Fused inverse-normal method for integrated differential expression analysis of RNA-seq data

TL;DR

This paper introduces a novel p-value combination method for meta-analysis of RNA-seq studies, improving detection of differentially expressed genes, especially when studies show conflicting gene expression directions.

Contribution

The proposed method extends the inverse-normal approach to better handle conflicting gene expression directions without increasing computational complexity.

Findings

Identified overexpression of RAD51 in glioblastoma.

Detected multiple GBM-related pathways and novel regulators.

Enhanced discovery of potential biomarkers with conflicting signals.

Abstract

Use of next-generation sequencing technologies to transcriptomics (RNA-seq) for gene expression profiling has found widespread application in studying different biological conditions including cancers. However, RNA-seq experiments are still small sample size experiments due to the cost. Recently, an increased focus has been on meta-analysis methods for integrated differential expression analysis for exploration of potential biomarkers. In this study, we propose a p-value combination method for meta-analysis of multiple related RNA-seq studies that accounts for sample size of a study and direction of expression of genes in individual studies. The proposed method generalizes the inverse-normal method without increase in computational complexity and does not pre- or post-hoc filter genes that have conflicting direction of expression in different studies. Thus, the proposed method, as compared to the inverse-normal, has better potential for the discovery of differentially expressed genes (DEGs) with potentially conflicting differential signals from multiple studies related to disease. We demonstrated the use of the proposed method in detection of biologically relevant DEGs in glioblastoma (GBM), the most aggressive brain cancer. Our approach notably enabled the identification of over-expression in GBM compared to healthy controls of the oncogene RAD51, which has recently been shown to be a target for inhibition to enhance radiosensitivity of GBM cells during treatment. Pathway analysis identified multiple aberrant GBM related pathways as well as novel regulators such as TCF7L2 and MAPT as important upstream regulators in GBM. The proposed method provides a way to establish differential expression status for genes with conflicting direction of expression in individual RNA-seq studies. Hence, leading to further exploration of them as potential biomarkers for the disease.