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

You might also read

Related Articles

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

Sort by
Same author

Comprehensive analysis of the RBP regulome reveals functional modules and drug candidates in liver cancer.

Scientific reports·2026
Same author

GeneSNAKE: a Python package for simulation of gene regulatory networks and perturbation-induced expression data.

Bioinformatics advances·2026
Same author

Computational decoding of cell-cycle phase effects on cancer hallmarks across breast cancer subtypes.

Breast cancer research : BCR·2025
Same author

Quest for Orthologs in the era of Data Deluge and AI: Challenges and Innovations in Orthology Prediction and Data Integration.

Journal of molecular evolution·2025
Same author

BiGSM: Bayesian inference of gene regulatory network via sparse modelling.

Bioinformatics (Oxford, England)·2025
Same author

Topology-based metrics for finding the optimal sparsity in gene regulatory network inference.

Bioinformatics (Oxford, England)·2025

Related Experiment Video

Updated: Aug 12, 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

17.7K

PathBIX-a web server for network-based pathway annotation with adaptive null models.

Miguel Castresana-Aguirre1, Emma Persson1, Erik L L Sonnhammer1

  • 1Department of Biochemistry and Biophysics, Science for Life Laboratory, Stockholm University, Stockholm 17121, Sweden.

Bioinformatics Advances
|January 26, 2023
PubMed
Summary
This summary is machine-generated.

PathBIX is a new web tool for network-based pathway analysis, improving upon existing methods. It uses the ANUBIX algorithm for more accurate pathway annotation across 21 species.

More Related Videos

Selecting Multiple Biomarker Subsets with Similarly Effective Binary Classification Performances
07:35

Selecting Multiple Biomarker Subsets with Similarly Effective Binary Classification Performances

Published on: October 11, 2018

7.6K
An Integrated Approach for Microprotein Identification and Sequence Analysis
09:37

An Integrated Approach for Microprotein Identification and Sequence Analysis

Published on: July 12, 2022

3.5K

Related Experiment Videos

Last Updated: Aug 12, 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

17.7K
Selecting Multiple Biomarker Subsets with Similarly Effective Binary Classification Performances
07:35

Selecting Multiple Biomarker Subsets with Similarly Effective Binary Classification Performances

Published on: October 11, 2018

7.6K
An Integrated Approach for Microprotein Identification and Sequence Analysis
09:37

An Integrated Approach for Microprotein Identification and Sequence Analysis

Published on: July 12, 2022

3.5K

Area of Science:

  • Life Sciences
  • Bioinformatics
  • Computational Biology

Background:

  • Pathway annotation is crucial for interpreting life science experimental data.
  • Network-based methods offer richer insights than gene-content-only approaches.
  • These methods analyze network crosstalk between query gene sets and known pathways.

Purpose of the Study:

  • To introduce PathBIX, a novel web application for network-based pathway analysis.
  • To leverage the accuracy of the ANUBIX algorithm for enhanced pathway annotation.
  • To provide a user-friendly platform integrating multiple data sources.

Main Methods:

  • Developed PathBIX, a web application implementing the ANUBIX algorithm.
  • Utilized prefetched and preprocessed network data from FunCoup 5.0.
  • Integrated pathway data from KEGG, Reactome, and WikiPathways databases.

Main Results:

  • PathBIX performs network-based pathway analysis for 21 species.
  • The application is based on the ANUBIX algorithm, noted for its accuracy.
  • It integrates data from extensive network and pathway databases.

Conclusions:

  • PathBIX offers an advanced tool for network-based pathway annotation.
  • The web application provides accurate analysis by utilizing the ANUBIX algorithm.
  • It serves as a valuable resource for researchers in life sciences and bioinformatics.