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Information Bottleneck for Pathway-Centric Gene Expression Analysis

  • Conference paper
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Pattern Recognition (GCPR 2014)

Part of the book series: Lecture Notes in Computer Science ((LNIP,volume 8753))

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Abstract

While DNA microarrays enable us to conveniently measure expression profiles in the scope of thousands of genes, the subsequent association studies typically suffer from a tremendous imbalance between number of variables (genes) and observations (subjects). Even more so, each gene is heavily perturbed by noise which prevents any meaningful analysis on the single-gene level [6]. Hence, the focus shifted to pathways as groups of functionally related genes [4], in the hope that aggregation potentiates the underlying signal. Technically, this leads to a problem of feature extraction which was previously tackled by principal component analysis [5]. We reformulate the task using an extension of the Meta-Gaussian Information Bottleneck method as a means to compress a gene set while preserving information about a relevance variable. This opens up new possibilities, enabling us to make use of clinical side information in order to uncover hidden characteristics in the data.

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Notes

  1. 1.

    \((A, \varSigma _\xi )\) and \((A^*, I_p)\) are equivalent under \(\mathcal {L}\) with a linear transformation between \(A\) and \(A^*\).

  2. 2.

    http://www.genome.jp/kegg/

  3. 3.

    http://www.broadinstitute.org/gsea/msigdb/

References

  1. Baffert, F., Thurston, G., Rochon-Duck, M., Le, T., Brekken, R., McDonald, D.M.: Age-related changes in vascular endothelial growth factor dependency and angiopoietin-1-induced plasticity of adult blood vessels. Circ. Res. 94(984), 984–992 (2004)

    Article  Google Scholar 

  2. Castle, S.C.: Clinical relevance of age-related immune dysfunction. Clin. Infect. Dis. 31(2), 578–585 (2000)

    Article  Google Scholar 

  3. Chechik, G., Globerson, A., Tishby, N., Weiss, Y.: Information Bottleneck for Gaussian Variables. J. Mach. Learn. Res. 6, 165–188 (2005)

    MathSciNet  MATH  Google Scholar 

  4. Curtis, R.K., Oresic, M., Vidal-Puig, A.: Pathways to the analysis of microarray data. Trends Biotechnol. 23(8), 429–435 (2005)

    Article  Google Scholar 

  5. Drier, Y., Sheffer, M., Domany, E.: Pathway-based personalized analysis of cancer. Proc. Natl. Acad. Sci. 110(16), 6388–6393 (2013)

    Article  Google Scholar 

  6. Ein-Dor, L., Zuk, O., Domany, E.: Thousands of samples are needed to generate a robust gene list for predicting outcome in cancer. Proc. Natl. Acad. Sci. 103, 5923–5928 (2006)

    Article  Google Scholar 

  7. Elsaleh, H., Joseph, D., Grieu, F., Zeps, N., Spry, N., Iacopetta, B.: Association of tumour site and sex with survival benefit from adjuvant chemotherapy in colorectal cancer. Lancet 355(9217), 1745–1750 (2000)

    Article  Google Scholar 

  8. Globerson, A., Tishby, N.: On the Optimality of the Gaussian Information Bottleneck Curve. The Hebrew University of Jerusalem. Technical report (2004)

    Google Scholar 

  9. Hoff, P.D.: Extending the rank likelihood for semiparametric copula estimation. Ann. Appl. Stat. 1(1), 265–283 (2007)

    Article  MathSciNet  MATH  Google Scholar 

  10. Licastro, F., Candore, G., Lio, D., Porcellini, E., Colonna-Romano, G., Franceschi, C., Caruso, C.: Innate immunity and inflammation in ageing: a key for understanding age-related diseases. Immun. Ageing 2(1), 8 (2005)

    Article  Google Scholar 

  11. Migliore, L., Coppede, F.: Genetic and environmental factors in cancer and neurodegenerative diseases. Mutat. Res. 512(2–3), 135–153 (2002)

    Article  Google Scholar 

  12. Pal, S.K., Hurria, A.: Impact of age, sex, and comorbidity on cancer therapy and disease progression. J. Clin. Oncol. 28(26), 4086–4093 (2010)

    Article  Google Scholar 

  13. Rey, M., Roth, V.: Meta-gaussian information bottleneck. Adv. Neural Inf. Process. Syst. 25, 1925–1933 (2012)

    Google Scholar 

  14. Sheffer, M., Bacolod, M.D., Zuk, O., Giardina, S.F., Pincas, H., Barany, F., Paty, P.B., Gerald, W.L., Notterman, D.A., Domany, E.: Association of survival and disease progression with chromosomal instability: a genomic exploration of colorectal cancer. Proc. Natl. Acad. Sci. 106(17), 7131–7136 (2009)

    Article  Google Scholar 

  15. Sklar, A.: Fonctions de répartition à n dimensions et leurs marges. Université Paris (1959)

    Google Scholar 

  16. Söderlund, S., Granath, F., Broström, O., Karlen, P., Löfberg, R., Ekbom, A., Askling, J.: Inflammatory bowel disease confers a lower risk of colorectal cancer to females than to males. Gastroenterology 138(5), 1697–1703 (2010)

    Article  Google Scholar 

  17. Tishby, N., Pereira, F.C., Bialek, W.: The information bottleneck method. In: Proceedings of the 37th Annual Allerton Conference on Communication, Control and Computing, pp. 368–377 (1999)

    Google Scholar 

  18. Wullschleger, S., Loewith, R., Hall, M.N.: TOR signaling in growth and metabolism. Cell 124(3), 471–484 (2006)

    Article  Google Scholar 

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Authors and Affiliations

  1. Department of Mathematics and Computer Science, University of Basel, Basel, Switzerland

    David Adametz, Mélanie Rey & Volker Roth

Authors
  1. David Adametz
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  2. Mélanie Rey
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  3. Volker Roth
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Corresponding author

Correspondence to David Adametz .

Editor information

Editors and Affiliations

  1. Department of Mathematics and Computer Science, University of Münster, Münster, Germany

    Xiaoyi Jiang

  2. Computer Science Department 5, University of Erlangen-Nürnberg, Erlangen, Germany

    Joachim Hornegger

  3. Department of Computer Science, University of Kiel, Kiel, Germany

    Reinhard Koch

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Adametz, D., Rey, M., Roth, V. (2014). Information Bottleneck for Pathway-Centric Gene Expression Analysis. In: Jiang, X., Hornegger, J., Koch, R. (eds) Pattern Recognition. GCPR 2014. Lecture Notes in Computer Science(), vol 8753. Springer, Cham. https://doi.org/10.1007/978-3-319-11752-2_7

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  • DOI: https://doi.org/10.1007/978-3-319-11752-2_7

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  • Publisher Name: Springer, Cham

  • Print ISBN: 978-3-319-11751-5

  • Online ISBN: 978-3-319-11752-2

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