Disease classification based on gene information has been of significance as the foundation for achieving precision medicine. Previous works focus on classifying diseases according to the gene expression data of patient samples, and constructing disease network based on the overlap of disease genes, as many genes have been confirmed to be associated with diseases. In this work, the effects of diseases on human biological functions are assessed from the perspective of gene network modules and pathways, and the distances between diseases are defined to carry out the classification models. In total, 1728 diseases are divided into 12 and 14 categories by the intensity and scope of effects on pathways, respectively. Each category is a mix of several types of diseases identified based on congenital and acquired factors as well as diseased tissues and organs. The disease classification models on the basis of gene network are parallel with traditional pathology classification based on anatomic and clinical manifestations, and enable us to look at diseases in the viewpoint of commonalities in etiology and pathology. Our models provide a foundation for exploring combination therapy of diseases, which in turn may inform strategies for future gene-targeted therapy.

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The gene interaction network is one of the most important biological networks and has been studied by many researchers. The gene interaction network provides information about whether the genes in the network can cause or heal diseases. As gene-gene interaction relations are constantly explored, gene interaction networks are evolving. To describe how much a gene has been studied, an approach based on a logistic model for each gene called gene saturation has been proposed, which in most cases, satisfies non-decreasing, correlation and robustness principles. The average saturation of a group of genes can be used to assess the network constructed by these genes. Saturation reflects the distance between known gene interaction networks and the real gene interaction network in a cell. Furthermore, the saturation values of 546 disease gene networks that belong to 15 categories of diseases have been calculated. The disease gene networks’ saturation for cancer is significantly higher than that of all other diseases, which means that the disease gene networks’ structure for cancer has been more deeply studied than other disease. Gene saturation provides guidance for selecting an experimental subject gene, which may have a large number of unknown interactions.

As the number of COVID-19 cases increases, the long-COVID symptoms become the focus of clinical attention. Based on the statistical analysis of long-COVID symptoms in European and Chinese populations, this study proposes the path module correlation coefficient, which can estimate the correlation between two modules in a network, to evaluate the correlation between SARS-CoV-2 infection and long-COVID symptoms, providing a theoretical support for analyzing the frequency of long-COVID symptoms in European and Chinese populations. The path module correlation coefficients between specific COVID-19-related genes in the European and Chinese populations and genes that may induce long-COVID symptoms were calculated. The results showed that the path module correlation coefficients were completely consistent with the frequency of long-COVID symptoms in the Chinese population, but slightly different in the European population. Furthermore, the cathepsin C (CTSC) gene was found to be a potential COVID-19-related gene by a path module correlation coefficient correction rate. Our study can help to explore other long-COVID symptoms that have not yet been discovered and provide a new perspective to research this syndrome. Meanwhile, the path module correlation coefficient correction rate can help to find more species-specific genes related to COVID-19 in the future.