We calculate measures of hierarchy in gene and tissue networks of breast cancer patients. We find that the likelihood of metastasis in the future is correlated with increased values of network hierarchy for expression networks of cancer-associated genes, due to the correlated expression of cancer-specific pathways. Conversely, future metastasis and quick relapse times are negatively correlated with the values of network hierarchy in the expression network of all genes, due to the dedifferentiation of gene pathways and circuits. These results suggest that the hierarchy of gene expression may be useful as an additional biomarker for breast cancer prognosis.