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
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
Genome Annotation and Assembly03:36

Genome Annotation and Assembly

18.8K
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.
18.8K
Predicting Reaction Outcomes02:24

Predicting Reaction Outcomes

8.3K
Kinetics describes the rate and path by which a reaction occurs. In contrast, thermodynamics deals with state functions and describes the properties, behavior, and components of a system. It is not concerned with the path taken by the process and cannot address the rate at which a reaction occurs. Although it does provide information about what can happen during a reaction process, it does not describe the detailed steps of what appears on an atomic or a molecular level. On the other hand,...
8.3K
Molecular Models02:00

Molecular Models

38.2K
Physical models representing molecular architectures of chemical compounds play essential roles in understanding chemistry. The use of molecular models makes it easier to visualize the structures and shapes of atoms and molecules.
38.2K
IP3/DAG Signaling Pathway01:11

IP3/DAG Signaling Pathway

12.0K
Membrane lipids such as phosphatidylinositol (PI) are precursors for several membrane-bound and soluble second messengers. Specific kinases phosphorylate PI and produce phosphorylated inositol phospholipids. One such inositol phospholipids are the  phosphatidylinositol-4,5 bisphosphate [PI(4,5)P2], present in the inner half of the lipid bilayer. Upon ligand binding, GPCR stimulates Gq proteins to turn on phospholipase Cꞵ. Activated phospholipase Cꞵ cleaves PI(4,5)P2 and...
12.0K

You might also read

Related Articles

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

Sort by
Same author

Green Tea Consumption and Risk of All-Cause Mortality: Findings from a Prospective Cohort Study.

Nutrients·2026
Same author

CD39 mRNA therapy attenuates localized acute inflammation: A novel anti-inflammatory strategy using cationic nanoliposomes.

Molecular therapy. Nucleic acids·2026
Same author

Immune microenvironment and noncoding RNA shape early colorectal carcinogenesis in patients with premalignant lesions.

Science translational medicine·2026
Same author

CSIE: cancer subtyping via inference and ensemble.

Briefings in bioinformatics·2026
Same author

Disruption of carotenoid metabolism in cavefish via loss of beta-carotene oxygenase 2a.

Current biology : CB·2026
Same author

Evaluation of the reliability of markerless tumor tracking with single-energy and dual-energy imaging using machine learning.

Journal of applied clinical medical physics·2026
Same journal

STED: flexible cross-modal topic modeling infers cell-type-specific regulatory landscapes from bulk epigenomics.

Briefings in bioinformatics·2026
Same journal

A knowledge-guided deep learning framework for quantitative nucleic acid testing.

Briefings in bioinformatics·2026
Same journal

Optimal transport for label transfer in single-cell multi-omics integration.

Briefings in bioinformatics·2026
Same journal

Continuous multi-omics pathway enrichment analysis resolves hidden functional heterogeneity.

Briefings in bioinformatics·2026
Same journal

Evaluating completeness, coherence, and consistency of genome-scale function annotations.

Briefings in bioinformatics·2026
Same journal

Transformers for single-cell RNA sequencing: a survey.

Briefings in bioinformatics·2026
See all related articles

Related Experiment Video

Updated: Jun 19, 2025

A Web Tool for Generating High Quality Machine-readable Biological Pathways
08:01

A Web Tool for Generating High Quality Machine-readable Biological Pathways

Published on: February 8, 2017

17.6K

CCPA: cloud-based, self-learning modules for consensus pathway analysis using GO, KEGG and Reactome.

Ha Nguyen1, Van-Dung Pham1, Hung Nguyen1

  • 1Department of Computer Science and Software Engineering, Auburn University, AL 36849, USA.

Briefings in Bioinformatics
|July 23, 2024
PubMed
Summary
This summary is machine-generated.

This study introduces a cloud-based learning module for Consensus Pathway Analysis, simplifying complex biological data interpretation for researchers. It offers interactive tutorials and supports multiple species, enhancing self-learning and comparative analysis capabilities.

Keywords:
NIGMS sandboxcloud computingjupyter notebookspathway analysisself-learning module

More Related Videos

Author Spotlight: Advancing Alzheimer's Research – Exploring Early Detection and Multi-Omics Approaches
09:47

Author Spotlight: Advancing Alzheimer's Research – Exploring Early Detection and Multi-Omics Approaches

Published on: December 15, 2023

1.0K
A Knowledge Graph Approach to Elucidate the Role of Organellar Pathways in Disease via Biomedical Reports
07:35

A Knowledge Graph Approach to Elucidate the Role of Organellar Pathways in Disease via Biomedical Reports

Published on: October 13, 2023

1.6K

Related Experiment Videos

Last Updated: Jun 19, 2025

A Web Tool for Generating High Quality Machine-readable Biological Pathways
08:01

A Web Tool for Generating High Quality Machine-readable Biological Pathways

Published on: February 8, 2017

17.6K
Author Spotlight: Advancing Alzheimer's Research – Exploring Early Detection and Multi-Omics Approaches
09:47

Author Spotlight: Advancing Alzheimer's Research – Exploring Early Detection and Multi-Omics Approaches

Published on: December 15, 2023

1.0K
A Knowledge Graph Approach to Elucidate the Role of Organellar Pathways in Disease via Biomedical Reports
07:35

A Knowledge Graph Approach to Elucidate the Role of Organellar Pathways in Disease via Biomedical Reports

Published on: October 13, 2023

1.6K

Area of Science:

  • Bioinformatics
  • Computational Biology
  • Genomics

Background:

  • Pathway analysis is crucial for understanding biological mechanisms but is hindered by method complexity, coding requirements, and limited species support.
  • Existing tools often lack the ability to compare results across different experiments and methods, complicating the identification of consensus findings.
  • Biomedical researchers face challenges in self-learning and efficiently performing pathway analysis due to these limitations.

Purpose of the Study:

  • To develop an interactive, cloud-based learning module for Consensus Pathway Analysis within the NIGMS Sandbox platform.
  • To provide a self-learning resource that addresses the difficulties biomedical researchers encounter in performing and interpreting pathway analyses.
  • To enable the comparison of results from multiple pathway analysis methods and experiments to identify consensus findings.

Main Methods:

  • Developed a module with five Jupyter Notebooks covering data processing, differential analysis (limma, t-test, edgeR, DESeq2), pathway database processing (GO, KEGG, Reactome), and pathway analysis (ORA, CAMERA, KS test, Wilcoxon test, FGSEA, GSA, SAFE, PADOG).
  • Integrated cloud resources for data access and analysis, supporting multiple model and non-model species.
  • Included examples, source code, explanations, and instructional videos for a comprehensive learning experience.

Main Results:

  • The module facilitates the processing of expression data and performs differential analysis using four distinct methods.
  • It enables pathway analysis using eight different methods and integrates results for consensus identification.
  • The resource supports a wide range of species, including human, mouse, fruit fly, and zebrafish, and is publicly available.

Conclusions:

  • The developed module effectively addresses the challenges in self-learning and performing consensus pathway analysis.
  • It provides a valuable, interactive, and cloud-based resource for training students and researchers in complex biological data analysis.
  • The module promotes efficient comparative analysis and supports a broad spectrum of species, enhancing its utility in biological research.