Method for identifying gene pathway based on PADOG

Abstract

The embodiment of the invention discloses a method for identifying a gene pathway based on PADOG. The method comprises the steps that a sample is obtained, signal pathways and genes of the sample are determined, the genes included in all the signal pathways are sorted, and the gene frequentness and gene outgoing degree of each gene are determined; the gene frequentness weight and correction fraction of each gene are determined, and pathway fraction of each signal pathway is calculated; the gene outgoing degree weight of each gene is determined after sorting; the gene outgoing degree weight of the same signal pathway is screened, pathway fractions of corresponding signal pathways are revised according to the gene outgoing degree weight of the same signal pathway, the revised pathway fractions are sorted, and it is determined that the change probability of the signal pathway corresponding to the maximum pathway fraction after sorting is maximum. By carrying out the method, the pathway identifying precision can be improved by considering the importance of the gene ratio for regulating and controlling a large number of genes on regulation and control of a small number of genes.

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 PADOG. 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 data...

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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