Genes, Vol. 10, Pages 931: HisCoM-PAGE: Hierarchical Structural Component Models for Pathway Analysis of Gene Expression Data
Genes, Vol. 10, Pages 931: HisCoM-PAGE: Hierarchical Structural Component Models for Pathway Analysis of Gene Expression Data
Genes doi: 10.3390/genes10110931
Authors:
Mok
Kim
Lee
Choi
Lee
Jang
Park
Although there have been several analyses for identifying cancer-associated pathways, based on gene expression data, most of these are based on single pathway analyses, and thus do not consider correlations between pathways. In this paper, we propose a hierarchical structural component model for pathway analysis of gene expression data (HisCoM-PAGE), which accounts for the hierarchical structure of genes and pathways, as well as the correlations among pathways. Specifically, HisCoM-PAGE focuses on the survival phenotype and identifies its associated pathways. Moreover, its application to real biological data analysis of pancreatic cancer data demonstrated that HisCoM-PAGE could successfully identify pathways associated with pancreatic cancer prognosis. Simulation studies comparing the performance of HisCoM-PAGE with other competing methods such as Gene Set Enrichment Analysis (GSEA), Global Test, and Wald-type Test showed HisCoM-PAGE to have the highest power to detect causal pathways in most simulation scenarios.
Source: Genes - Category: Genetics & Stem Cells Authors: Mok Kim Lee Choi Lee Jang Park Tags: Article Source Type: research