Investigation of the usefulness of liver-specific deconvolution method by establishing a liver benchmark dataset.

ABSTRACT: Immune responses in the liver are related to the development and progression of liver failure, and precise prediction of their behavior is important. Deconvolution is a methodology for estimating the immune cell proportions from the transcriptome, and it is mainly applied to blood-derived samples and tumor tissues. However, the influence of tissue-specific modeling on the estimation results has rarely been investigated. Here, we constructed a system to evaluate the performance of the deconvolution method on liver transcriptome data. We prepared seven mouse liver injury models using small-molecule compounds and established a benchmark dataset with corresponding liver bulk RNA-Seq and immune cell proportions. RNA-Seq expression for nine leukocyte subsets and four liver-associated cell types

SUBMITTER: Azuma I 

PROVIDER: S-EPMC10768887 | biostudies-literature | 2024 Mar

REPOSITORIES: biostudies-literature