Embracing the dropouts in single-cell RNA-seq analysis.

Nature Communications
Peng Qiu

Abstract

One primary reason that makes single-cell RNA-seq analysis challenging is dropouts, where the data only captures a small fraction of the transcriptome of each cell. Almost all computational algorithms developed for single-cell RNA-seq adopted gene selection, dimension reduction or imputation to address the dropouts. Here, an opposite view is explored. Instead of treating dropouts as a problem to be fixed, we embrace it as a useful signal. We represent the dropout pattern by binarizing single-cell RNA-seq count data, and present a co-occurrence clustering algorithm to cluster cells based on the dropout pattern. We demonstrate in multiple published datasets that the binary dropout pattern is as informative as the quantitative expression of highly variable genes for the purpose of identifying cell types. We expect that recognizing the utility of dropouts provides an alternative direction for developing computational algorithms for single-cell RNA-seq analysis.

References

Mar 29, 2001·Physiological Reviews·N Baumann, D Pham-Dinh
Sep 24, 2013·Nature Methods·Simone PicelliRickard Sandberg
May 20, 2014·Nature Methods·Peter V KharchenkoDavid T Scadden
Apr 14, 2015·Nature Biotechnology·Rahul SatijaAviv Regev
Mar 11, 2016·Nature Biotechnology·Jacob O Kitzman
Mar 24, 2016·BMC Bioinformatics·Justina Žurauskienė, Christopher Yau
Apr 29, 2016·Genome Biology·Tamar HashimshonyItai Yanai
May 15, 2016·Nucleic Acids Research·Zhicheng Ji, Hongkai Ji
Jan 31, 2017·Nature Methods·Sarah A VitakAndrew Adey
Mar 10, 2018·Nature Communications·Wei Vivian Li, Jingyi Jessica Li
Apr 3, 2018·Nature Methods·Vladimir Yu KiselevMartin Hemberg
Apr 10, 2018·Nature Methods·Josip S HermanDominic Grün
Jun 27, 2018·Nature Methods·Mo HuangNancy R Zhang
Aug 11, 2018·Molecular Therapy. Methods & Clinical Development·Aisha A AlJanahiCynthia E Dunbar
Oct 5, 2018·Nature·UNKNOWN Tabula Muris ConsortiumUNKNOWN Principal investigators
Dec 28, 2018·Bioinformatics·Tallulah S Andrews, Martin Hemberg
Apr 3, 2019·Nature Biotechnology·Wouter SaelensYvan Saeys
Apr 25, 2019·Nature Communications·Huidong ChenLuca Pinello
Jul 14, 2019·BMC Bioinformatics·Sam TracyRuben Dries

❮ Previous
Next ❯

Citations

Jul 28, 2020·The Journal of Investigative Dermatology·Anna DuboisMuzlifah Haniffa
Dec 4, 2020·Arteriosclerosis, Thrombosis, and Vascular Biology·Holger Winkels, Dennis Wolf
Apr 30, 2021·Circulation Research·Mark C BlaserElena Aikawa
May 8, 2021·Briefings in Bioinformatics·Philip DaviesDaniel Hebenstreit
May 22, 2021·Frontiers in Plant Science·Laura Serrano-RonMiguel A Moreno-Risueno
May 20, 2021·Trends in Endocrinology and Metabolism : TEM·Juan Domínguez-BendalaRicardo Luis Pastori
Jun 7, 2021·BMC Genomics·Xinlei WangAngela Ruohao Wu
Aug 13, 2021·Journal of Neurogenetics·Aaron M Allen, Marla B Sokolowski
Sep 2, 2021·Annual Review of Biomedical Data Science·Angela Oliveira PiscoAaron McGeever

❮ Previous
Next ❯

Methods Mentioned

BETA
scRNA-seq
PCA

Software Mentioned

SAVER
scImpute
MAGIC
TSCAN
CEL
RaceID3
pcaReduce
Seurat
MNN
M3Drop

Related Concepts

Trending Feeds

COVID-19

Coronaviruses encompass a large family of viruses that cause the common cold as well as more serious diseases, such as the ongoing outbreak of coronavirus disease 2019 (COVID-19; formally known as 2019-nCoV). Coronaviruses can spread from animals to humans; symptoms include fever, cough, shortness of breath, and breathing difficulties; in more severe cases, infection can lead to death. This feed covers recent research on COVID-19.

Blastomycosis

Blastomycosis fungal infections spread through inhaling Blastomyces dermatitidis spores. Discover the latest research on blastomycosis fungal infections here.

Nuclear Pore Complex in ALS/FTD

Alterations in nucleocytoplasmic transport, controlled by the nuclear pore complex, may be involved in the pathomechanism underlying multiple neurodegenerative diseases including Amyotrophic Lateral Sclerosis and Frontotemporal Dementia. Here is the latest research on the nuclear pore complex in ALS and FTD.

Applications of Molecular Barcoding

The concept of molecular barcoding is that each original DNA or RNA molecule is attached to a unique sequence barcode. Sequence reads having different barcodes represent different original molecules, while sequence reads having the same barcode are results of PCR duplication from one original molecule. Discover the latest research on molecular barcoding here.

Chronic Fatigue Syndrome

Chronic fatigue syndrome is a disease characterized by unexplained disabling fatigue; the pathology of which is incompletely understood. Discover the latest research on chronic fatigue syndrome here.

Evolution of Pluripotency

Pluripotency refers to the ability of a cell to develop into three primary germ cell layers of the embryo. This feed focuses on the mechanisms that underlie the evolution of pluripotency. Here is the latest research.

Position Effect Variegation

Position Effect Variagation occurs when a gene is inactivated due to its positioning near heterochromatic regions within a chromosome. Discover the latest research on Position Effect Variagation here.

STING Receptor Agonists

Stimulator of IFN genes (STING) are a group of transmembrane proteins that are involved in the induction of type I interferon that is important in the innate immune response. The stimulation of STING has been an active area of research in the treatment of cancer and infectious diseases. Here is the latest research on STING receptor agonists.

Microbicide

Microbicides are products that can be applied to vaginal or rectal mucosal surfaces with the goal of preventing, or at least significantly reducing, the transmission of sexually transmitted infections. Here is the latest research on microbicides.

Related Papers

BioRxiv : the Preprint Server for Biology
Peng Qiu
Advances in Experimental Medicine and Biology
Yukie KashimaYutaka Suzuki
Canadian Psychiatric Association Journal
C M Rosenberg, A E Raynes
Zeitschrift für Psychosomatische Medizin und Psychotherapie
Ute MartensMartin Teufel
Archives of General Psychiatry
I D Yalom
© 2021 Meta ULC. All rights reserved