doi:

DOI: 10.3724/SP.J.1206.2012.00410

Progress in Biochemistry and Biophysics (生物化学与生物物理进展) 2013/40:12 PP.1256-1264

A Method of Pathway Enrichment Analysis Based Gene Expression Variability


Abstract:
Current pathway enrichment method is mainly based on the gene that are differentially expressed, andno enrichment method considers pathway variability (variance). We observed that in the phenotype of disease,some pathways have a significant increase or decrease in variability describing appropriate statistics. Therefore, inthis article, we hypothesize that the variation of single pathway is significantly different between two phenotypes.We designed fourteen types of statistics coupled with their test methods to analyze pathways variation and thepathways enrichment significance between two phenotypes, and we compared the results with those obtained bydocument retrieval. At the same time, the results of five different data preprocessing methods on data wereinvestigated. The results show that RMA is stable in the five gene expression data preprocessing methods. Thepathway variation is different between the two phenotypes. According to the literature research results, thepermutation test coupled with the variance of Euclidean distance of each gene (the eleventh method) can identifysignificant pathways more efficiently than GSEA. In conclusion, pathway enrichment analysis strategy based on thepathway variation is feasible, which could be a theoretical guideline for enrichment analysis and a new biologicalinsights of study in human diseases.

Key words:variation,pathway,enrichment analysis,preprocessing method

ReleaseDate:2015-04-18 09:14:52



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