Analysis of images obtained from two-dimensional gel electrophoresis (2D-GE) is a topic of utmost importance in bioinformatics research, since commercial and academic software available currently has proven to be neither completely effective nor fully automatic, often requiring manual revision 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, the algorithm reveals overexposed areas, where spots may be truncated, and plateau regions caused by smeared and overlapping spots. Next, it reconstructs the correct distribution of pixel values in these overexposed areas and plateau regions, using a two-dimensional least-squares fitting based on a generalized Gaussian distribution. Pixel correction in saturated and smeared spots allows more accurate quantification, providing more reliable image analysis results. The method is validated for processing highly exposed 2D-GE images, comparing reconstructed spots with the corresponding non-saturated image, demonstrating that the algorithm enables correct spot quantification.

A Novel Gaussian Extrapolation Approach for 2D Gel Electrophoresis Saturated Protein Spots / Natale, Massimo; Caiazzo, A.; Bucci, E. M.; Ficarra, Elisa. - In: GENOMICS, PROTEOMICS & BIOINFORMATICS. - ISSN 1672-0229. - 10:6(2012), pp. 336-344. [10.1016/j.gpb.2012.06.005]

A Novel Gaussian Extrapolation Approach for 2D Gel Electrophoresis Saturated Protein Spots

FICARRA, ELISA
2012-01-01

Abstract

Analysis of images obtained from two-dimensional gel electrophoresis (2D-GE) is a topic of utmost importance in bioinformatics research, since commercial and academic software available currently has proven to be neither completely effective nor fully automatic, often requiring manual revision 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, the algorithm reveals overexposed areas, where spots may be truncated, and plateau regions caused by smeared and overlapping spots. Next, it reconstructs the correct distribution of pixel values in these overexposed areas and plateau regions, using a two-dimensional least-squares fitting based on a generalized Gaussian distribution. Pixel correction in saturated and smeared spots allows more accurate quantification, providing more reliable image analysis results. The method is validated for processing highly exposed 2D-GE images, comparing reconstructed spots with the corresponding non-saturated image, demonstrating that the algorithm enables correct spot quantification.
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A Novel Gaussian Extrapolation Approach for 2D Gel Electrophoresis Saturated Protein Spots / Natale, Massimo; Caiazzo, A.; Bucci, E. M.; Ficarra, Elisa. - In: GENOMICS, PROTEOMICS & BIOINFORMATICS. - ISSN 1672-0229. - 10:6(2012), pp. 336-344. [10.1016/j.gpb.2012.06.005]
Natale, Massimo; Caiazzo, A.; Bucci, E. M.; Ficarra, Elisa
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Utilizza questo identificativo per citare o creare un link a questo documento: https://hdl.handle.net/11380/1240393
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