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

Genome Annotation and Assembly03:36

Genome Annotation and Assembly

18.7K
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.
18.7K
Epistasis Analysis01:09

Epistasis Analysis

4.9K
Although Mendel chose seven unrelated traits in peas to study gene segregation, most traits involve multiple gene interactions that create a spectrum of phenotypes. When the interaction of various genes or alleles at different locations influences a phenotype, this is called epistasis. Epistasis often involves one gene masking or interfering with the expression of another (antagonistic epistasis). Epistasis often occurs when different genes are part of the same biochemical pathway. The...
4.9K
Genome-wide Association Studies-GWAS01:11

Genome-wide Association Studies-GWAS

12.2K
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...
12.2K
What is Genetic Engineering?00:49

What is Genetic Engineering?

72.8K
Overview
72.8K
Genomics02:02

Genomics

35.3K
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...
35.3K
DNA Microarrays02:34

DNA Microarrays

17.1K
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...
17.1K

You might also read

Related Articles

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

Sort by
Same author

ChEA-KG and ChEA-KG-TS: a network-based transcription factor enrichment analysis tool with an accompanying time-series workflow.

Nucleic acids research·2026
Same author

A tool based on objective data to identify patients at elevated risk of hospital-onset <i>Staphylococcus aureus</i> bacteremia: a nested case-control study.

Antimicrobial stewardship & healthcare epidemiology : ASHE·2026
Same author

sc2DAT: workflow for targeting tumor subpopulations of single cells.

Bioinformatics advances·2025
Same author

Creating an Interactive Web Interface for Networks Stored in Knowledge Graph Databases.

Current protocols·2025
Same author

A Gene Set Foundation Model Pre-Trained on a Massive Collection of Diverse Gene Sets.

bioRxiv : the preprint server for biology·2025
Same author

L2S2: chemical perturbation and CRISPR KO LINCS L1000 signature search engine.

Nucleic acids research·2025
Same journal

NanoporeDB: A Structural Resource Of Multimeric Protein Nanopores For Single-Molecule Sensing.

GigaScience·2026
Same journal

From the Brain Cell Atlas to Precision Neurology: A review of the application of AI-driven multi-omics in brain science.

GigaScience·2026
Same journal

Comparison of Deep Learning Approaches for Extreme Low-SNR Image Restoration.

GigaScience·2026
Same journal

ScopeViewer: A Browser-Based Solution for Visualizing Large Biological Images.

GigaScience·2026
Same journal

ChatMDV: Reducing Technical Barriers in Bioinformatics Analysis using Large Language Models.

GigaScience·2026
Same journal

ClusterGraph: a new tool for visualisation and compression of multidimensional data.

GigaScience·2026
See all related articles

Related Experiment Video

Updated: May 15, 2025

A Protocol for Using Gene Set Enrichment Analysis to Identify the Appropriate Animal Model for Translational Research
09:35

A Protocol for Using Gene Set Enrichment Analysis to Identify the Appropriate Animal Model for Translational Research

Published on: August 16, 2017

17.7K

GeneSetCart: assembling, augmenting, combining, visualizing, and analyzing gene sets.

Giacomo B Marino1, Stephanie Olaiya1, John Erol Evangelista1

  • 1Mount Sinai Center for Bioinformatics, Department of Pharmacological Sciences, Department of Artificial Intelligence and Human Health, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA.

Gigascience
|April 10, 2025
PubMed
Summary
This summary is machine-generated.

GeneSetCart is a web platform for biologists to integrate multiomics data into gene sets. It aids in data management, analysis, and visualization, facilitating knowledge discovery without programming expertise.

Keywords:
Alexander diseaseChrome extensionGeneshotSuperVennUpSetVennagingexercisegene set intersectionintegrative analysis

More Related Videos

Transcriptomic Analysis of C. elegans RNA Sequencing Data Through the Tuxedo Suite on the Galaxy Project
10:19

Transcriptomic Analysis of C. elegans RNA Sequencing Data Through the Tuxedo Suite on the Galaxy Project

Published on: April 8, 2017

17.3K
Author Spotlight: Investigating the Role of Repetitive DNA Misregulation in Cancer Initiation and Immunotherapy Resistance
04:58

Author Spotlight: Investigating the Role of Repetitive DNA Misregulation in Cancer Initiation and Immunotherapy Resistance

Published on: December 13, 2024

1.9K

Related Experiment Videos

Last Updated: May 15, 2025

A Protocol for Using Gene Set Enrichment Analysis to Identify the Appropriate Animal Model for Translational Research
09:35

A Protocol for Using Gene Set Enrichment Analysis to Identify the Appropriate Animal Model for Translational Research

Published on: August 16, 2017

17.7K
Transcriptomic Analysis of C. elegans RNA Sequencing Data Through the Tuxedo Suite on the Galaxy Project
10:19

Transcriptomic Analysis of C. elegans RNA Sequencing Data Through the Tuxedo Suite on the Galaxy Project

Published on: April 8, 2017

17.3K
Author Spotlight: Investigating the Role of Repetitive DNA Misregulation in Cancer Initiation and Immunotherapy Resistance
04:58

Author Spotlight: Investigating the Role of Repetitive DNA Misregulation in Cancer Initiation and Immunotherapy Resistance

Published on: December 13, 2024

1.9K

Area of Science:

  • Bioinformatics
  • Computational Biology
  • Genomics

Background:

  • Multiomics datasets require effective gene set management for integrated analysis and knowledge discovery.
  • Existing tools often lack comprehensive management capabilities for gene sets from diverse sources.

Purpose of the Study:

  • To introduce GeneSetCart, an interactive web-based platform for comprehensive gene set management and analysis.
  • To enable biologists, regardless of programming expertise, to integrate and analyze multiomics data.

Main Methods:

  • GeneSetCart allows gathering gene sets from various sources, augmenting them with coexpression and interaction data.
  • It supports set operations (union, intersection, consensus) and visualization using Venn diagrams, heatmaps, UMAP, SuperVenn, and UpSet plots.
  • The platform integrates with external tools for enrichment analysis and uses a large language model (LLM) for interpreting overlapping gene sets and generating reports.

Main Results:

  • GeneSetCart provides a centralized environment for gene set manipulation, visualization, and analysis.
  • It facilitates the identification of similarities and overlaps between gene sets from different sources.
  • The platform successfully demonstrated its utility through two use cases, including LLM-assisted interpretation of gene set overlaps.

Conclusions:

  • GeneSetCart empowers biologists to perform complex gene set analyses, promoting data integration and hypothesis generation.
  • The platform enhances accessibility to advanced bioinformatics tools for researchers without coding skills.
  • GeneSetCart serves as a valuable resource for advancing biological research through integrated multiomics data analysis.