Structural matching of 2D electrophoresis gels using deformed graphs

Authors:
Alexandre Noma;Alvaro Pardo;Roberto M. Cesar, Jr.
Affiliations:
Institute of Mathematics and Statistics - IME, University of São Paulo - USP, Rua do Matão, 1010, 05508-090 São Paulo, Brazil;Department of Electrical Engineering, Faculty of Engineering and Technologies, Catholic University of Uruguay, Av. 8 de octubre 2801, CP11600 Montevideo, Uruguay;Institute of Mathematics and Statistics - IME, University of São Paulo - USP, Rua do Matão, 1010, 05508-090 São Paulo, Brazil
Venue:
Pattern Recognition Letters
Year:
2011

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Abstract

2D electrophoresis is a well-known method for protein separation which is extremely useful in the field of proteomics. Each spot in the image represents a protein accumulation and the goal is to perform a differential analysis between pairs of images to study changes in protein content. It is thus necessary to register two images by finding spot correspondences. Although it may seem a simple task, generally, the manual processing of this kind of images is very cumbersome, especially when strong variations between corresponding sets of spots are expected (e.g. strong non-linear deformations and outliers). In order to solve this problem, this paper proposes a new quadratic assignment formulation together with a correspondence estimation algorithm based on graph matching which takes into account the structural information between the detected spots. Each image is represented by a graph and the task is to find a maximum common subgraph. Successful experimental results using real data are presented, including an extensive comparative performance evaluation with ground-truth data.