Evaluation of combining several statistical methods with a flexible cutoff for identifying differentially expressed genes in pairwise comparison of EST sets

Lindlöf, AngelicaHögskolan i Skövde,Institutionen för kommunikation och information,Forskningscentrum för Systembiologi,Bioinformatik, Bioinformatics (author)

The detection of differentially expressed genes from EST data is of importance for the discovery of potential biological or pharmaceutical targets, especially when studying biological processes in less characterized organisms and where large-scale microarrays are not an option. We present a comparison of ﬁve different statistical methods for identifying up-regulated genes through pairwise comparison of EST sets, where one of the sets is generated from a treatment and the other one serves as a control. In addition, we speciﬁcally address situations where the sets are relatively small (~2,000– 10,000 ESTs) and may differ in size. The methods were tested on both simulated and experimentally derived data, and compared to a collection of cold stress induced genes identiﬁed by microarrays. We found that combining the method pro- posed by Audic and Claverie with Fisher’s exact test and a method based on calculating the difference in relative frequency was the best combination for maximizing the detection of up-regulated genes. We also introduced the use of a ﬂexible cutoff, which takes the size of the EST sets into consideration. This could be considered as an alternative to a static cutoff. Finally, the detected genes showed a low overlap with those identiﬁed by microarrays, which indicates, as in previous studies, low overall concordance between the two platforms.

Bräutigam, MarcusGöteborg University (author)
Chawade, AakashGöteborg University (author)
Olsson, OlofGöteborg University (author)
Olsson, Björn,1962-Högskolan i Skövde,Institutionen för kommunikation och information,Forskningscentrum för Systembiologi,Bioinformatik, Bioinformatics,Bioinformatik, Bioinformatics(Swepub:his)olsb (author)
Högskolan i SkövdeInstitutionen för kommunikation och information (creator_code:org_t)

In:Bioinformatics and Biology Insights: Libertas Academica2, s. 215-2371177-9322

By the author/editor: Lindlöf, Angelic ...; Bräutigam, Marcu ...; Chawade, Aakash; Olsson, Olof; Olsson, Björn, 1 ...

About the subject

NATURAL SCIENCES: NATURAL SCIENCES; and Biological Scien ...; and Bioinformatics a ...

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