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 Experiment Videos

Array2BIO: from microarray expression data to functional annotation of co-regulated genes.

Gabriela G Loots1, Patrick S G Chain, Shalini Mabery

  • 1Lawrence Livermore National Laboratory, Livermore, California 94550, USA. loots1@llnl.gov

BMC Bioinformatics
|June 20, 2006
PubMed
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

Amplicon and metagenomic data from fumarole-associated geothermal features of Hawai'i.

Scientific data·2026
Same author

Brain and knee joint degeneration following anterior cruciate ligament injury in a mouse model of Alzheimer's disease.

JBMR plus·2026
Same author

Methods for evaluating bacterial dispersal on hyphal networks.

microLife·2026
Same author

Using Deep Learning Models of Gene Regulation to Guide Drug Prioritization.

bioRxiv : the preprint server for biology·2026
Same author

<i>N</i>-acyl-homoserine lactone-based quorum sensing beyond canonical lineages: insights from Actinomycetota.

Frontiers in microbiology·2026
Same author

Significance and challenges in dissecting cancer-bacteriome interactions.

BJC reports·2026
Same journal

OpenIMC: an open-source platform for analyzing single-cell and spatial proteomics by imaging mass cytometry.

BMC bioinformatics·2026
Same journal

NAP: an open source pipeline for cross-domain microbiome profiling using Nanopore sequencing-derived amplicon data.

BMC bioinformatics·2026
Same journal

SurvGME: an R package for survival analysis with graphical and measurement error models.

BMC bioinformatics·2026
Same journal

SimMapNet: a Bayesian framework for gene regulatory network inference using gene ontology similarities as external hint.

BMC bioinformatics·2026
Same journal

Dual channel drug-drug interactions extraction based on cross attention.

BMC bioinformatics·2026
Same journal

FeSseqdb: a curated sequence-level database and interpretable machine learning framework for identifying iron-sulfur proteins.

BMC bioinformatics·2026
See all related articles

Array2BIO is a new web-based toolkit that integrates multiple analytical methods for comprehensive Affymetrix microarray expression data analysis. It automates gene expression analysis, functional annotation, and regulatory element prediction.

Area of Science:

  • Bioinformatics
  • Computational Biology
  • Genomics

Background:

  • Existing tools for microarray expression data analysis are fragmented.
  • There is a need for an integrated, user-friendly, and automated solution.

Purpose of the Study:

  • To develop Array2BIO, a web-based application for comprehensive Affymetrix microarray expression data analysis.
  • To couple multiple analytical methods into a single, automated utility.

Main Methods:

  • Array2BIO converts raw intensities to probe expression values and maps them to genes.
  • It employs comparative analysis and clustering to identify co-expressed genes.
  • Functional annotation is achieved using Gene Ontology and KEGG pathways.

Main Results:

Related Experiment Videos

  • The tool handles low-expressor genes and incorporates statistical methods like Benjamini-Hochberg and Bonferroni corrections.
  • It integrates with ECR Browser for evolutionary conservation analysis and Crème for gene regulatory element prediction.
  • Array2BIO links expression data to comparative genomics tools and predicts gene co-regulation mechanisms.

Conclusions:

  • Array2BIO provides a rapid and comprehensive analysis of Affymetrix microarray expression data.
  • It facilitates the translation of co-expression data into gene co-regulation mechanisms.
  • The tool is publicly accessible at http://array2bio.dcode.org.