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

Genomics02:02

Genomics

38.3K
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...
38.3K
Genome Annotation and Assembly03:36

Genome Annotation and Assembly

19.7K
The genome refers to all of the genetic material in an organism. It can range from a few million base pairs in microbial cells to several billion base pairs in many eukaryotic organisms. Genome assembly refers to the process of taking the DNA sequencing data and putting it all back together in a correct order to create a close representation of the original genome. This is followed by the identification of functional elements on the newly assembled genome, a process called genome annotation.
19.7K
DNA Microarrays02:34

DNA Microarrays

19.4K
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...
19.4K
Synthetic Biology02:55

Synthetic Biology

5.1K
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...
5.1K
Genome-wide Association Studies-GWAS01:11

Genome-wide Association Studies-GWAS

14.8K
Genome-wide association studies or GWAS are used to identify whether common SNPs are associated with certain diseases. Suppose specific SNPs are more frequently observed in individuals with a particular disease than those without the disease. In that case, those SNPs are said to be associated with the disease. Chi-square analysis is performed to check the probability of the allele likely to be associated with the disease.
GWAS does not require the identification of the target gene involved in...
14.8K
Next-generation Sequencing03:00

Next-generation Sequencing

95.2K
The first human genome sequencing project cost $2.7 billion and was declared complete in 2003, after 15 years of international cooperation and collaboration between several research teams and funding agencies. Today, with the advent of next-generation sequencing technologies, the cost and time of sequencing a human genome have dropped over 100 fold.
Next-Generation Sequencing Methods
Although all next-generation methods use different technologies, they all share a set of standard features....
95.2K

You might also read

Related Articles

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

Sort by
Same author

Association Between Deep Gray Matter Iron Deposition Dysregulation and Cognitive Performance in Type 2 Diabetes Mellitus Patients: A Quantitative Susceptibility Mapping Study.

Journal of magnetic resonance imaging : JMRI·2026
Same author

Spatiotemporal prediction of sneeze pollutants in enclosed spaces: a CNN-LSTM approach validated by field measurements and CFD-Robotics arm twin system.

Frontiers in robotics and AI·2026
Same author

mRNA-laden LNP-enabled in situ CAR-macrophage alleviates liver fibrosis via inhibiting activated HSCs and modulating the immune microenvironment.

Proceedings of the National Academy of Sciences of the United States of America·2026
Same author

Plasma proteomic profiles reveal proteins and characteristic patterns associated with hypertension: A prospective cohort study.

Journal of hypertension·2026
Same author

BMAL1 regulates circadian rhythms via phase separation-mediated transcriptional hub formation.

Signal transduction and targeted therapy·2026
Same author

NEK7 Cys298 is important for NLRP3 inflammasome and targetable by dimethyl fumarate.

Cell chemical biology·2026

Related Experiment Video

Updated: Nov 4, 2025

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

2.4K

eVITTA: a web-based visualization and inference toolbox for transcriptome analysis.

Xuanjin Cheng1,2,3, Junran Yan1,2,4, Yongxing Liu1,2,3

  • 1Centre for Molecular Medicine and Therapeutics, The University of British Columbia, Vancouver, British Columbia, Canada.

Nucleic Acids Research
|May 21, 2021
PubMed
Summary
This summary is machine-generated.

eVITTA is a new tool for transcriptome analysis, enabling exploration of public gene expression data. It helps identify gene changes in diseases like COVID-19 and in model organisms.

More Related Videos

Comprehensive Workflow for the Genome-wide Identification and Expression Meta-analysis of the ATL E3 Ubiquitin Ligase Gene Family in Grapevine
10:40

Comprehensive Workflow for the Genome-wide Identification and Expression Meta-analysis of the ATL E3 Ubiquitin Ligase Gene Family in Grapevine

Published on: December 22, 2017

10.7K
Leveraging CyVerse Resources for De Novo Comparative Transcriptomics of Underserved Non-model Organisms
10:41

Leveraging CyVerse Resources for De Novo Comparative Transcriptomics of Underserved Non-model Organisms

Published on: May 9, 2017

9.4K

Related Experiment Videos

Last Updated: Nov 4, 2025

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

2.4K
Comprehensive Workflow for the Genome-wide Identification and Expression Meta-analysis of the ATL E3 Ubiquitin Ligase Gene Family in Grapevine
10:40

Comprehensive Workflow for the Genome-wide Identification and Expression Meta-analysis of the ATL E3 Ubiquitin Ligase Gene Family in Grapevine

Published on: December 22, 2017

10.7K
Leveraging CyVerse Resources for De Novo Comparative Transcriptomics of Underserved Non-model Organisms
10:41

Leveraging CyVerse Resources for De Novo Comparative Transcriptomics of Underserved Non-model Organisms

Published on: May 9, 2017

9.4K

Area of Science:

  • Genomics and Bioinformatics
  • Molecular Biology
  • Computational Biology

Background:

  • Transcriptome profiling is crucial for understanding gene regulation in development and disease.
  • Existing web tools for transcriptome analysis are limited in functionality, data integration, and visualization.
  • There is a lack of systematic methods for exploring the vast NCBI GEO transcriptome repository.

Purpose of the Study:

  • To develop eVITTA, an accessible end-to-end platform for transcriptome data analysis and exploration.
  • To overcome limitations of current tools by integrating up-to-date, species-specific information and advanced visualization.
  • To facilitate systematic exploration of data within the NCBI GEO repository.

Main Methods:

  • Development of eVITTA, featuring modules for NCBI GEO data exploration (easyGEO), functional profiling (easyGSEA), and group comparisons (easyVizR).
  • Application of eVITTA to analyze transcriptomes of SARS-CoV-2 infected human samples.
  • Utilized eVITTA to analyze transcriptomes of Caenorhabditis elegans with altered S-adenosylmethionine metabolism.

Main Results:

  • eVITTA identified downregulation of olfactory signal transducers in SARS-CoV-2 infected samples, correlating with anosmia.
  • Analysis of Caenorhabditis elegans transcriptomes confirmed innate immune response activation and feedback induction of one-carbon cycle genes.
  • Demonstrated eVITTA's capability to capture both broad and granular transcriptomic changes across species.

Conclusions:

  • eVITTA provides a streamlined and accessible interface for complex transcriptome analysis workflows.
  • The platform effectively integrates and analyzes data from public repositories like NCBI GEO.
  • eVITTA advances the study of gene regulation in both human diseases and model organisms.