In Silico ascription of gene expression differences to tumor and stromal cells in a model to study impact on breast cancer outcome

We present a method for identifying and ascribing differentially expressed genes to tumor epithelial and/or stromal cells, by utilizing pathologic information and weighted t-statistics Sets of differentially expressed gene-probes were identified in tumors from patients who developed distant metastasis compared with those who did not, by weighing the contribution from each tumor with the relative content of stromal and tumor epithelial cells in their individual tumor specimen. The analyses were performed under various assumptions of mRNA transcription level from tumor epithelial cells compared with stromal cells. Supplementary files: Human_AB1700_Annotations_09_06.txt: This file includes control probes and obsolete probes not listed in GPL2986. Raw_data.txt: This file includes control probes not listed in GPL2986.