Singular Spectrum Analysis of Gene Expression Profiles of Early <i>Drosophila embryo</i>: Exponential-in-Distance Patterns

Alexandrov, T.; Golyandina, N.; Spirov, A.

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Research Letters in Signal Processing
Volume 2008 (2008), Article ID 825758, 5 pages
doi:10.1155/2008/825758

Research Letter

Singular Spectrum Analysis of Gene Expression Profiles of Early Drosophila embryo: Exponential-in-Distance Patterns

T. Alexandrov,¹ N. Golyandina,² and A. Spirov³

¹Center for Industrial Mathematics, Department of Mathematics, University of Bremen, 28334 Bremen, Germany
²Department of Mathematics and Mechanics, St. Petersburg State University, 198504 St. Petersburg, Russia
³Department of Applied Mathematics and Statistics and Center for Developmental Genetics, State University of New York, Stony Brook, NY 11794, USA

Received 19 May 2008; Accepted 26 June 2008

Academic Editor: Andreas Jakobsson

Copyright © 2008 T. Alexandrov et al. This is an open access article distributed under the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.

Abstract

We present investigation of gene expression profiles by means of singular spectrum analysis (SSA). The biological problem under investigation is the decomposition of bicoid protein profiles of Drosophila melanogaster into the sum of a signal and noise, where the former consists of an exponential-in-distance pattern and is close to constant nonspecific component, or “background.” The signal processing problems addressed are (i) trend extraction from a noisy signal, (ii) batch processing of similar data, and (iii) analytical approximation of the signal components by the sum of exponential and constant-like functions. The proposed methods are evaluated on the given 17 series.