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Global Gene Expression Analysis Using a Zebrafish Oligonucleotide Microarray Platform
Published on: August 10, 2009
Evaluating annotations of an Agilent expression chip suggests that many features cannot be interpreted.
E Michael Gertz1, Kundan Sengupta, Michael J Difilippantonio
1Computational Biology Branch, National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, DHHS, Bethesda, MD 20892, USA. gertz@ncbi.nlm.nih.gov
BMC Genomics
|December 2, 2009
Summary
Many Agilent human expression chip reporters lack valid gene annotations. A bioinformatics analysis revealed 40% of reporters were invalid, impacting gene expression data accuracy.
Area of Science:
- Genomics
- Bioinformatics
- Gene Expression Analysis
Background:
- Reanalysis of Agilent 4x44 human expression chip data revealed issues with oligonucleotide feature annotations.
- Some 60-mer oligonucleotide features could not be uniquely mapped to single human genes, aligning with multiple transcripts.
Purpose of the Study:
- To systematically assess the validity of oligonucleotide annotations on human autosomes and the X chromosome using bioinformatics methods.
- To identify and quantify reporters with ambiguous or incorrect gene mappings in expression datasets.
Main Methods:
- Bioinformatic analysis of Agilent 4x44 human expression chip data.
- Systematic evaluation of oligonucleotide reporter annotations against human genome and transcript databases.
- Alignment tests and identifier checks to determine reporter validity.
Main Results:
- Out of 42,683 reporters, 60% (25,505) were deemed "fully valid" with unique gene associations.
- 23% (9,964) of reporters had invalid identifiers, incorrect chromosome mapping, or failed alignment tests.
- 17% (7,214) of reporters mapped to unique genes or intergenic locations but lacked RefSeq transcript mapping, with further validity partitioning.
Conclusions:
- Expression array studies necessitate rigorous evaluation and removal of reporters with suspect annotations.
- Systematic and semi-automated validation methods are crucial for ensuring data integrity.
- Dynamic updates in data sources require ongoing re-evaluation of reporter validation status.
