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

C4 Pathway and CAM01:27

C4 Pathway and CAM

48.8K
Most plants use the C3 pathway for carbon fixation. However, some plants, such as sugar cane, corn, and cacti that grow in hot conditions, use alternative pathways to fix carbon and conserve energy loss due to photorespiration. Photorespiration is the process that occurs when the oxygen concentration is high. Under such conditions, the rubisco enzyme in the Calvin cycle binds O2 instead of CO2, which halts photosynthesis and consumes energy.
C4 Pathway
The C4 pathway is used by plants such as...
48.8K
What is Gene Expression?01:42

What is Gene Expression?

194.7K
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...
194.7K
Other Glycolytic Pathways01:24

Other Glycolytic Pathways

839
The pentose phosphate pathway (PPP) operates in parallel with glycolysis, facilitating the metabolism of both pentoses and glucose. This pathway consists of two distinct phases: the oxidative and non-oxidative phases. While it does not directly generate ATP, the intermediates formed during the process can integrate into glycolysis, contributing to cellular energy metabolism when required.Oxidative Phase: NADPH ProductionThe oxidative phase of the pentose phosphate pathway is primarily...
839
mRNA Stability and Gene Expression02:51

mRNA Stability and Gene Expression

6.5K
The structure and stability of mRNA molecules regulates gene expression, as mRNAs are a key step in the pathway from gene to protein. In eukaryotes, the half-life of mRNA varies from a few minutes up to several days. mRNA stability is essential in growth and development. The absence of the proteins regulating its stability, such as tristetraprolin in mice, can cause systemic issues, including bone marrow overgrowth, inflammation, and autoimmunity.
Cis-acting Elements involved in mRNA stability
6.5K
Respiration Pathways01:26

Respiration Pathways

720
Cellular respiration is a fundamental metabolic process that enables organisms to generate energy from organic molecules. One of its central pathways is the tricarboxylic acid (TCA) cycle, also known as the Krebs cycle, which plays a crucial role in energy production and biosynthetic processes.Conversion of Pyruvate to Acetyl-CoAThe pyruvate generated from glycolysis undergoes oxidative decarboxylation by the pyruvate dehydrogenase complex, producing acetyl-CoA, one molecule of NADH, and one...
720
Auditory Pathway01:15

Auditory Pathway

7.1K
Auditory pathways constitute the complex neural circuits responsible for transmitting and interpreting auditory information from the peripheral auditory system to the brain. Sound waves are initially captured by the outer ear, funneled through the ear canal, and reach the tympanic membrane (eardrum). These vibrations are transmitted via the middle ear's ossicles to the inner ear's cochlea.
When viewed cross-sectionally, the cochlea reveals the scala vestibuli and scala tympani flanking...
7.1K

You might also read

Related Articles

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

Sort by
Same author

The Pathway-Informed Deep Learning Models in Cancer Research: A Survey.

IEEE transactions on computational biology and bioinformatics·2025
Same author

Identify Modules Associated with Immunotherapy Response from Mouse Tumor Profiles for Stratifying Cancer Patients.

Interdisciplinary sciences, computational life sciences·2025
Same author

Predicting Drug-Disease Associations Through Similarity Network Fusion and Multi-View Feature Projection Representation.

IEEE journal of biomedical and health informatics·2023
Same author

Early myeloid-derived suppressor cells accelerate epithelial-mesenchymal transition by downregulating ARID1A in luminal A breast cancer.

Frontiers in bioengineering and biotechnology·2022
Same author

Prediction performance of twelve tumor mutation burden panels in melanoma and non-small cell lung cancer.

Critical reviews in oncology/hematology·2021
Same author

Dual functional dinuclear platinum complex with selective reactivity towards c-myc G-quadruplex.

Scientific reports·2018

Related Experiment Video

Updated: Jan 20, 2026

Sample Preparation and Analysis of RNASeq-based Gene Expression Data from Zebrafish
11:42

Sample Preparation and Analysis of RNASeq-based Gene Expression Data from Zebrafish

Published on: October 27, 2017

11.4K

A network-based pathway-extending approach using DNA methylation and gene expression data to identify altered

Jie Li1, Qiaosheng Zhang2,3, Zhuo Chen1

  • 1Harbin Institute of Technology, School of Computer Science and Technology, Harbin, 150001, P.R. China.

Scientific Reports
|August 16, 2019
PubMed
Summary

This study introduces a new network-based method to integrate DNA methylation and gene expression data for cancer pathway analysis. The approach effectively identifies altered cancer pathways by extending existing ones using gene interaction networks.

More Related Videos

Author Spotlight: Exploring ShiDuGao's Multi-Target Approach in Anus Eczema Treatment
12:34

Author Spotlight: Exploring ShiDuGao's Multi-Target Approach in Anus Eczema Treatment

Published on: January 12, 2024

1.2K
siRNA Screening to Identify Ubiquitin and Ubiquitin-like System Regulators of Biological Pathways in Cultured Mammalian Cells
10:43

siRNA Screening to Identify Ubiquitin and Ubiquitin-like System Regulators of Biological Pathways in Cultured Mammalian Cells

Published on: May 24, 2014

11.8K

Related Experiment Videos

Last Updated: Jan 20, 2026

Sample Preparation and Analysis of RNASeq-based Gene Expression Data from Zebrafish
11:42

Sample Preparation and Analysis of RNASeq-based Gene Expression Data from Zebrafish

Published on: October 27, 2017

11.4K
Author Spotlight: Exploring ShiDuGao's Multi-Target Approach in Anus Eczema Treatment
12:34

Author Spotlight: Exploring ShiDuGao's Multi-Target Approach in Anus Eczema Treatment

Published on: January 12, 2024

1.2K
siRNA Screening to Identify Ubiquitin and Ubiquitin-like System Regulators of Biological Pathways in Cultured Mammalian Cells
10:43

siRNA Screening to Identify Ubiquitin and Ubiquitin-like System Regulators of Biological Pathways in Cultured Mammalian Cells

Published on: May 24, 2014

11.8K

Area of Science:

  • Bioinformatics
  • Computational Biology
  • Cancer Genomics

Background:

  • Pathway analysis is crucial for understanding cancer molecular mechanisms.
  • High-throughput multi-omics data and biological networks aid in identifying cancer-related pathways.
  • Integrating multidimensional data, pathway databases, and interaction networks is a promising strategy.

Purpose of the Study:

  • To present a novel network-based approach for the integrative analysis of DNA methylation and gene expression data.
  • To extend original pathways by incorporating multi-omics information.
  • To identify cancer-related altered pathways using this extended pathway information.

Main Methods:

  • Developed a novel network-based approach for integrative analysis of DNA methylation and gene expression data.
  • Extended original pathways using gene interaction networks.
  • Applied classical gene set analysis (ORA and FCS) to extended pathway gene lists.

Main Results:

  • Pathway extension provides a basis for discovering new pathway components.
  • The method facilitates understanding crosstalk between pathways in large biological networks.
  • Identified altered pathways correlated with specific cancers across TCGA datasets (BRCA, LUAD, COAD).

Conclusions:

  • The integration of DNA methylation and gene expression data via gene interaction networks is effective for identifying altered cancer pathways.
  • This network-based approach enhances pathway analysis for cancer research.
  • The extended pathways offer deeper insights into cancer mechanisms and inter-pathway communication.