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The paper presents the information technology of gene expression profiles processing in order to reconstruct gene regulatory networks. The information technology is presented as a structural block-chart, which contains all stages of studied data processing. DNA microchips of patients, which were studied on different types of diseases, were used as experimental data. The relative criteria of validation for all reconstructed networks were calculated during simulation process. The obtained results show high efficiency of the proposed technology. High values of the validation criteria indicate a high level of the obtained gene networks objectivity.