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J Proteome Res. 2012 May 4;11(5):2955-67. doi: 10.1021/pr300038b. Epub 2012 Apr 21.

Multimodel pathway enrichment methods for functional evaluation of expression regulation.

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  • 1Department of Immunotechnology, Lund University Biomedical Centre D13, SE-221 84 Lund, Sweden.

Abstract

Functional analysis of quantitative expression data is becoming common practice within the proteomics and transcriptomics fields; however, a gold standard for this type of analysis has yet not emerged. To grasp the systemic changes in biological systems, efficient and robust methods are needed for data analysis following expression regulation experiments. We discuss several conceptual and practical challenges potentially hindering the emergence of such methods and present a novel method, called FEvER, that utilizes two enrichment models in parallel. We also present analysis of three disparate differential expression data sets using our method and compare our results to other established methods. With many useful features such as pathway hierarchy overview, we believe the FEvER method and its software implementation will provide a useful tool for peers in the field of proteomics. Furthermore, we show that the method is also applicable to other types of expression data.

PMID:
22471554
[PubMed - indexed for MEDLINE]
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