Isoform-level gene expression patterns in single-cell RNA-sequencing data

Bioinformatics
Trung Nghia VuMattias Rantalainen

Abstract

RNA sequencing of single cells enables characterization of transcriptional heterogeneity in seemingly homogeneous cell populations. Single-cell sequencing has been applied in a wide range of researches fields. However, few studies have focus on characterization of isoform-level expression patterns at the single-cell level. In this study, we propose and apply a novel method, ISOform-Patterns (ISOP), based on mixture modeling, to characterize the expression patterns of isoform pairs from the same gene in single-cell isoform-level expression data. We define six principal patterns of isoform expression relationships and describe a method for differential-pattern analysis. We demonstrate ISOP through analysis of single-cell RNA-sequencing data from a breast cancer cell line, with replication in three independent datasets. We assigned the pattern types to each of 16 562 isoform-pairs from 4929 genes. Among those, 26% of the discovered patterns were significant (P<0.05), while remaining patterns are possibly effects of transcriptional bursting, drop-out and stochastic biological heterogeneity. Furthermore, 32% of genes discovered through differential-pattern analysis were not detected by differential-expression analysis. Finally, the ...Continue Reading

References

Mar 11, 2003·Annual Review of Biochemistry·Douglas L Black
Apr 21, 2005·Bioinformatics·Yudi PawitanAlexander Ploner
Jun 16, 2005·Nature Reviews. Molecular Cell Biology·Arianne J MatlinChristopher W J Smith
Dec 22, 2005·Bioinformatics·Alexander PlonerYudi Pawitan
Nov 4, 2008·Nature·Eric T WangChristopher B Burge
Mar 6, 2009·Genome Biology·Ben LangmeadSteven L Salzberg
Mar 18, 2009·Bioinformatics·Cole TrapnellSteven L Salzberg
Apr 8, 2009·Nature Methods·Fuchou TangM Azim Surani
Feb 13, 2010·Nucleic Acids Research·Hugues RichardMarie-Laure Yaspo
Nov 12, 2010·Nucleic Acids Research·David CroftLincoln Stein
Apr 1, 2011·Nature Methods·Fuchou TangM Azim Surani
Jul 24, 2012·Nature Biotechnology·Daniel RamsköldRickard Sandberg
Oct 22, 2013·Nature Methods·Angela R WuStephen R Quake
Jun 29, 2014·BMC Bioinformatics·Krishna R KalariJean-Pierre A Kocher
Sep 16, 2014·Genome Biology·Nicholas E Navin
Apr 14, 2015·Nature Biotechnology·Kaia AchimJohn C Marioni
May 21, 2015·Nucleic Acids Research·Jose Manuel RodriguezMichael L Tress
May 23, 2015·Molecular Cell·Yong Wang, Nicholas E Navin
Jun 5, 2015·Molecular Systems Biology·Lars VeltenLars M Steinmetz
Jan 8, 2016·Nucleic Acids Research·Joshua D WelchJan F Prins
Apr 5, 2016·Nature Biotechnology·Nicolas L BrayLior Pachter
May 7, 2016·Bioinformatics·Aaron DiazArnold Kriegstein
May 7, 2016·Bioinformatics·Trung Nghia VuYudi Pawitan
Aug 10, 2016·Nature Biotechnology·Nicolas L BrayLior Pachter
Feb 6, 2017·BMC Genomics·Kasper Karlsson, Sten Linnarsson
Aug 9, 2017·Nature Reviews. Immunology·Efthymia Papalexi, Rahul Satija
Aug 25, 2017·Nature Reviews. Cancer·Timour Baslan, James Hicks
Nov 7, 2017·Briefings in Functional Genomics·Mattias Rantalainen

❮ Previous
Next ❯

Citations

Sep 9, 2020·PLoS Computational Biology·Wei Xiong WenSupat Thongjuea
Feb 27, 2020·Computational and Structural Biotechnology Journal·Wei Xiong WenSupat Thongjuea
Jan 28, 2021·Trends in Cancer·Zhaoqi Liu, Raul Rabadan
May 16, 2021·Cell Death Discovery·Lili RenJing Tang

❮ Previous
Next ❯

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.