Development of a technique for the reconstruction and validation of gene network models based on gene expression profiles

An Evaluation of Information Technology of Gene Expression Profiles Processing Stability for Different Levels of Noise Component

“…The analysis of the obtained charts allows us to conclude that the existence of the noise component decreases the degree of the adequacy of the gene networks reconstructed based on the biclusters to the network reconstructed on the basis of complete data. The average of the relative validation criterion for the obtained models of gene networks are significantly less than the appropriate value of this criterion in the case of gene networks reconstruction based on the gene expression profiles without noise [30]. Moreover, the analysis of the charts in Figure 12 has shown that the increase of the noise level in the data decreases the average of the relative validation criterion.…”

“…Ten largest biclusters from each of the studied data were selected for the further analysis. Reconstruction of the gene regulatory networks and validation of the obtained models were performed based on Cytoscape software with the use of correlation inference algorithm [26].Detailed description of the used information technology for the reconstruction and validation of gene networks is presented in [30]. Figures 8-11 presents the charts of general Harrington desirability index versus the value of thresholding coefficient for both the data without noise and data with different levels of noise component.…”

“…The comparative analysis of the character of the appropriate genes interconnection in the gene networks reconstructed based on the complete data and the obtained biclusters respectively with the calculation of the errors of both the first and second types was performed at this stage. Further, the relative validation criterion was calculated according to the method described in details in [30]. A Higher value of this criterion corresponds to a higher level of adequacy of the networks reconstructed based on the selected biclusters to the network reconstructed based on the complete data in terms of the direct links between the appropriate genes in different networks existence.…”

Construction of a method for the structural functional-cost modeling of a complex hierarchic system

“…An option to overcome such difficulties may be the use of neural algorithms. This approach is used in papers [10,11]. However, even in this case, the derivation of the parametric description of a complex system in the analytical form was not considered.…”

A Hybrid Model of 1-D Signal Adaptive Filter Based on the Complex Use of Huang Transform and Wavelet Analysis

“…The optimal wavelet and the level of wavelet decomposition are determined based on the maximum value of the Shannon entropy for the allocated noise component and the thresholding coefficient optimal value is determined based on the minimum value of the Shannon entropy for filtered data within the framework of the proposed technology. The proposed by the authors technology was successfully implemented for the gene expression profiles filtering within the framework of the information technology of gene expression profiles processing for the purpose of gene regulatory networks reconstruction [29,30]. In this paper we propose the model of the wavelet filter optimal parameters determination based on the use of ratio of the Shannon entropies for the filtered signal and the allocated noise component.…”