DeCompress: tissue compartment deconvolution of targeted mRNA expression panels using compressed sensing.

ABSTRACT: Targeted mRNA expression panels, measuring up to 800 genes, are used in academic and clinical settings due to low cost and high sensitivity for archived samples. Most samples assayed on targeted panels originate from bulk tissue comprised of many cell types, and cell-type heterogeneity confounds biological signals. Reference-free methods are used when cell-type-specific expression references are unavailable, but limited feature spaces render implementation challenging in targeted panels. Here, we present DeCompress, a semi-reference-free deconvolution method for targeted panels. DeCompress leverages a reference RNA-seq or microarray dataset from similar tissue to expand the feature space of targeted panels using compressed sensing. Ensemble reference-free deconvolution is performed on this

SUBMITTER: Bhattacharya A 

PROVIDER: S-EPMC8096278 | biostudies-literature | 2021 May

REPOSITORIES: biostudies-literature