The development of the technology makes it possible to measure large amount of genes expressions simultaneously. Since biological functions are mostly coordinated by multiple genes, called “gene pathway”, it is interesting to identify differential gene pathways which are associated with clinical phenotype. Principal component analysis has been proposed to identify differential gene pathways in several literatures, while sparse principal component analysis (SPCA) has not drawn any attention. We proposed to use SPCA to identify differential gene pathways. The results show that, comparing to PCA, SPCA could identify more differential expressed gene pathways, especially when the higher-order interactions among genes are considered.