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Re-Annotator: Annotation Pipeline for Microarrays

Janine Arloth, Daniel Magnus Bader, Simone Röh, Andre Altmann
doi: https://doi.org/10.1101/019596
Janine Arloth
1.Translational Research Department, Max Planck Institute of Psychiatry, Kraepelinstrasse 2-10, 80804, Munich, Germany
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Daniel Magnus Bader
1.Translational Research Department, Max Planck Institute of Psychiatry, Kraepelinstrasse 2-10, 80804, Munich, Germany
2.Gene Center Munich, Ludwig-Maximillians-Universität München, Feodor-Lynen Strasse 25, 81377, Munich, Germany
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Simone Röh
1.Translational Research Department, Max Planck Institute of Psychiatry, Kraepelinstrasse 2-10, 80804, Munich, Germany
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Andre Altmann
3.Department of Neurology and Neurological Sciences, Stanford University, School of Medicine, 780 Welch Road, CJ350 C38, CA-94304 Palo Alto, USA
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Abstract

Background Microarray technologies are established approaches for high throughput gene expression, methylation and genotyping analysis. An accurate mapping of the array probes is essential to generate reliable biological findings. Manufacturers typically provide incomplete and outdated annotation tables, which often rely on older genome and transcriptome versions differing substantially from up-to-date sequence databases.

Results Here, we present the Re-Annotator, a re-annotation pipeline for microarrays. It is primarily designed for gene expression microarrays but can be adapted to other types of microarrays. The Re-Annotator is based on a custom-built mRNA reference, used to identify the positions of gene expression array probe sequences. A comparison of our re-annotation of the Human-HT12-v4 microarray to the manufacturer’s annotation led to over 25% differently interpreted probes.

Conclusions A thorough re-annotation of probe information is crucial to any microarray analysis. The Re-Annotator pipeline consists of Perl and Shell scripts, freely available at http://sourceforge.net/projects/reannotator. Re-annotation files for Illumina microarrays Human HT-12 v3/v4 and MouseRef-8 v2 are available as well.

Copyright 
The copyright holder for this preprint is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under a CC-BY-NC-ND 4.0 International license.
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Posted May 21, 2015.
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Re-Annotator: Annotation Pipeline for Microarrays
Janine Arloth, Daniel Magnus Bader, Simone Röh, Andre Altmann
bioRxiv 019596; doi: https://doi.org/10.1101/019596
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Re-Annotator: Annotation Pipeline for Microarrays
Janine Arloth, Daniel Magnus Bader, Simone Röh, Andre Altmann
bioRxiv 019596; doi: https://doi.org/10.1101/019596

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