Search research articles

ABOUT JoVE

Overview Leadership Blog JoVE Help Center

AUTHORS

Publishing Process Editorial Board Scope & Policies Peer Review FAQ Submit

LIBRARIANS

Testimonials Subscriptions Access Resources Library Advisory Board FAQ

RESEARCH

JoVE Journal Methods Collections JoVE Encyclopedia of Experiments Archive

EDUCATION

JoVE Core JoVE Business JoVE Science Education JoVE Lab Manual Faculty Resource Center Faculty Site

Terms & Conditions of Use

Search research articles

Related Experiment Videos

Characterizing gene sets with FuncAssociate.

Gabriel F Berriz¹, Oliver D King, Barbara Bryant

¹Harvard Medical School, Department of Biological Chemistry and Molecular Pharmacology, 250 Longwood Avenue, Boston, MA 02115, USA.

Bioinformatics (Oxford, England)

|December 12, 2003

Summary

This summary is machine-generated.

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

Image-based, pooled phenotyping reveals multidimensional, disease-specific variant effects.

Cell·2026

Same author

Global genetic interaction network of a human cell maps conserved principles and informs functional interpretation of gene co-essentiality profiles.

Cell·2026

Same author

Experimental assessment of AI-based interactome mapping.

Nature communications·2026

Same author

The 2025 Westlake Autumn Symposium for Al Proteomics and Virtual Cell.

Genomics, proteomics & bioinformatics·2026

Same author

A scalable approach to resolving variants of uncertain significance.

bioRxiv : the preprint server for biology·2026

Same author

Pertpy: an end-to-end framework for perturbation analysis.

Nature methods·2025

Same journal

MCFST: Spatial domain identification method based on multi-view graph convolutional network and graph fusion network.

Bioinformatics (Oxford, England)·2026

Same journal

SpaBiT: Enhancing Spatial Transcriptomics Resolution via Bidirectional Attention Transformers.

Bioinformatics (Oxford, England)·2026

Same journal

EDEL: Enhancing Dense Retrievers for Curation of Biomedical Knowledge Bases.

Bioinformatics (Oxford, England)·2026

Same journal

Informative Relational Learning for Adverse Reaction Prediction with Enhanced Generalization to Novel Drugs.

Bioinformatics (Oxford, England)·2026

Same journal

An interpretable deep learning framework uncovers features governing CRISPR-Cas9 genome-editing efficiency.

Bioinformatics (Oxford, England)·2026

Same journal

3DICE: Interpretable 3D Cross-Modal Learning for Drug-Target Interaction Prediction and Large-Scale Drug Discovery.

Bioinformatics (Oxford, England)·2026

See all related articles

FuncAssociate is a web tool that uses Gene Ontology attributes to analyze large gene sets from experiments. It offers a more accurate significance determination using Monte Carlo simulations for 10 different organisms.

Area of Science:

Bioinformatics
Computational Biology
Genomics

Background:

FuncAssociate is a freely accessible web-based tool.
Source code is available for academic users.

Purpose of the Study:

To provide researchers with a tool for characterizing large gene sets using Gene Ontology (GO) attributes.
To offer a more statistically robust method for determining significance in gene set analysis.

Main Methods:

Utilizes Gene Ontology attributes for gene set characterization.
Employs a Monte Carlo simulation approach for significance testing.
Handles ranked input lists.

Main Results:

FuncAssociate supports the analysis of gene sets across 10 different organisms.

Related Experiment Videos

The tool provides a more appropriate method for determining statistical significance compared to traditional corrections like Bonferroni or Šidák.

Conclusions:

FuncAssociate is a valuable web-based tool for researchers analyzing large gene sets.
Its unique features, including ranked list handling and Monte Carlo simulations, enhance the accuracy of biological interpretation.