Robustness and applicability of transcription factor and pathway analysis tools on single-cell RNA-seq data.

ABSTRACT:

Background

Many functional analysis tools have been developed to extract functional and mechanistic insight from bulk transcriptome data. With the advent of single-cell RNA sequencing (scRNA-seq), it is in principle possible to do such an analysis for single cells. However, scRNA-seq data has characteristics such as drop-out events and low library sizes. It is thus not clear if functional TF and pathway analysis tools established for bulk sequencing can be applied to scRNA-seq in a meaningful way.

Results

To address this question, we perform benchmark studies on simulated and real scRNA-seq data. We include the bulk-RNA tools PROGENy, GO enrichment, and DoRothEA that estimate pathway and transcription factor (TF) activities, respectively, and compare them against the tools S

SUBMITTER: Holland CH 

PROVIDER: S-EPMC7017576 | biostudies-literature | 2020 Feb

REPOSITORIES: biostudies-literature