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 corresponding non-saturated image, confirming that the method can effectively fix the saturated spots and enable correct spots quantification.

A novel Gaussian fitting approach for 2D gel electrophoresis saturated protein spots / Natale, Massimo; Caiazzo, A.; Bucci, E. M.; Ficarra, Elisa. - (2012), pp. 335-338. ((Intervento presentato al convegno International Conference on Bioinformatics Models, Methods and Algorithms, BIOINFORMATICS 2012 tenutosi a Vilamoura, Algarve, Portugal nel 1-4 Feb. 2012 [10.5220/0003789803350338].

A novel Gaussian fitting approach for 2D gel electrophoresis saturated protein spots

FICARRA, ELISA
2012-01-01

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 corresponding non-saturated image, confirming that the method can effectively fix the saturated spots and enable correct spots quantification.
International Conference on Bioinformatics Models, Methods and Algorithms, BIOINFORMATICS 2012
Vilamoura, Algarve, Portugal
1-4 Feb. 2012
335
338
Natale, Massimo; Caiazzo, A.; Bucci, E. M.; Ficarra, Elisa
A novel Gaussian fitting approach for 2D gel electrophoresis saturated protein spots / Natale, Massimo; Caiazzo, A.; Bucci, E. M.; Ficarra, Elisa. - (2012), pp. 335-338. ((Intervento presentato al convegno International Conference on Bioinformatics Models, Methods and Algorithms, BIOINFORMATICS 2012 tenutosi a Vilamoura, Algarve, Portugal nel 1-4 Feb. 2012 [10.5220/0003789803350338].
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Utilizza questo identificativo per citare o creare un link a questo documento: https://hdl.handle.net/11380/1240350
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