IDEAS home Printed from https://ideas.repec.org/a/eee/csdana/v53y2009i4p1414-1426.html
   My bibliography  Save this article

Adaptive clustering for time series: Application for identifying cell cycle expressed genes

Author

Listed:
  • Douzal-Chouakria, Ahlame
  • Diallo, Alpha
  • Giroud, Françoise

Abstract

The biological problem of identifying the active genes during the cell division process is addressed. The cell division ensures the proliferation of cells, which is drastically aberrant in cancer cells. The studied genes are described by their expression profiles during the cell division cycle. Commonly, the identification process is a supervised approach based on an a priori set of reference genes, assumed as well-characterizing the cell cycle phases. Each studied gene is then classified by its peak similarity to one pre-specified reference gene. This classical approach suffers from two limitations. On the one hand, there is no consensus between biologists about the set of reference genes to consider for the identification process. On the other hand, the proximity measures used for genes expression profiles are unjustified and mainly based on the expression values regardless of the genes expression behavior. To identify genes expression profiles, a new adaptive clustering approach is proposed which consists of two main points. First, it allows in an unsupervised way the selection of a well-justified set of reference genes, to be compared with the pre-specified ones. Secondly, it enables the users to learn the appropriate proximity measure to use for genes expression data, a measure which will cover both proximity on values and on behavior. The adaptive clustering method is compared to a correlation-based approach through public and simulated genes expression data.

Suggested Citation

  • Douzal-Chouakria, Ahlame & Diallo, Alpha & Giroud, Françoise, 2009. "Adaptive clustering for time series: Application for identifying cell cycle expressed genes," Computational Statistics & Data Analysis, Elsevier, vol. 53(4), pages 1414-1426, February.
    • Handle: RePEc:eee:csdana:v:53:y:2009:i:4:p:1414-1426
    as

    Download full text from publisher

    File URL: http://www.sciencedirect.com/science/article/pii/S0167-9473(08)00567-7
    Download Restriction: Full text for ScienceDirect subscribers only.
    ---><---

    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. Liu, Xueli & Lee, Sheng-Chien & Casella, George & Peter, Gary F., 2008. "Assessing agreement of clustering methods with gene expression microarray data," Computational Statistics & Data Analysis, Elsevier, vol. 52(12), pages 5356-5366, August.
    2. Caiado, Jorge & Crato, Nuno & Pena, Daniel, 2006. "A periodogram-based metric for time series classification," Computational Statistics & Data Analysis, Elsevier, vol. 50(10), pages 2668-2684, June.
    3. Scrucca, Luca, 2007. "Class prediction and gene selection for DNA microarrays using regularized sliced inverse regression," Computational Statistics & Data Analysis, Elsevier, vol. 52(1), pages 438-451, September.
    4. Park, Changyi & Koo, Ja-Yong & Kim, Sujong & Sohn, Insuk & Lee, Jae Won, 2008. "Classification of gene functions using support vector machine for time-course gene expression data," Computational Statistics & Data Analysis, Elsevier, vol. 52(5), pages 2578-2587, January.
    5. Liang, Faming, 2007. "Use of SVD-based probit transformation in clustering gene expression profiles," Computational Statistics & Data Analysis, Elsevier, vol. 51(12), pages 6355-6366, August.
    6. Zhang, Chunming & Fu, Haoda & Jiang, Yuan & Yu, Tao, 2007. "High-dimensional pseudo-logistic regression and classification with applications to gene expression data," Computational Statistics & Data Analysis, Elsevier, vol. 52(1), pages 452-470, September.
    7. Kim, Yongdai & Kwon, Sunghoon & Heun Song, Seuck, 2006. "Multiclass sparse logistic regression for classification of multiple cancer types using gene expression data," Computational Statistics & Data Analysis, Elsevier, vol. 51(3), pages 1643-1655, December.
    8. Luis Angel Garcia-Escudero & Alfonso Gordaliza, 2005. "A Proposal for Robust Curve Clustering," Journal of Classification, Springer;The Classification Society, vol. 22(2), pages 185-201, September.
    9. Serban, Nicoleta & Wasserman, Larry, 2005. "CATS: Clustering After Transformation and Smoothing," Journal of the American Statistical Association, American Statistical Association, vol. 100, pages 990-999, September.
    10. He, Yi & Pan, Wei & Lin, Jizhen, 2006. "Cluster analysis using multivariate normal mixture models to detect differential gene expression with microarray data," Computational Statistics & Data Analysis, Elsevier, vol. 51(2), pages 641-658, November.
    Full references (including those not matched with items on IDEAS)

    Citations

    Citations are extracted by the CitEc Project, subscribe to its RSS feed for this item.
    as


    Cited by:

    1. Liu, Shen & Maharaj, Elizabeth Ann, 2013. "A hypothesis test using bias-adjusted AR estimators for classifying time series in small samples," Computational Statistics & Data Analysis, Elsevier, vol. 60(C), pages 32-49.
    2. Slaets, Leen & Claeskens, Gerda & Hubert, Mia, 2012. "Phase and amplitude-based clustering for functional data," Computational Statistics & Data Analysis, Elsevier, vol. 56(7), pages 2360-2374.
    3. Vilar, J.A. & Alonso, A.M. & Vilar, J.M., 2010. "Non-linear time series clustering based on non-parametric forecast densities," Computational Statistics & Data Analysis, Elsevier, vol. 54(11), pages 2850-2865, November.
    4. Liu, Shen & Maharaj, Elizabeth Ann & Inder, Brett, 2014. "Polarization of forecast densities: A new approach to time series classification," Computational Statistics & Data Analysis, Elsevier, vol. 70(C), pages 345-361.

