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AILUN: reannotating gene expression data automatically

Nature Methods volume 4, page 879 (2007)Cite this article

To the editor:

Gene Expression Omnibus (GEO)1 is a public repository for gene expression data. While the amount of data in GEO has grown exponentially, the number of publications citing GEO has only grown linearly. The difficulty in data reuse is the mapping of probes in GEO datasets to established gene identifiers, which can change as annotations for the underlying sequences change2. Therefore, microarray results need to be reevaluated with the latest probe annotations. There have been several previous efforts to reannotate microarray probe identifiers3,4, but only for a few platforms and species.

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References

  1. Barrett, T. et al. Nucleic Acids Res. 35, D760–D765 (2007).

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Acknowledgements

Supported by Lucile Packard Foundation for Children's Health, US National Library of Medicine (K22 LM008261), National Institute of General Medical Sciences (R01 GM079719), Howard Hughes Medical Institute, and Pharmaceutical Research and Manufacturers of America Foundation. We thank A. Skrenchuk for computer support and A. Chiang for manuscript review.

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Authors and Affiliations

  1. Department of Medicine, Stanford Medical Informatics, Stanford University School of Medicine, 251 Campus Drive, Stanford, 94305, California, USA

    Rong Chen & Atul J Butte

  2. Department of Pediatrics, Stanford University School of Medicine, 251 Campus Drive, Stanford, 94305, California, USA

    Li Li & Atul J Butte

  3. Lucile Packard Children's Hospital, 725 Welch Road, Palo Alto, 94304, California, USA

    Atul J Butte

Authors
  1. Rong Chen
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  2. Li Li
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  3. Atul J Butte
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Supplementary Fig. 1, Supplementary Table 1–3, Supplementary Discussion and Supplementary Methods (PDF 308 kb)

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Chen, R., Li, L. & Butte, A. AILUN: reannotating gene expression data automatically. Nat Methods 4, 879 (2007). https://doi.org/10.1038/nmeth1107-879

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