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Identification of dominant signaling pathways from proteomics expression data
Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology.
Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology.
Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology.
Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology.
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2008 (English)In: Journal of Proteomics, ISSN 1874-3919, Vol. 71, no 1, 89-96 p.Article in journal (Refereed) Published
Abstract [en]

The availability of the results of high-throughput analyses coming from 'omic' technologies has been one of the major driving forces of pathway biology. Analytical pathway biology strives to design a 'pathway search engine', where the input is the 'omic' data and the output is the list of activated or dominant pathways in a given sample. Here we describe the first attempt to design and validate such a pathway search engine using as input expression proteomics data. The engine represents a specific workflow in computational tools developed originally for mRNA analysis (BMC Bioinformatics 2006, 7 (Suppl 2), S13). Using our own datasets as well as data from recent proteomics literature we demonstrate that different dominant pathways (EGF, TGF(beta), stress, and Fas pathways) can be correctly identified even from limited datasets. Pathway search engines can find application in a variety of proteomics-related fields, from fundamental molecular biology to search for novel types of disease biomarkers.

Place, publisher, year, edition, pages
2008. Vol. 71, no 1, 89-96 p.
Keyword [en]
Proteins, Genes, Protein identification, Tandem mass spectrometry, Pathway analysis
National Category
Biochemistry and Molecular Biology
Identifiers
URN: urn:nbn:se:uu:diva-107094DOI: 10.1016/j.jprot.2008.01.004ISI: 000260744300008OAI: oai:DiVA.org:uu-107094DiVA: diva2:227654
Available from: 2009-07-16 Created: 2009-07-16 Last updated: 2009-07-16Bibliographically approved

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