iEDGE Overview

iEDGE is a computational tool for performing integrative analysis of epi-DNA and gene expression data. This tool was based on methods described in Monti, Chapuy, et. al. (Cancer Cell, 2012) for integrating copy number alteration with gene expression data for studying Diffuse Large B cell Lymphoma, and has since been extended to TCGA pan-cancer analysis of Somatic Copy Number (SCNA) and Gene Expression Data in 19 cancer types. The generalized pipeline performs integrative analysis of epi-genomic data (methylation, copy number alteration, mutation, microRNA, etc) and gene-expression data arising from overlapping samples and consists of 3 major modules:

1. Cis/trans differential expression based analysis of epi-DNA and gene expression data
2. Pathway enrichment analysis of significant cis and trans genes correlated with the epi-DNA alterations
3. Pruning of associations between epi-DNA alterations and cis and trans gene expression using a statistical mediation model

Citation:

• Li A, Chapuy B, Varelas X, Sebastiani P, Monti S. Identification of candidate cancer drivers by integrative Epi-DNA and Gene Expression (iEDGE) data analysis. Sci. Rep. 9, 16904 (2019). PMID: 31729402

Here, we present the web portal reports from the TCGA pancancer analysis. Detailed reports in additional formats (.txt) are available upon request.