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

DNA Microarrays02:34

DNA Microarrays

23.1K
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...
23.1K
What is Gene Expression?01:42

What is Gene Expression?

200.6K
Overview
Gene expression is the process in which DNA directs the synthesis of functional products, that is, proteins. Cells can regulate gene expression at various stages. It allows organisms to generate different cell types and enables cells to adapt to internal and external factors.
Genetic Information Flows from DNA to RNA to Protein
A gene is a stretch of DNA that serves as the blueprint for functional RNAs and proteins. Since DNA is made up of nucleotides and proteins consist of amino...
200.6K

You might also read

Related Articles

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

Sort by
Same author

Laboratory Validation of a Fully Automated Point-of-Care Device for High-Order Multiplexing Real-Time PCR Detection of Respiratory Pathogens.

Diagnostics (Basel, Switzerland)·2025
Same author

Inflammatory signaling pathways in pancreatic β-cell: New insights into type 2 diabetes pathogenesis.

Pharmacological research·2025
Same author

Development of a YouthFit Index to assess health-related quality of life in Hong Kong children.

Jornal de pediatria·2025
Same author

Physical Fitness and Body Mass Index Status of Hong Kong Primary Schoolchildren across the COVID-19 Pandemic, before and after School Closure.

The Journal of pediatrics·2023
Same author

Lipotoxicity-polarised macrophage-derived exosomes regulate mitochondrial fitness through Miro1-mediated mitophagy inhibition and contribute to type 2 diabetes development in mice.

Diabetologia·2023
Same author

A high fat diet in glutamate 3-/Y mice causes changes in behavior that resemble human intellectual disability.

Physiology & behavior·2022

Related Experiment Video

Updated: Apr 11, 2026

Analyzing Multifactorial RNA-Seq Experiments with DiCoExpress
05:22

Analyzing Multifactorial RNA-Seq Experiments with DiCoExpress

Published on: July 29, 2022

4.1K

DECODE: an integrated differential co-expression and differential expression analysis of gene expression data.

Thomas W H Lui1, Nancy B Y Tsui2, Lawrence W C Chan3

  • 1Department of Health Technology and Informatics, The Hong Kong Polytechnic University, Hung Hom, Kowloon, Hong Kong. tlui27@yahoo.com.

BMC Bioinformatics
|June 1, 2015
PubMed
Summary

We developed DECODE (Differential Co-expression and Differential Expression), a new method to analyze gene expression and co-expression. DECODE enhances the detection of disease-related gene functions by integrating both differential expression and differential co-expression analyses.

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

42.9K
High-Throughput Transcriptome Analysis for Investigating Host-Pathogen Interactions
14:58

High-Throughput Transcriptome Analysis for Investigating Host-Pathogen Interactions

Published on: March 5, 2022

5.0K

Related Experiment Videos

Last Updated: Apr 11, 2026

Analyzing Multifactorial RNA-Seq Experiments with DiCoExpress
05:22

Analyzing Multifactorial RNA-Seq Experiments with DiCoExpress

Published on: July 29, 2022

4.1K
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

42.9K
High-Throughput Transcriptome Analysis for Investigating Host-Pathogen Interactions
14:58

High-Throughput Transcriptome Analysis for Investigating Host-Pathogen Interactions

Published on: March 5, 2022

5.0K

Area of Science:

  • Genomics
  • Bioinformatics
  • Systems Biology

Background:

  • Differential expression (DE) and differential co-expression (DC) analyses are key for understanding gene regulation in complex diseases.
  • The combined performance of DE and DC analyses has not been previously explored.

Purpose of the Study:

  • To introduce DECODE (Differential Co-expression and Differential Expression), a novel analytical approach integrating DE and DC analyses.
  • To explore the combined features of DE and DC for each transcript between two conditions.

Main Methods:

  • DECODE systematically defines optimal thresholds for gene expression and co-expression changes using chi-square maximization.
  • Genes are categorized into four groups based on high or low DE and DC characteristics.
  • The approach was applied to a large breast cancer microarray dataset of 2000 tumor samples.

Main Results:

  • DECODE improved the detection of functional gene sets, including those related to immune response, metastasis, and metabolism.
  • Identification of genes with high DE and high DC provides deeper insights into complex disease mechanisms.
  • Further investigation of identified genes and pathways can enhance understanding of disease biology.

Conclusions:

  • DECODE complements existing DC and traditional DE analyses, offering a valuable method for studying disease-associated genes.
  • It reveals biological functions that may be missed by analyzing DE or DC alone.
  • The DECODE R package is available on CRAN.