    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. Liu, Shen & Maharaj, Elizabeth Ann, 2013. "A hypothesis test using bias-adjusted AR estimators for classifying time series in small samples," Computational Statistics & Data Analysis, Elsevier, vol. 60(C), pages 32-49.
    2. Liu, Shen & Maharaj, Elizabeth Ann & Inder, Brett, 2014. "Polarization of forecast densities: A new approach to time series classification," Computational Statistics & Data Analysis, Elsevier, vol. 70(C), pages 345-361.
    3. Allison, David B. & Visscher, Peter M. & Rosa, Guilherme J.M. & Amos, Christopher I., 2009. "Statistical genetics & statistical genomics: Where biology, epistemology, statistics, and computation collide," Computational Statistics & Data Analysis, Elsevier, vol. 53(5), pages 1531-1534, March.
    4. Li, Pai-Ling & Chiou, Jeng-Min, 2011. "Identifying cluster number for subspace projected functional data clustering," Computational Statistics & Data Analysis, Elsevier, vol. 55(6), pages 2090-2103, June.
    5. Pierpaolo D’Urso & Livia Giovanni & Riccardo Massari & Dario Lallo, 2013. "Noise fuzzy clustering of time series by autoregressive metric," METRON, Springer;Sapienza Università di Roma, vol. 71(3), pages 217-243, November.
    6. Edler, Lutz & Lee, Jae Won & Mittlböck, Martina & Niland, Joyce & Victor, Norbert, 2009. "Computational statistics within clinical research," Computational Statistics & Data Analysis, Elsevier, vol. 53(3), pages 583-585, January.
    7. Liu, Xueli & Yang, Mark C.K., 2009. "Simultaneous curve registration and clustering for functional data," Computational Statistics & Data Analysis, Elsevier, vol. 53(4), pages 1361-1376, February.
    8. João A. Bastos & Jorge Caiado, 2014. "Clustering financial time series with variance ratio statistics," Quantitative Finance, Taylor & Francis Journals, vol. 14(12), pages 2121-2133, December.
    9. Vincent, Martin & Hansen, Niels Richard, 2014. "Sparse group lasso and high dimensional multinomial classification," Computational Statistics & Data Analysis, Elsevier, vol. 71(C), pages 771-786.
    10. Umberto Triacca, 2016. "Measuring the Distance between Sets of ARMA Models," Econometrics, MDPI, vol. 4(3), pages 1-11, July.
    11. Li, Pai-Ling & Chiou, Jeng-Min & Shyr, Yu, 2017. "Functional data classification using covariate-adjusted subspace projection," Computational Statistics & Data Analysis, Elsevier, vol. 115(C), pages 21-34.
    12. Juan Vilar & José Vilar & Sonia Pértega, 2009. "Classifying Time Series Data: A Nonparametric Approach," Journal of Classification, Springer;The Classification Society, vol. 26(1), pages 3-28, April.
    13. Mahdi Massahi & Masoud Mahootchi & Alireza Arshadi Khamseh, 2020. "Development of an efficient cluster-based portfolio optimization model under realistic market conditions," Empirical Economics, Springer, vol. 59(5), pages 2423-2442, November.
    14. Marie Chavent & Stéphane Girard & Vanessa Kuentz-Simonet & Benoit Liquet & Thi Nguyen & Jérôme Saracco, 2014. "A sliced inverse regression approach for data stream," Computational Statistics, Springer, vol. 29(5), pages 1129-1152, October.
    15. Beibei Zhang & Rong Chen, 2018. "Nonlinear Time Series Clustering Based on Kolmogorov-Smirnov 2D Statistic," Journal of Classification, Springer;The Classification Society, vol. 35(3), pages 394-421, October.
    16. Mahmoudi, Mohammad Reza, 2021. "A computational technique to classify several fractional Brownian motion processes," Chaos, Solitons & Fractals, Elsevier, vol. 150(C).
    17. De Gregorio, Alessandro & Maria Iacus, Stefano, 2010. "Clustering of discretely observed diffusion processes," Computational Statistics & Data Analysis, Elsevier, vol. 54(2), pages 598-606, February.
    18. Elizabeth Ann Maharaj & Pierpaolo D’Urso & Don Galagedera, 2010. "Wavelet-based Fuzzy Clustering of Time Series," Journal of Classification, Springer;The Classification Society, vol. 27(2), pages 231-275, September.
    19. Tyler Roick & Dimitris Karlis & Paul D. McNicholas, 2021. "Clustering discrete-valued time series," Advances in Data Analysis and Classification, Springer;German Classification Society - Gesellschaft für Klassifikation (GfKl);Japanese Classification Society (JCS);Classification and Data Analysis Group of the Italian Statistical Society (CLADAG);International Federation of Classification Societies (IFCS), vol. 15(1), pages 209-229, March.
    20. Jentsch, Carsten & Pauly, Markus, 2012. "A note on using periodogram-based distances for comparing spectral densities," Statistics & Probability Letters, Elsevier, vol. 82(1), pages 158-164.

    More about this item

    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:eee:csdana:v:53:y:2009:i:4:p:1414-1426. 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: Catherine Liu (email available below). General contact details of provider: http://www.elsevier.com/locate/csda .

    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.