SCADIE: simultaneous estimation of cell type proportions and cell type-specific gene expressions using SCAD-based iterative estimating procedure

A challenge in bulk gene differential expression analysis is to differentiate changes due to cell type-specific gene expression and cell type proportions. SCADIE is an iterative algorithm that simultaneously estimates cell type-specific gene expression profiles and cell type proportions, and perform...

Full description

Saved in:
Bibliographic Details
Published inGenome Biology Vol. 23; no. 1; p. 129
Main Authors Tang, Daiwei, Park, Seyoung, Zhao, Hongyu
Format Journal Article
LanguageEnglish
Published England BioMed Central 15.06.2022
BMC
Subjects
Accuracy
Algorithms
Cell differentiation
Cell type-specific differential expression
Deconvolution
Gene Expression
Gene Expression Profiling - methods
Hypotheses
Hypothesis testing
Method
RNA-Seq
SCAD
scRNA-seq
Sequence Analysis, RNA
Single-Cell Analysis - methods
Deconvolution
scRNA-seq
RNA-Seq
SCAD
Cell type-specific differential expression
Online AccessGet full text

Cover

More Information
Summary:A challenge in bulk gene differential expression analysis is to differentiate changes due to cell type-specific gene expression and cell type proportions. SCADIE is an iterative algorithm that simultaneously estimates cell type-specific gene expression profiles and cell type proportions, and performs cell type-specific differential expression analysis at the group level. Through its unique penalty and objective function, SCADIE more accurately identifies cell type-specific differentially expressed genes than existing methods, including those that may be missed from single cell RNA-Seq data. SCADIE has robust performance with respect to the choice of deconvolution methods and the sources and quality of input data.
Bibliography:ObjectType-Article-1
SourceType-Scholarly Journals-1
ObjectType-Feature-2
content type line 23
ISSN:1474-760X
1474-7596
1474-760X
DOI:10.1186/s13059-022-02688-w