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Differential Shannon entropy and differential coefficient of variation: alternatives and augmentations to differential expression in the search for disease-related genes
University of Tennessee, Knoxville, USA.
University of Tennessee, Knoxville, USA.
National Institute for Computational Sciences, Oak Ridge, Tennessee, USA.
Linköpings universitet, Institutionen för klinisk och experimentell medicin, Avdelningen för cellbiologi. Linköpings universitet, Hälsouniversitetet.
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2014 (engelsk)Inngår i: International journal of computational biology and drug design, ISSN 1756-0756, Vol. 7, nr 2-3, s. 183-94Artikkel i tidsskrift (Fagfellevurdert) Published
Abstract [en]

Differential expression has been a standard tool for analysing case-control transcriptomic data since the advent of microarray technology. It has proved invaluable in characterising the molecular mechanisms of disease. Nevertheless, the expression profile of a gene across samples can be perturbed in ways that leave the expression level unaltered, while a biological effect is nonetheless present. This paper describes and analyses differential Shannon entropy and differential coefficient of variation, two alternate techniques for identifying genes of interest. Ontological analysis across 16 human disease datasets demonstrates that these alternatives are effective at identifying disease-related genes not found by mere differential expression alone. Because the two alternate techniques are based on somewhat different mathematical formulations, they tend to produce somewhat different gene lists. Moreover, each may pinpoint genes completely overlooked by the other. Thus, measures of entropy and variation can be used to replace or better yet augment standard differential expression computations.

sted, utgiver, år, opplag, sider
InderScience Publishers, 2014. Vol. 7, nr 2-3, s. 183-94
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URN: urn:nbn:se:liu:diva-109422DOI: 10.1504/IJCBDD.2014.061656PubMedID: 24878729OAI: oai:DiVA.org:liu-109422DiVA, id: diva2:738329
Tilgjengelig fra: 2014-08-18 Laget: 2014-08-18 Sist oppdatert: 2019-02-11bibliografisk kontrollert

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