Fig. 1

DE tools assessment work flow. The study has four components: evaluation of five normalization methods, concordance analysis of DE tools, evaluating the capability of DE tools to recover genes with known biological evidence of differential expression, and simulation procedures to study the statistical properties of DE tools, such as their ability to control the FDR and their sensitivity for the detection of differential expression. Six diverse types of RNA-seq datasets were used for comparison of the normalization methods and concordance analysis of DE tools. RNA-seq datasets were obtained from two cultured cell line datasets (CRC AZA and NGP nutlin), inbred animals (Bottomly and Hammer), normal human tissues (GTEx), and human cancer cells (Zhang). Three series of simulations were performed, each starting from a different RNA-seq source dataset: Zhang, NGP nutlin, and GTEx data. Results of the simulation study are made available through a user-friendly web application