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Related Experiment Video

Updated: Jun 26, 2026

Microarray Analysis for Saccharomyces cerevisiae

Microarray Analysis for Saccharomyces cerevisiae

Published on: April 7, 2011

ArrayIDer: automated structural re-annotation pipeline for DNA microarrays.

Bart Hj van den Berg¹, Jay H Konieczka, Fiona M McCarthy

¹Department of Basic Science, PO Box 6100, College of Veterinary Medicine, Mississippi State University, Mississippi State, MS 39762,USA. bvandenberg@cvm.msstate.edu

BMC Bioinformatics

|January 27, 2009

Summary

ArrayIDer computationally re-annotates microarrays using EST clone names, improving data accuracy for systems biology. This tool rapidly generates updated database accessions, crucial for non-traditional model organisms.

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Microarray Analysis for Saccharomyces cerevisiae

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A Rapid High-throughput Method for Mapping Ribonucleoproteins (RNPs) on Human pre-mRNA

A Rapid High-throughput Method for Mapping Ribonucleoproteins (RNPs) on Human pre-mRNA

Published on: December 2, 2009

Area of Science:

Bioinformatics
Genomics
Systems Biology

Background:

Accurate microarray annotation is essential for systems biology modeling.
Existing annotations for non-traditional model organisms are often outdated.
Microarray analysis tools struggle with EST clone names, hindering data utilization.

Purpose of the Study:

To develop a computational tool (ArrayIDer) for rapid microarray re-annotation.
To improve the accuracy and completeness of microarray functional annotation.
To facilitate systems biology modeling in non-traditional biomedical model organisms.

Main Methods:

ArrayIDer retrieves current accession mapping files from public databases.
The tool processes EST clone names or accessions for re-annotation.
Automated generation of database accessions for entire microarrays.

Main Results:

Structurally re-annotated 55% of a 13K chicken cDNA array.
Reduced non-chicken functional annotations by twofold.
Identified 290 pseudogenes, including 66 previously misannotated ones.

Conclusions:

ArrayIDer enables fast, automated structural re-annotation of microarrays.
The tool provides multiple accession types for downstream functional analysis.
ArrayIDer is particularly valuable for systems biology in non-traditional model organisms.