IDEAS home Printed from https://ideas.repec.org/a/bpj/sagmbi/v15y2016i1p1-18n1.html
   My bibliography  Save this article

Identification of consistent functional genetic modules

Author

Listed:
  • Miecznikowski Jeffrey C.

    (Department of Biostatistics, SUNY University at Buffalo, Buffalo NY 14214, USA)

  • Gaile Daniel P.

    (Department of Biostatistics, SUNY University at Buffalo, Buffalo NY 14214, USA)

  • Chen Xiwei

    (Department of Biostatistics, SUNY University at Buffalo, Buffalo NY 14214, USA)

  • Tritchler David L.

    (Department of Biostatistics, SUNY University at Buffalo, Buffalo NY 14214, USA Division of Biostatistics, University of Toronto, ON M5T 3M7, Toronto, Canada)

Abstract

It is often of scientific interest to find a set of genes that may represent an independent functional module or network, such as a functional gene expression module causing a biological response, a transcription regulatory network, or a constellation of mutations jointly causing a disease. In this paper we are specifically interested in identifying modules that control a particular outcome variable such as a disease biomarker. We discuss the statistical properties that functional networks should possess and introduce the concept of network consistency which should be satisfied by real functional networks of cooperating genes, and directly use the concept in the pathway discovery method we present. Our method gives superior performance for all but the simplest functional networks.

Suggested Citation

  • Miecznikowski Jeffrey C. & Gaile Daniel P. & Chen Xiwei & Tritchler David L., 2016. "Identification of consistent functional genetic modules," Statistical Applications in Genetics and Molecular Biology, De Gruyter, vol. 15(1), pages 1-18, March.
    • Handle: RePEc:bpj:sagmbi:v:15:y:2016:i:1:p:1-18:n:1
    DOI: 10.1515/sagmb-2015-0026
    as

    Download full text from publisher

    File URL: https://doi.org/10.1515/sagmb-2015-0026
    Download Restriction: For access to full text, subscription to the journal or payment for the individual article is required.
    File URL: https://libkey.io/10.1515/sagmb-2015-0026?utm_source=ideas
    LibKey link: if access is restricted and if your library uses this service, LibKey will redirect you to where you can use your library subscription to access this item
    ---><---

    As the access to this document is restricted, you may want to search for a different version of it.

    References listed on IDEAS

    as
    1. Peter Hall & J. S. Marron & Amnon Neeman, 2005. "Geometric representation of high dimension, low sample size data," Journal of the Royal Statistical Society Series B, Royal Statistical Society, vol. 67(3), pages 427-444, June.
    2. Zhang Bin & Horvath Steve, 2005. "A General Framework for Weighted Gene Co-Expression Network Analysis," Statistical Applications in Genetics and Molecular Biology, De Gruyter, vol. 4(1), pages 1-45, August.
    3. Luis Milan & Joe Whittaker, 1995. "Application of the Parametric Bootstrap to Models that Incorporate a Singular Value Decomposition," Journal of the Royal Statistical Society Series C, Royal Statistical Society, vol. 44(1), pages 31-49, March.
    4. Jeongyoun Ahn & J. S. Marron & Keith M. Muller & Yueh-Yun Chi, 2007. "The high-dimension, low-sample-size geometric representation holds under mild conditions," Biometrika, Biometrika Trust, vol. 94(3), pages 760-766.
    Full references (including those not matched with items on IDEAS)

