Method for identifying gene pathways based on GSA

Abstract

The embodiment of the invention discloses a method for identifying gene pathways based on GSA. The method includes the steps of obtaining samples, determining the signal pathways and genes of the samples, and sorting the genes contained in all the signal pathways; determining the total number of the genes in each signal pathway and the average value of the positive and negative points of each gene, and calculating the pathway fraction of each signal pathway; obtaining the gene out-degree of each gene, calculating out the maximum and minimum gene out-degree, and working out the gene out-degree weight of each gene; screening the gene out-degree weight in the same signal pathway out, revising the pathway fraction of the corresponding signal pathway according to the gene out-degree weight of the same signal pathway, and sorting the modified pathway fraction to determine that the changing probability of the signal pathway corresponding to the maximum pathway fraction after sorting pathway is maximum. By the method, the importance of regulating a large number of genes compared with only regulating a small number of genes is considered, and therefore the recognition accuracy of the pathways is improved.

Description

technical field [0001] The invention relates to the technical field of systems biology research, in particular to a method for identifying gene pathways based on GSA. Background technique [0002] Microarray-based high-throughput technology produces a large amount of gene expression data. How to gain insights from these massive gene expression data and then understand the mechanism of life phenomena is still a severe challenge for scientists all over the world. A biological pathway is a group of interactions between genes that perform specific functions, mainly including signal transduction pathways and metabolic pathways. In a signaling pathway, nodes represent genes (or gene products), and edges represent signals transduced from one gene to another. In metabolic pathways, nodes represent biochemical compounds and edges represent biochemical reactions between compounds encoded by enzymes, which encode genes. Commonly used pathway databases include KEGG and Reactome databa...

AI Technical Summary

Problems solved by technology

In the signal pathway impact analysis method SPIA, only the influence of the upstream and downstream positions of genes on the propagation of perturbation signals is considered, but the genes that regulate a large number of genes in the pathway should be more important than the genes that only regulate a small number of genes. Their differences It has a greater influence on the function of pathways, and in PADOG, an overlapping gene weight reduction method, although the GSA method is combined to reduce the influence of "common genes" that frequently appear in many pathways, it does not take into account Genes that regulate a large number of genes in a pathway should be more important than genes that regulate only a few genes, and their differences have a greater impact on the function of the pathway

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