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

Protein Networks02:26

Protein Networks

3.9K
An organism can have thousands of different proteins, and these proteins must cooperate to ensure the health of an organism. Proteins bind to other proteins and form complexes to carry out their functions. Many proteins interact with multiple other proteins creating a complex network of protein interactions.
These interactions can be represented through maps depicting protein-protein interaction networks, represented as nodes and edges. Nodes are circles that are representative of a protein,...
3.9K
Genomics02:02

Genomics

36.1K
Genomics is the science of genomes: it is the study of all the genetic material of an organism. In humans, the genome consists of information carried in 23 pairs of chromosomes in the nucleus, as well as mitochondrial DNA. In genomics, both coding and non-coding DNA is sequenced and analyzed. Genomics allows a better understanding of all living things, their evolution, and their diversity. It has a myriad of uses: for example, to build phylogenetic trees, to improve productivity and...
36.1K
Proteomics01:33

Proteomics

7.2K
A proteome is the entire set of proteins that a cell type produces. We can study proteomes using the knowledge of genomes because genes code for mRNAs, and the mRNAs encode proteins. Although mRNA analysis is a step in the right direction, not all mRNAs are translated into proteins.
Proteomics is the study of proteomes' function. It involves the large-scale systematic study of the proteome to denote the protein complement expressed by a genome. Scientist Mark Wilkins coined the term...
7.2K
Synthetic Biology02:55

Synthetic Biology

4.7K
Synthetic biology is an interdisciplinary science that involves using principles from disciplines such as engineering, molecular biology, cell biology, and systems biology. It involves remodeling existing organisms from nature or constructing completely new synthetic organisms for applications such as protein or enzyme production, bioremediation, value-added macromolecule production, and the addition of desirable traits to crops, to name a few.
Golden rice
Golden rice is a genetically modified...
4.7K

You might also read

Related Articles

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

Sort by
Same author

Vagal activation inhibits insulin release through neuronal nitric oxide synthase in obese male mice.

Science signaling·2026
Same author

Potential and challenges of natural product inhaled formulations in the treatment of pulmonary diseases.

International journal of pharmaceutics·2026
Same author

Intervention of ginseng-derived macromolecular drugs in Alzheimer's disease: exploring mechanisms and assessing potential.

Frontiers in aging neuroscience·2026
Same author

Use of continuous glucose monitoring to stratify individuals without diabetes.

Communications medicine·2026
Same author

Global loss of metabolic responsiveness and elevated enzyme in leptin deficient obese mice during starvation.

NPJ systems biology and applications·2026
Same author

Tracing lactate and its functions in adipose thermogenesis.

The Journal of physiology·2026
Same journal

Region-aware bridge modeling enables interpretable mesoscale representation of spatial transcriptomic tissue sections.

Bioinformatics advances·2026
Same journal

Microbiome differential abundance methodologies to detect relevant taxa associated with chemotherapy toxicity rate in colorectal cancer.

Bioinformatics advances·2026
Same journal

maldipickr dereplicates microbial MALDI-TOF spectra to facilitate multiplexed isolation.

Bioinformatics advances·2026
Same journal

RAM-MSA: an anytime memory-bounded method for exact multiple sequence alignment using path finding.

Bioinformatics advances·2026
Same journal

Interpretable machine learning for low-sample multi-omics: a case study of ferret vaccine response.

Bioinformatics advances·2026
Same journal

DeepTaxa: a hybrid CNN-BERT framework for 16S rRNA taxonomic classification.

Bioinformatics advances·2026
See all related articles

Related Experiment Video

Updated: Jun 9, 2025

Author Spotlight: Unveiling the Role of TMOD3 in Platinum Resistance and Immune Infiltration in Ovarian Cancer
09:40

Author Spotlight: Unveiling the Role of TMOD3 in Platinum Resistance and Immune Infiltration in Ovarian Cancer

Published on: August 2, 2024

2.6K

iTraNet: a web-based platform for integrated trans-omics network visualization and analysis.

Hikaru Sugimoto1, Keigo Morita2,3, Dongzi Li2

  • 1Department of Biochemistry and Molecular Biology, Graduate School of Medicine, The University of Tokyo, Tokyo 113-0033, Japan.

Bioinformatics Advances
|October 23, 2024
PubMed
Summary
This summary is machine-generated.

iTraNet visualizes and analyzes trans-omics networks, integrating gene regulatory, protein-protein interaction, and metabolic data. This tool revealed differences in molecular responses to glucose between wild-type and obese mice.

More Related Videos

JUMPn: A Streamlined Application for Protein Co-Expression Clustering and Network Analysis in Proteomics
07:28

JUMPn: A Streamlined Application for Protein Co-Expression Clustering and Network Analysis in Proteomics

Published on: October 19, 2021

3.1K
Inherent Dynamics Visualizer, an Interactive Application for Evaluating and Visualizing Outputs from a Gene Regulatory Network Inference Pipeline
10:44

Inherent Dynamics Visualizer, an Interactive Application for Evaluating and Visualizing Outputs from a Gene Regulatory Network Inference Pipeline

Published on: December 7, 2021

2.1K

Related Experiment Videos

Last Updated: Jun 9, 2025

Author Spotlight: Unveiling the Role of TMOD3 in Platinum Resistance and Immune Infiltration in Ovarian Cancer
09:40

Author Spotlight: Unveiling the Role of TMOD3 in Platinum Resistance and Immune Infiltration in Ovarian Cancer

Published on: August 2, 2024

2.6K
JUMPn: A Streamlined Application for Protein Co-Expression Clustering and Network Analysis in Proteomics
07:28

JUMPn: A Streamlined Application for Protein Co-Expression Clustering and Network Analysis in Proteomics

Published on: October 19, 2021

3.1K
Inherent Dynamics Visualizer, an Interactive Application for Evaluating and Visualizing Outputs from a Gene Regulatory Network Inference Pipeline
10:44

Inherent Dynamics Visualizer, an Interactive Application for Evaluating and Visualizing Outputs from a Gene Regulatory Network Inference Pipeline

Published on: December 7, 2021

2.1K

Area of Science:

  • Systems biology
  • Bioinformatics
  • Computational biology

Background:

  • Understanding biological systems relies on analyzing diverse molecular networks, including gene regulatory, protein-protein interaction, and metabolic networks.
  • Analyzing these networks is complex due to varied databases and intricate analysis methods.
  • Metabolic networks involve substrates, products, and enzymes, influenced by allosteric regulation and gene expression.

Purpose of the Study:

  • To develop a web application, iTraNet, for visualizing and analyzing integrated trans-omics networks.
  • To investigate differences in molecular responses to glucose administration in wild-type versus obese (ob/ob) mice using network analysis.

Main Methods:

  • Development of iTraNet, a web application integrating gene regulatory, protein-protein interaction, metabolic, and metabolite exchange networks.
  • Application of iTraNet to analyze trans-omics data from wild-type and ob/ob mice.
  • Comparative analysis of network hub molecule responses to glucose administration.

Main Results:

  • iTraNet successfully visualizes and analyzes integrated trans-omics networks.
  • In wild-type mice, key network molecules responded to glucose administration.
  • This response pattern was absent in ob/ob mice, indicating altered metabolic regulation.

Conclusions:

  • iTraNet provides a valuable tool for researchers to explore complex biological networks.
  • Network analysis using iTraNet can revealSystemic differences in physiological responses, such as those related to obesity and glucose metabolism.
  • The findings highlight potential disruptions in molecular signaling pathways in obesity.