The present invention calls utilized genes differentially expressed in target cells to design vaccines to generate an immune response. Unlike prior art methods that seek to identify antigenic proteins from phenotypic analysis, the subject method applies functional genomics for antigen identification. The method is exemplified herein and therefore provides compositions and methods for inducing an immune response against gp 100 melanoma cells and for inducing an immune response against HER-2+cells. Cancer vaccines and adoptive immunotherapeutic methods to treat and prevent conditions associated with the presence of these cells in a subject also are provided. The methods can be practiced by administering the appropriate gene or cancer vaccine, antibody, protein, polypeptide, antigen-presenting cell or immune effector cell.