A NOVEL GAUSSIAN FITTING APPROACH FOR 2D GEL ELECTROPHORESIS SATURATED PROTEIN SPOTS

Massimo Natale, Alfonso Caiazzo, Enrico M. Bucci, Elisa Ficarra

Abstract

Analysis of 2D-GE images is a hot topic in bioinformatics research, since currently available commercial and academic software has proven to be not really effective and not completely automatic, often requiring manual revision of spots detection and refinement of computer generated matches. In this work, we present an effective technique for the detection and the reconstruction of over-saturated protein spots. Firstly, it reveals overexposed areas where spots may be truncated, and plateau regions caused by smeared and overlapped spots. As next, the correct distribution of pixel values in the overexposed areas and plateau regions is recovered by a two-dimensional fitting based on a generalized Gaussian distribution approximating the spots volume. Pixel correction according to the generalized Gaussian curve in saturated and smeared spots allows more accurate quantifications, providing more reliable image analysis results. As validation, we process highly exposed 2D-GE image, containing saturate spots, with respect to the corre-sponding non-saturated image, confirming that the method can effectively fix the saturated spots and enable correct spots quantification.

References

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Paper Citation


in Harvard Style

Natale M., Caiazzo A., M. Bucci E. and Ficarra E. (2012). A NOVEL GAUSSIAN FITTING APPROACH FOR 2D GEL ELECTROPHORESIS SATURATED PROTEIN SPOTS . In Proceedings of the International Conference on Bioinformatics Models, Methods and Algorithms - Volume 1: BIOINFORMATICS, (BIOSTEC 2012) ISBN 978-989-8425-90-4, pages 335-338. DOI: 10.5220/0003789803350338


in Bibtex Style

@conference{bioinformatics12,
author={Massimo Natale and Alfonso Caiazzo and Enrico M. Bucci and Elisa Ficarra},
title={A NOVEL GAUSSIAN FITTING APPROACH FOR 2D GEL ELECTROPHORESIS SATURATED PROTEIN SPOTS},
booktitle={Proceedings of the International Conference on Bioinformatics Models, Methods and Algorithms - Volume 1: BIOINFORMATICS, (BIOSTEC 2012)},
year={2012},
pages={335-338},
publisher={SciTePress},
organization={INSTICC},
doi={10.5220/0003789803350338},
isbn={978-989-8425-90-4},
}


in EndNote Style

TY - CONF
JO - Proceedings of the International Conference on Bioinformatics Models, Methods and Algorithms - Volume 1: BIOINFORMATICS, (BIOSTEC 2012)
TI - A NOVEL GAUSSIAN FITTING APPROACH FOR 2D GEL ELECTROPHORESIS SATURATED PROTEIN SPOTS
SN - 978-989-8425-90-4
AU - Natale M.
AU - Caiazzo A.
AU - M. Bucci E.
AU - Ficarra E.
PY - 2012
SP - 335
EP - 338
DO - 10.5220/0003789803350338