Method for recognizing gene pathway based on PAGIS

Abstract

An embodiment of the invention discloses a method for recognizing gene pathway based on PAGIS; the method comprises acquiring a sample, determining signal pathways and genes of the sample, and further acquiring gene frequency and gene outdegree of each gene; statistically acquiring maximum gene frequency, minimum gene frequency, maximum gene frequency and minimum gene frequency according to the gene frequency and gene outdegree of each gene so as to obtain gene frequency weight and gene outdegree weight of each gene; calculating comprehensive weight of each gene according to the gene frequency weight and gene outdegree weight of each gene to obtain weight of each signal pathway, sorting the weights of the signal pathways to determine that the signal pathway corresponding to the maximum signal pathway weight has the highest probability to vary. By implementing the embodiment of the invention to recognize pathways in conjunction with gene importance and specificity, and pathway recognition precision 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 PAGIS. 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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