It became possible to see all the expressed genes present in a cell (transcriptome) at once using microarray. We have applied microarray technology to various studies regarding allergic diseases. Although we and others have discovered various novel molecules crucially involved in the pathogenesis of the disease, transcriptome assay is now expected as a tool for understanding the whole molecule balancing, i.e., system biology. Here I introduce examples of our trials for understanding the whole functional roles of a certain cell type related to allergy as has been published in the web database. In the near future, we will be able to construct human inflammatory cell models in silico (in a computer) by analyzing integrative information regarding the genome, transcriptome and proteome of mast cells and can test our hypothesis without performing in vitro testing.