CdtGRN: Construction of qualitative time-delayed gene regulatory networks with a deep learning method

Background:Gene regulations often change over time rather than being constant. But many of gene regulatory networks extracted from databases are static. The tumor suppressor gene $P53$ is involved in the pathogenesis of many tumors, and its inhibition effects occur after a certain period. Therefore, it is of great significance to elucidate the regulation mechanism over time points. Result:A qualitative method for representing dynamic gene regulatory network is developed, called CdtGRN. It adopts the combination of convolutional neural networks(CNN) and fully connected networks(DNN) as the core mechanism of prediction. The ionizing radiation Affymetrix dataset (E-MEXP-549) was obtained at ArrayExpress, by microarray gene expression levels predicting relations between regulation. CdtGRN is tested against a time-delayed gene regulatory network with $22,284$ genes related to $P53$. The accuracy of CdtGRN reaches 92.07$\%$ on the classification of conservative verification set, and a kappa coefficient reaches $0.84$ and an average AUC accuracy is 94.25$\%$. This resulted in the construction of. Conclusion:The algorithm and program we developed in our study would be useful for identifying dynamic gene regulatory networks, and objectively analyze the delay of the regulatory relationship by analyzing the gene expression levels at different time points. The time-delayed gene regulatory network of $P53$ is also inferred and represented qualitatively, which is helpful to understand the pathological mechanism of tumors.