Jove
Visualize
Contact Us
JoVE
x logofacebook logolinkedin logoyoutube logo
ABOUT JoVE
OverviewLeadershipBlogJoVE Help Center
AUTHORS
Publishing ProcessEditorial BoardScope & PoliciesPeer ReviewFAQSubmit
LIBRARIANS
TestimonialsSubscriptionsAccessResourcesLibrary Advisory BoardFAQ
RESEARCH
JoVE JournalMethods CollectionsJoVE Encyclopedia of ExperimentsArchive
EDUCATION
JoVE CoreJoVE BusinessJoVE Science EducationJoVE Lab ManualFaculty Resource CenterFaculty Site
Terms & Conditions of Use
Privacy Policy
Policies

Related Concept Videos

Ribosome Profiling02:24

Ribosome Profiling

3.6K
Ribosome profiling or ribo-sequencing is a deep sequencing technique that produces a snapshot of active translation in a cell. It selectively sequences the mRNAs protected by ribosomes to get an insight into a cell’s translation landscape at any given point in time.
Applications of ribosome profiling
Ribosome profiling has many applications, including in vivo monitoring of translation inside a particular organ or tissue type and quantifying new protein synthesis levels.
The technique...
3.6K
DNA Microarrays02:34

DNA Microarrays

17.8K
Microarrays are high-throughput and relatively inexpensive assays that can be automated to analyze large quantities of data at a time. They are used in genome-wide studies to compare gene or protein expression under two varied conditions, such as healthy and diseased states. Microarrays consist of glass or silica slides on which probe molecules are covalently attached through surface functionalization. Most commonly, the slides are prepared through the chemisorption of silanes to silica...
17.8K

You might also read

Related Articles

Articles linked to this work by shared authors, journal, and citation graph.

Sort by
Same author

GWAS SVatalog: a visualization tool to aid fine-mapping of GWAS loci with structural variations.

Heredity·2025
Same author

On the analysis of genetic association with long-read sequencing data.

PLoS genetics·2025
Same author

Large-scale genome-wide association analyses identify novel genetic loci and mechanisms in hypertrophic cardiomyopathy.

Nature genetics·2025
Same author

Directional integration and pathway enrichment analysis for multi-omics data.

Nature communications·2024
Same author

SLCO5A1 and synaptic assembly genes contribute to impulsivity in juvenile myoclonic epilepsy.

NPJ genomic medicine·2023
Same author

HostSeq: a Canadian whole genome sequencing and clinical data resource.

BMC genomic data·2023

Related Experiment Video

Updated: Aug 3, 2025

Analyzing Multifactorial RNA-Seq Experiments with DiCoExpress
05:22

Analyzing Multifactorial RNA-Seq Experiments with DiCoExpress

Published on: July 29, 2022

3.6K

RoPE: A robust profile likelihood method for differential gene expression analysis.

Lehang Zhong1,2, Lisa J Strug1,2,3

  • 1Division of Biostatistics, Dalla Lana School of Public Health, University of Toronto, Toronto, Ontario, Canada.

Genetic Epidemiology
|April 12, 2023
PubMed
Summary

Researchers developed RoPE, a new method for analyzing RNA-Seq data to detect differential gene expression (DE). RoPE improves accuracy with larger sample sizes and identified a gene downregulated during Pseudomonas aeruginosa infection.

Keywords:
RNA-Seqcystic fibrosis lung infectiondifferential expression analysisoverdispersionprofile likelihood inferencerobust adjustment

More Related Videos

Three Differential Expression Analysis Methods for RNA Sequencing: limma, EdgeR, DESeq2
10:10

Three Differential Expression Analysis Methods for RNA Sequencing: limma, EdgeR, DESeq2

Published on: September 18, 2021

37.9K
Gene Expression Profiling of Infecting Microbes Using a Digital Bar-coding Platform
09:13

Gene Expression Profiling of Infecting Microbes Using a Digital Bar-coding Platform

Published on: January 13, 2016

8.1K

Related Experiment Videos

Last Updated: Aug 3, 2025

Analyzing Multifactorial RNA-Seq Experiments with DiCoExpress
05:22

Analyzing Multifactorial RNA-Seq Experiments with DiCoExpress

Published on: July 29, 2022

3.6K
Three Differential Expression Analysis Methods for RNA Sequencing: limma, EdgeR, DESeq2
10:10

Three Differential Expression Analysis Methods for RNA Sequencing: limma, EdgeR, DESeq2

Published on: September 18, 2021

37.9K
Gene Expression Profiling of Infecting Microbes Using a Digital Bar-coding Platform
09:13

Gene Expression Profiling of Infecting Microbes Using a Digital Bar-coding Platform

Published on: January 13, 2016

8.1K

Area of Science:

  • Bioinformatics
  • Computational Biology
  • Genomics

Background:

  • RNA-sequencing (RNA-Seq) data presents significant modeling challenges for differential gene expression (DE) analysis.
  • Existing statistical methods for DE analysis, such as empirical Bayes and non-parametric tests, often yield conflicting results, particularly with small sample sizes.
  • The advent of larger sample sizes necessitates the exploration of novel DE analysis paradigms.

Purpose of the Study:

  • To develop a robust and data-driven method for differential gene expression analysis in RNA-Seq data.
  • To improve the performance and error rate control of DE analysis, especially as sample sizes increase.
  • To identify specific gene expression changes associated with Pseudomonas aeruginosa infection.

Main Methods:

  • Development of RoPE (Robust Profile Likelihood Ratio Test for DE), a novel DE analysis tool.
  • RoPE incorporates a data-driven adjustment for variation inherent in RNA-Seq data.
  • Utilizes a robust profile likelihood ratio test for accurate DE detection.

Main Results:

  • Simulation studies demonstrated that RoPE outperforms existing DE analysis tools with increasing sample sizes.
  • RoPE exhibited superior control over error rates compared to conventional methods.
  • Application of RoPE revealed that active Pseudomonas aeruginosa infection leads to the downregulation of the SLC9A3 gene, a modifier of Cystic Fibrosis.

Conclusions:

  • RoPE offers an improved and reliable approach for differential gene expression analysis, particularly beneficial for studies with larger sample sizes.
  • The method provides more accurate and consistent DE detection, enhancing the reliability of biological findings.
  • The study identified a specific gene expression signature associated with Pseudomonas aeruginosa infection, highlighting the role of SLC9A3 in Cystic Fibrosis pathogenesis.