A method for analyzing a tissue specimen that includes obtaining a first digital tissue sample image and a second digital tissue sample image showing a first and a second tissue sample, respectively. The first tissue sample and the second tissue sample are stained for a first biomarker and a second biomarker, respectively. Both digital tissue sample images are analyzed to identify portions of the first tissue sample positive for the first biomarker and for the second biomarker, respectively. A co-expression analysis to create a biomarker co-expression profile. The co-expression analysis identifies at least a portion of the tissue specimen positive for both the first biomarker and the second biomarker, at least a portion of the tissue specimen positive for only the first biomarker, and at least a portion of the tissue specimen positive for only the second biomarker. The biomarker co-expression profile is displayed.