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Briefings in Functional Genomics and Proteomics Advance Access published online on July 19, 2008
Briefings in Functional Genomics and Proteomics, doi:10.1093/bfgp/eln033
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©The Author 2008. Published by Oxford University Press. All rights reserved. For permissions, please email: journals.permissions@oxfordjournals.org

Uncharacterized/hypothetical proteins in biomedical ‘omics’ experiments: is novelty being swept under the carpet?

Krzysztof Pawlowski

Corresponding author. Krzysztof Pawlowski, Nencki Institute of Experimental Biology, PAS, ul. Pasteura 3, 02-093 Warszawa, Poland and Warsaw University of Life Sciences, Warszawa, Poland. Tel: +48 22 5892 222; Fax: +48 22 822 53 42. E-mail: k.pawlowski{at}nencki.gov.pl

Many ‘omics’ studies, gene expression microarray experiments in particular, aim at charting the molecular mechanisms of physiology, disease and drug response. This short review discusses the bias present in many such studies whereas the focus is set on the well understood and established molecular scenarios. The under-reporting rate of ‘hypothetical’ or uncharacterized genes and proteins, differentially regulated in disease context, is assessed here. Reasons for this bias are discussed. Particular examples from the genomics studies on respiratory diseases are presented. This review aims at increasing awareness of the unexplored genomics data and proposes remedies in order to refocus genomics studies on the less-charted territories of the genome, transcriptome and proteome. It is suggested that routine use of function prediction methods in conjunction with omics analyses may allow better interpretation of the data, and facilitate discovery of true novelty.

Keywords: gene expression analysis, hypothetical proteins, uncharacterized genes, biomedicine, function prediction


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