Biopolym. Cell. 2013; 29(6):521-526.
http://dx.doi.org/10.7124/bc.000844
Bioinformatics
Evaluation criteria of rat hepatocytes transcriptome analysis under the influence of interferon alpha by DNA microarray
1Kuklin A. V., 1Tokovenko B. T., 1Obolenska M. Yu.
  1. Institute of Molecular Biology and Genetics, NAS of Ukraine
    150, Akademika Zabolotnoho Str., Kyiv, Ukraine, 03680

Abstract

The changes induced in transcriptome of rat hepatocytes treated with interferon alpha (IFN) during three and six hours were analyzed by DNA microarray. Aim. To conduct a stepwise analysis of the results of microarray experiment and to determine whether they meet/fail to the conventional requirements. Methods. The files obtained after scanning microarrays were subjected to the analysis in statistical environment R by Bioconductor’s packages «affy», «simpleaffy», «affyPLM» and BRB Array Tools software for paired T-test. Results. All microarrays had quality metrics lying within recommended ranges, passed quality control, were normalized and are comparable with each other. The T-test revealed 28 and 124 differentially expressed genes after three and six hours of cells cultivation with IFNα , respectively. Conclusions. The obtained data meet the conventional criteria of quality and are applicable for further evaluation of their biological significance. The R-codes used in this study can be used for the analysis of the microarrays data.
Keywords: DNA microarrays, interferon alpha, statistical environment R, Bioconductor, normalization
Full text: (PDF, in Ukrainian)

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