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Volume 12   Issue 2   Year 2017
Projection to Latent Structures as a Strategy for Peptides Microarray Data Analysis

Anisimov D.S., Podlesnykh S.V., Kolosova E.A., Shcherbakov D.N., Petrova V.D., Johnston S.A., Lazarev A.F., Oskorbin N.N., Shapoval A.I., Ryazanov M.A.

Russian-American Anti-Cancer Center, Altai State University, Barnaul, Russia
Center for Innovations in Medicine, Biodesign Institute, Arizona State University, Tempe, Arizona, United States of America
Altai Branch of Blokhin N.N. Russian Cancer Research Center, Barnaul, Russia
Department of Theoretical Cybernetics and Applied Mathematics, Altai State University, Barnaul, Russia

Abstract. Currently various microarrays platforms containing nucleotides, proteins, peptides, glycans and other molecules are used in biomedical  research. Number and density of immobilized molecules on microarrays are constantly increasing. Microarray data handling requires optimization of methods for their analysis. Peptide microarrays data analysis has certain characteristics that require non-conventional statistical methods. In this paper we present the results of antibody repertoire analysis in breast cancer patients sera utilizing microchips containing 330,000 peptides. We investigated methods for space dimension reduction such as projective methods and methods for selection of informative features. We have shown that method of projection to latent structures can detect an effective data dimension, reduce overfitting of the model and increase the quality of object recognition. Accuracy of the experimental results was assessed with the ROC-curve; the best quality was achieved with three latent structures without normalization and reduction of total numbers of peptides.
Key words: microarrays, peptides, normalization, latent variables, clustering, ROC, method of projection to latent structures.
Table of Contents Original Article
Math. Biol. Bioinf.
doi: 10.17537/2017.12.435
published in Russian

Abstract (rus.)
Abstract (eng.)
Full text (rus., pdf)


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