The invention relates to an apparatus and method for transcriptome analysis. With the use of nucleotide sequence data concerning transcription products, transcriptome analysis is performed with higherprecision. Concerning a plurality of data sets including the objective variable data and the gene expression level data, a plurality of subdata sets are generated by randomly deleting the gene expression level data, and the method of regularization is applied to the plurality of subdata sets to calculate relevant estimation formulae and then generate the lists of genes included in the estimationformula.