Evaluation of two-dimensional gel electrophoresis maps by local tangent space alignment: An application to neuroproteomics

Saveria Mazzara, Antonio Conti, Stefano Olivieri, Sandro Iannaccone, Massimo Alessio, Sergio Cerutti, Linda Pattini

Research output: Chapter in Book/Report/Conference proceedingConference contribution

Abstract

Proteomic analysis may be useful to investigate disorders of the central nervous system, in order to explore the protein content of cells and of biological fluids in respect of the onset and evolution of diseases. Today, one of the most used proteomic approach includes the separation and visualization of proteins by means of two-dimensional gel electrophoresis (2DE). However the development of fully automatic strategies in extracting information from gel images is still a challenging task. In this paper we applied a computational strategy to the aim of obtaining a compact representation of the original data. This method was applied to an experimental protocol including two different clinical groups of amyotrophic lateral sclerosis (ALS) and peripheral neuropathy patients : 32 2DE maps generated from cerebrospinal fluid (24 pathologic and 8 control subjects) were processed. Quantitative features were extracted to describe each image and dealt with the dimension reduction technique of local tangent space alignment (LTSA). The discovered low-dimensional structure allows to see the gel of the dataset as separable, according to their clinical conditions, showing the informativeness of the adopted descriptors and providing the bases for classification of this kind of samples.

Original languageEnglish
Title of host publication8th IEEE International Conference on BioInformatics and BioEngineering, BIBE 2008
DOIs
Publication statusPublished - 2008
Event8th IEEE International Conference on BioInformatics and BioEngineering, BIBE 2008 - Athens, Greece
Duration: Oct 8 2008Oct 10 2008

Other

Other8th IEEE International Conference on BioInformatics and BioEngineering, BIBE 2008
CountryGreece
CityAthens
Period10/8/0810/10/08

Fingerprint

Electrophoresis, Gel, Two-Dimensional
Electrophoresis
Proteomics
Gels
Central Nervous System Diseases
Amyotrophic Lateral Sclerosis
Peripheral Nervous System Diseases
Cerebrospinal fluid
Proteins
Cerebrospinal Fluid
Neurology
Visualization
Fluids
Datasets

ASJC Scopus subject areas

  • Biotechnology
  • Bioengineering

Cite this

Mazzara, S., Conti, A., Olivieri, S., Iannaccone, S., Alessio, M., Cerutti, S., & Pattini, L. (2008). Evaluation of two-dimensional gel electrophoresis maps by local tangent space alignment: An application to neuroproteomics. In 8th IEEE International Conference on BioInformatics and BioEngineering, BIBE 2008 [4696672] https://doi.org/10.1109/BIBE.2008.4696672

Evaluation of two-dimensional gel electrophoresis maps by local tangent space alignment : An application to neuroproteomics. / Mazzara, Saveria; Conti, Antonio; Olivieri, Stefano; Iannaccone, Sandro; Alessio, Massimo; Cerutti, Sergio; Pattini, Linda.

8th IEEE International Conference on BioInformatics and BioEngineering, BIBE 2008. 2008. 4696672.

Research output: Chapter in Book/Report/Conference proceedingConference contribution

Mazzara, S, Conti, A, Olivieri, S, Iannaccone, S, Alessio, M, Cerutti, S & Pattini, L 2008, Evaluation of two-dimensional gel electrophoresis maps by local tangent space alignment: An application to neuroproteomics. in 8th IEEE International Conference on BioInformatics and BioEngineering, BIBE 2008., 4696672, 8th IEEE International Conference on BioInformatics and BioEngineering, BIBE 2008, Athens, Greece, 10/8/08. https://doi.org/10.1109/BIBE.2008.4696672
Mazzara S, Conti A, Olivieri S, Iannaccone S, Alessio M, Cerutti S et al. Evaluation of two-dimensional gel electrophoresis maps by local tangent space alignment: An application to neuroproteomics. In 8th IEEE International Conference on BioInformatics and BioEngineering, BIBE 2008. 2008. 4696672 https://doi.org/10.1109/BIBE.2008.4696672
Mazzara, Saveria ; Conti, Antonio ; Olivieri, Stefano ; Iannaccone, Sandro ; Alessio, Massimo ; Cerutti, Sergio ; Pattini, Linda. / Evaluation of two-dimensional gel electrophoresis maps by local tangent space alignment : An application to neuroproteomics. 8th IEEE International Conference on BioInformatics and BioEngineering, BIBE 2008. 2008.
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