ScMAPA: Identification of cell-type-specific alternative polyadenylation in complex tissues.

ABSTRACT:

Background

Alternative polyadenylation (APA) causes shortening or lengthening of the 3'-untranslated region (3'-UTR) of genes (APA genes) in diverse cellular processes such as cell proliferation and differentiation. To identify cell-type-specific APA genes in scRNA-Seq data, current bioinformatic methods have several limitations. First, they assume certain read coverage shapes in the scRNA-Seq data, which can be violated in multiple APA genes. Second, their identification is limited between 2 cell types and not directly applicable to the data of multiple cell types. Third, they do not control undesired source of variance, which potentially introduces noise to the cell-type-specific identification of APA genes.

Findings

We developed a combination of a computational change-poi

SUBMITTER: Bai Y 

PROVIDER: S-EPMC9055853 | biostudies-literature | 2022 Apr

REPOSITORIES: biostudies-literature