    Most related items

    These are the items that most often cite the same works as this one and are cited by the same works as this one.
    1. Yata, Kazuyoshi & Aoshima, Makoto, 2013. "PCA consistency for the power spiked model in high-dimensional settings," Journal of Multivariate Analysis, Elsevier, vol. 122(C), pages 334-354.
    2. Jung, Sungkyu & Sen, Arusharka & Marron, J.S., 2012. "Boundary behavior in High Dimension, Low Sample Size asymptotics of PCA," Journal of Multivariate Analysis, Elsevier, vol. 109(C), pages 190-203.
    3. Wang, Shao-Hsuan & Huang, Su-Yun, 2022. "Perturbation theory for cross data matrix-based PCA," Journal of Multivariate Analysis, Elsevier, vol. 190(C).
    4. Kazuyoshi Yata & Makoto Aoshima, 2012. "Inference on High-Dimensional Mean Vectors with Fewer Observations Than the Dimension," Methodology and Computing in Applied Probability, Springer, vol. 14(3), pages 459-476, September.
    5. Yugo Nakayama & Kazuyoshi Yata & Makoto Aoshima, 2020. "Bias-corrected support vector machine with Gaussian kernel in high-dimension, low-sample-size settings," Annals of the Institute of Statistical Mathematics, Springer;The Institute of Statistical Mathematics, vol. 72(5), pages 1257-1286, October.
    6. Borysov, Petro & Hannig, Jan & Marron, J.S., 2014. "Asymptotics of hierarchical clustering for growing dimension," Journal of Multivariate Analysis, Elsevier, vol. 124(C), pages 465-479.
    7. Chung, Hee Cheol & Ahn, Jeongyoun, 2021. "Subspace rotations for high-dimensional outlier detection," Journal of Multivariate Analysis, Elsevier, vol. 183(C).
    8. Shen, Dan & Shen, Haipeng & Marron, J.S., 2013. "Consistency of sparse PCA in High Dimension, Low Sample Size contexts," Journal of Multivariate Analysis, Elsevier, vol. 115(C), pages 317-333.
    9. Jun Li, 2018. "Asymptotic normality of interpoint distances for high-dimensional data with applications to the two-sample problem," Biometrika, Biometrika Trust, vol. 105(3), pages 529-546.
    10. Makoto Aoshima & Kazuyoshi Yata, 2014. "A distance-based, misclassification rate adjusted classifier for multiclass, high-dimensional data," Annals of the Institute of Statistical Mathematics, Springer;The Institute of Statistical Mathematics, vol. 66(5), pages 983-1010, October.
    11. Nakayama, Yugo & Yata, Kazuyoshi & Aoshima, Makoto, 2021. "Clustering by principal component analysis with Gaussian kernel in high-dimension, low-sample-size settings," Journal of Multivariate Analysis, Elsevier, vol. 185(C).
    12. Yata, Kazuyoshi & Aoshima, Makoto, 2012. "Effective PCA for high-dimension, low-sample-size data with noise reduction via geometric representations," Journal of Multivariate Analysis, Elsevier, vol. 105(1), pages 193-215.
    13. Jung, Sungkyu, 2018. "Continuum directions for supervised dimension reduction," Computational Statistics & Data Analysis, Elsevier, vol. 125(C), pages 27-43.
    14. Yata, Kazuyoshi & Aoshima, Makoto, 2010. "Effective PCA for high-dimension, low-sample-size data with singular value decomposition of cross data matrix," Journal of Multivariate Analysis, Elsevier, vol. 101(9), pages 2060-2077, October.
    15. Modarres, Reza, 2022. "A high dimensional dissimilarity measure," Computational Statistics & Data Analysis, Elsevier, vol. 175(C).
    16. Yata, Kazuyoshi & Aoshima, Makoto, 2013. "Correlation tests for high-dimensional data using extended cross-data-matrix methodology," Journal of Multivariate Analysis, Elsevier, vol. 117(C), pages 313-331.
    17. Wang, Shao-Hsuan & Huang, Su-Yun & Chen, Ting-Li, 2020. "On asymptotic normality of cross data matrix-based PCA in high dimension low sample size," Journal of Multivariate Analysis, Elsevier, vol. 175(C).
    18. Lee, Myung Hee, 2012. "On the border of extreme and mild spiked models in the HDLSS framework," Journal of Multivariate Analysis, Elsevier, vol. 107(C), pages 162-168.
    19. Joost Ginkel & Pieter Kroonenberg, 2014. "Using Generalized Procrustes Analysis for Multiple Imputation in Principal Component Analysis," Journal of Classification, Springer;The Classification Society, vol. 31(2), pages 242-269, July.
    20. Yixuan Qiu & Jing Lei & Kathryn Roeder, 2023. "Gradient-based sparse principal component analysis with extensions to online learning," Biometrika, Biometrika Trust, vol. 110(2), pages 339-360.

    More about this item

    Keywords

    module; network; pathway;
    All these keywords.

    Statistics

    Access and download statistics

    Corrections

    All material on this site has been provided by the respective publishers and authors. You can help correct errors and omissions. When requesting a correction, please mention this item's handle: RePEc:bpj:sagmbi:v:15:y:2016:i:1:p:1-18:n:1. See general information about how to correct material in RePEc.

    If you have authored this item and are not yet registered with RePEc, we encourage you to do it here. This allows to link your profile to this item. It also allows you to accept potential citations to this item that we are uncertain about.

    If CitEc recognized a bibliographic reference but did not link an item in RePEc to it, you can help with this form .

    If you know of missing items citing this one, you can help us creating those links by adding the relevant references in the same way as above, for each refering item. If you are a registered author of this item, you may also want to check the "citations" tab in your RePEc Author Service profile, as there may be some citations waiting for confirmation.

    For technical questions regarding this item, or to correct its authors, title, abstract, bibliographic or download information, contact: Peter Golla (email available below). General contact details of provider: https://www.degruyter.com .

    Please note that corrections may take a couple of weeks to filter through the various RePEc services.

    IDEAS is a RePEc service. RePEc uses bibliographic data supplied by the respective publishers.