Inner and rosette leaves of Chinese cabbage (Brassica rapa) have different characteristics in terms of nutritional value, appearance, taste, color and texture. Many researchers have utilized differentially expressed genes for exploring the difference between inner and rosette leaves of Brassica rapa. The functional characteristics of a gene, however, is determined by complex interactions between genes. Hence, a noble network approach is required for elucidating such functional difference that is not captured by gene expression profiles alone. In this study, we measured gene expression in the standard cabbage genome by RNA-Sequencing and constructed rosette and inner leaf networks based on the gene expression profiles. Furthermore, we compared the topological and functional characteristics of these networks. We found significant functional difference between the rosette and inner leaf networks. Specifically, we found that the genes in the rosette leaf network were associated with homeostasis and response to external stimuli whereas the genes in the inner leaf network were mainly related to the glutamine biosynthesis processes and developmental processes with hormones. Overall, the network approach provides an insight into the functional difference of the two leaves. (C) 2017 Elsevier Inc. All rights reserved.