High heterogeneity undermines generalization of differential expression results in RNA-Seq analysis.

ABSTRACT:

Background

RNA sequencing (RNA-Seq) has been widely applied in oncology for monitoring transcriptome changes. However, the emerging problem that high variation of gene expression levels caused by tumor heterogeneity may affect the reproducibility of differential expression (DE) results has rarely been studied. Here, we investigated the reproducibility of DE results for any given number of biological replicates between 3 and 24 and explored why a great many differentially expressed genes (DEGs) were not reproducible.

Results

Our findings demonstrate that poor reproducibility of DE results exists not only for small sample sizes, but also for relatively large sample sizes. Quite a few of the DEGs detected are specific to the samples in use, rather than genuinely differentially

SUBMITTER: Cui W 

PROVIDER: S-EPMC7845028 | biostudies-literature | 2021 Jan

REPOSITORIES: biostudies-literature