The paper presents the research results concerning an effectiveness evaluation of information technology of gene expression profiles processing for purpose of gene regulatory networks reconstruction. The information technology is presented as a structural block-chart of step-by-step stages of the studied data processing. The DNA microchips of patients, who were investigated on different types of cancer, were used as experimental data. The optimal parameters of data processing algorithm at appropriate stage of this process implementation by quantity criteria of data processing quality were determined during simulation. Validation of the reconstructed gene networks was performed with the use of ROC-analysis by comparison of character of genes interconnection in both the basic network and networks reconstructed based on the obtained biclusters.