Proteomic feature maps: a new visualization approach in proteomics analysis
Proteomic feature maps: a new visualization approach in proteomics analysis
The different steps of a proteomics analysis workflow generate a plethora of features for each extracted proteomic object (a protein spot in 2D gel electrophoresis (2-DE), or a peptide peak in liquid chromatography–mass spectrometry (LC–MS) analysis). Yet, the joint visualization of multiple object features on 2D gel-like maps is rather limited in currently available proteomics software packages. We introduce a new, simple, and intuitive visualization method that utilizes spheres to represent proteomic objects on proteomic feature maps, and exploits the spheres size and color to provide simultaneous visualization of user-selected feature pairs. Our contribution, a unified and flexible visualization mechanism that can be easily applied at any stage of a 2-DE or a LC–MS based differential proteomics study, is demonstrated and discussed using five representative scenarios. The joint visualization of proteomic object features and their spatial distribution is a powerful tool for inspecting and comparing the proteomics analysis results, attracting the users attention to useful information, such as differential expression trends and patterns, and even assisting in the evaluation and refinement of a proteomics experiment.
644-653
Giannopoulou, E.G.
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Garbis, S.D.
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Vlahou, A.
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Kossida, S.
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Lepouras, G.
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Manolakos, S.
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August 2009
Giannopoulou, E.G.
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Garbis, S.D.
7067fd19-50c9-4d42-9611-f370289470bd
Vlahou, A.
dcb37329-7d10-4bee-b233-41a6153b041f
Kossida, S.
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Lepouras, G.
1cc67bdc-9aee-455f-b5d9-e716631af3ad
Manolakos, S.
abaebc74-6dee-47b3-ba0f-1543695ea00b
Giannopoulou, E.G., Garbis, S.D., Vlahou, A., Kossida, S., Lepouras, G. and Manolakos, S.
(2009)
Proteomic feature maps: a new visualization approach in proteomics analysis.
Journal of Biomedical Informatics, 42 (4), .
(doi:10.1016/j.jbi.2009.01.007).
(PMID:19535004)
Abstract
The different steps of a proteomics analysis workflow generate a plethora of features for each extracted proteomic object (a protein spot in 2D gel electrophoresis (2-DE), or a peptide peak in liquid chromatography–mass spectrometry (LC–MS) analysis). Yet, the joint visualization of multiple object features on 2D gel-like maps is rather limited in currently available proteomics software packages. We introduce a new, simple, and intuitive visualization method that utilizes spheres to represent proteomic objects on proteomic feature maps, and exploits the spheres size and color to provide simultaneous visualization of user-selected feature pairs. Our contribution, a unified and flexible visualization mechanism that can be easily applied at any stage of a 2-DE or a LC–MS based differential proteomics study, is demonstrated and discussed using five representative scenarios. The joint visualization of proteomic object features and their spatial distribution is a powerful tool for inspecting and comparing the proteomics analysis results, attracting the users attention to useful information, such as differential expression trends and patterns, and even assisting in the evaluation and refinement of a proteomics experiment.
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e-pub ahead of print date: 4 February 2009
Published date: August 2009
Organisations:
Cancer Sciences
Identifiers
Local EPrints ID: 395421
URI: http://eprints.soton.ac.uk/id/eprint/395421
ISSN: 1532-0464
PURE UUID: 80857492-c9d2-4c6a-8320-aa27097cfe8f
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Date deposited: 18 Jul 2016 10:19
Last modified: 21 Aug 2025 10:53
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Contributors
Author:
E.G. Giannopoulou
Author:
S.D. Garbis
Author:
A. Vlahou
Author:
S. Kossida
Author:
G. Lepouras
Author:
S. Manolakos
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