The rapidly growing collection of diverse genome-scale data from multiple tumor 
types sheds light on various aspects of the underlying tumor biology. With the 
objective to identify genes of importance for breast tumorigenesis in men and to 
enable comparisons with genes important for breast cancer development in women, 
we applied the computational framework COpy Number and EXpression In Cancer 
(CONEXIC) to detect candidate driver genes among all altered passenger genes. 
Unique to this approach is that each driver gene is associated with several gene 
modules that are believed to be altered by the driver. Thirty candidate drivers 
were found in the male breast cancers and 67 in the female breast cancers. We 
identified many known drivers of breast cancer and other types of cancer, in the 
female dataset (e.g. GATA3, CCNE1, GRB7, CDK4). In contrast, only three known 
cancer genes were found among male breast cancers; MAP2K4, LHP, and ZNF217. Many 
of the candidate drivers identified are known to be involved in processes 
associated with tumorigenesis, including proliferation, invasion and 
differentiation. One of the modules identified in male breast cancer was 
regulated by THY1, a gene involved in invasion and related to 
epithelial-mesenchymal transition. Furthermore, men with THY1 positive breast 
cancers had significantly inferior survival. THY1 may thus be a promising novel 
prognostic marker for male breast cancer. Another module identified among male 
breast cancers, regulated by SPAG5, was closely associated with proliferation. 
Our data indicate that male and female breast cancers display highly different 
landscapes of candidate driver genes, as only a few genes were found in common 
between the two. Consequently, the pathobiology of male breast cancer may differ 
from that of female breast cancer and can be associated with differences in 
prognosis; men diagnosed with breast cancer may consequently require different 
management and treatment strategies than women.