Genomics | Bioinformatics | Gastrointestinal Cancers
Proteomics Signature Profiling (PSP) - a novel contextualization approach for proteomics
Wilson Wen Bin Goh*, Lee YieHou, Ramdzan M Zubaidah, Marek Sergot, Maxey CM Chung, Limsoon Wong
*Corresponding author: Wilson Wen Bin Goh
Department of Computing, Imperial College London, London, UK
Department of Computer Science, National University of Singapore, Singapore, Singapore
F1000Posters 2012, 3: 832 (poster) [English]
International Conference on Intelligent Systems for Molecular Biology (ISMB) 2012, 14 - 16 Jul 2012, P000
Traditional proteomics analysis is plagued by the use of arbitrary thresholds that results in large loss of information. We propose a novel method in proteomics that utilizes all detected proteins. We demonstrate its efficacy in a proteomics screen for five and seven liver cancer patients in the moderate and late stage, respectively.
Although consistency of individual proteins between patients is low, we found the reported proteins tend to hit clusters in a meaningful and informative manner. By extracting this information in the form of a Proteomics Signature Profile (PSP), we confirm that this information is conserved and can be used for (1) clustering of patient samples, (2) identification of significant clusters based on real biological complexes, and (3) overcoming consistency and coverage issues prevalent in proteomics data sets.
No relevant competing interests disclosed.
Wellcome Trust, 83701/Z/07/Z
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