Tissue heterogeneity is prevalent in gene expression studies.

ABSTRACT: Lack of reproducibility in gene expression studies is a serious issue being actively addressed by the biomedical research community. Besides established factors such as batch effects and incorrect sample annotations, we recently reported tissue heterogeneity, a consequence of unintended profiling of cells of other origins than the tissue of interest, as a source of variance. Although tissue heterogeneity exacerbates irreproducibility, its prevalence in gene expression data remains unknown. Here, we systematically analyse 2 667 publicly available gene expression datasets covering 76 576 samples. Using two independent data compendia and a reproducible, open-source software pipeline, we find a prevalence of tissue heterogeneity in gene expression data that affects between 1 and 40% of

SUBMITTER: Sturm G 

PROVIDER: S-EPMC8415427 | biostudies-literature | 2021 Sep

REPOSITORIES: biostudies-literature