Correcting for the bias due to expression specificity improves the estimation of constrained evolution of expression between mouse and human.

Bioinformatics
Barbara PiaseckaSven Bergmann

Abstract

Comparative analyses of gene expression data from different species have become an important component of the study of molecular evolution. Thus methods are needed to estimate evolutionary distances between expression profiles, as well as a neutral reference to estimate selective pressure. Divergence between expression profiles of homologous genes is often calculated with Pearson's or Euclidean distance. Neutral divergence is usually inferred from randomized data. Despite being widely used, neither of these two steps has been well studied. Here, we analyze these methods formally and on real data, highlight their limitations and propose improvements. It has been demonstrated that Pearson's distance, in contrast to Euclidean distance, leads to underestimation of the expression similarity between homologous genes with a conserved uniform pattern of expression. Here, we first extend this study to genes with conserved, but specific pattern of expression. Surprisingly, we find that both Pearson's and Euclidean distances used as a measure of expression similarity between genes depend on the expression specificity of those genes. We also show that the Euclidean distance depends strongly on data normalization. Next, we show that the ran...Continue Reading

References

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Citations

Apr 13, 2013·BMC Genomics·Maurice H T LingSteven X Ge
Oct 12, 2012·PloS One·Lydie ChevalAlain Doucet
Mar 13, 2014·Genome Biology and Evolution·Igor B RogozinEugene V Koonin
Jul 13, 2013·Proceedings of the National Academy of Sciences of the United States of America·Andrew R OsterburgGeorge F Babcock
Feb 20, 2016·Briefings in Bioinformatics·Nadezda Kryuchkova-Mostacci, Marc Robinson-Rechavi
Oct 27, 2016·Journal of Experimental Zoology. Part B, Molecular and Developmental Evolution·Hang RuanXun Gu
Dec 29, 2016·PLoS Computational Biology·Nadezda Kryuchkova-Mostacci, Marc Robinson-Rechavi
May 4, 2013·Breeding Science·Miyako Kusano, Atsushi Fukushima
Apr 14, 2015·Journal of Experimental Zoology. Part B, Molecular and Developmental Evolution·Julien RouxMarc Robinson-Rechavi

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Methods Mentioned

BETA
RNA-seq

Software Mentioned

Ensembl
LOESS
gcrma R package

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