to the transcriptome of invasive breast cancers. Two of these 6 genes were specifically expressed by the stromal cells within the invasive carcinoma; however, 1 (collagen 1alpha1) was expressed throughout the stromal response (panstromal expression), whereas the second (osteonectin) was specifically expressed within the juxtatumoral stromal cells, indicating a critical "regionality" of gene expression within the stromal response itself. A comparison of the gene expression profiles of the juxtatumoral stroma in breast and pancreatic carcinomas indicated important differences between the two, suggesting tumor-specific or organ-specific differences in the desmoplastic responses. Some of the genes presented are novel markers of the invasive process, imply communication at the host/tumor interface, and suggest potential therapeutic targets.