Visualizing Meta-Features in Proteomic Maps

被引:1
|
作者
Giannopoulou, Eugenia G. [1 ,3 ]
Lepouras, George [3 ]
Manolakos, Elias S. [2 ]
机构
[1] Weill Cornell Med Coll, HRH Prince Alwaleed Bin Talal Bin Abdulaziz Alsau, New York, NY 10021 USA
[2] Univ Athens, Dept Informat & Telecommun, Athens, Greece
[3] Univ Peloponnese, Dept Comp Sci & Technol, Tripolis, Greece
来源
BMC BIOINFORMATICS | 2011年 / 12卷
关键词
2-DIMENSIONAL GEL-ELECTROPHORESIS; MASS-SPECTROMETRY; CHROMATOGRAPHY; PATHWAYS; CANCER; TOOL;
D O I
10.1186/1471-2105-12-308
中图分类号
Q5 [生物化学];
学科分类号
071010 ; 081704 ;
摘要
Background: The steps of a high-throughput proteomics experiment include the separation, differential expression and mass spectrometry-based identification of proteins. However, the last and more challenging step is inferring the biological role of the identified proteins through their association with interaction networks, biological pathways, analysis of the effect of post-translational modifications, and other protein-related information. Results: In this paper, we present an integrative visualization methodology that allows combining experimentally produced proteomic features with protein meta-features, typically coming from meta-analysis tools and databases, in synthetic Proteomic Feature Maps. Using three proteomics analysis scenarios, we show that the proposed visualization approach is effective in filtering, navigating and interacting with the proteomics data in order to address visually challenging biological questions. The novelty of our approach lies in the ease of integration of any user-defined proteomic features in easy-to-comprehend visual representations that resemble the familiar 2D-gel images, and can be adapted to the user's needs. The main capabilities of the developed VIP software, which implements the presented visualization methodology, are also highlighted and discussed. Conclusions: By using this visualization and the associated VIP software, researchers can explore a complex heterogeneous proteomics dataset from different perspectives in order to address visually important biological queries and formulate new hypotheses for further investigation. VIP is freely available at http://pelopas.uop.gr/similar to egian/VIP/index.html.
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页数:13
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