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SNPs matter: impact on detection of differential expression

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Figure 1: Acyp2 is an example of a false negative induced by SNPs.

References

  1. Frazer, K.A. et al. Genome Res. 14, 1493–1500 (2004).

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Acknowledgements

Supported by US National Institutes of Health grants AA010760, DA05228 and AA011114, and a Department of Veterans Affairs Merit Award.

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Authors and Affiliations

  1. Department of Behavioral Neuroscience, Oregon Health & Science University, 3181 SW Sam Jackson Park Road, Portland, 97239, Oregon, USA

    Nicole A R Walter, John K Belknap, Robert Hitzemann & Kari J Buck

  2. Portland Alcohol Research Center, Oregon Health & Science University, 3181 SW Sam Jackson Park Road, Portland, 97239, Oregon, USA

    Nicole A R Walter, Shannon K McWeeney, John K Belknap, Robert Hitzemann & Kari J Buck

  3. Division of Biostatistics, Oregon Health Sciences University Cancer Institute, Oregon Clinical and Translational Research Institute, Public Health and Prevention Medicine, Oregon Health & Science University, 3181 SW Sam Jackson Park Road, Portland, 97239, Oregon, USA

    Shannon K McWeeney

  4. Vollum Institute, Oregon Health & Science University, 3181 SW Sam Jackson Park Road, Portland, 97239, Oregon, USA

    Sandra T Peters

  5. Portland Veterans Affairs Medical Center, 3710 SW US Veterans Hospital Road, Portland, 97239, Oregon, USA

    Nicole A R Walter, John K Belknap, Robert Hitzemann & Kari J Buck

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  1. Nicole A R Walter
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  2. Shannon K McWeeney
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The authors declare no competing financial interests.

Supplementary information

Supplementary Text and Figures

Supplementary Figures 1–2, Supplementary Tables 1–3, Supplementary Methods (PDF 221 kb)

Supplementary Data 1

SNP Mask file for the Affymetrix MOE 430 2.0 array (Mas 5.0 format) which incorporates all known SNPs between the B6 and D2 strains at the time of publication. (TXT 106 kb)

Supplementary Data 2

SNP Mask file for the Affymetrix MOE 430 2.0 array (RMA format) which incorporates all known SNPs between the B6 and D2 strains at the time of publication. (TXT 228 kb)

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Walter, N., McWeeney, S., Peters, S. et al. SNPs matter: impact on detection of differential expression. Nat Methods 4, 679–680 (2007). https://doi.org/10.1038/nmeth0907-679

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