A nitty-gritty aspect of correlation and network inference from gene expression data.

Biology Direct
Lev B Klebanov, Andrei Yu Yakovlev

Abstract

All currently available methods of network/association inference from microarray gene expression measurements implicitly assume that such measurements represent the actual expression levels of different genes within each cell included in the biological sample under study. Contrary to this common belief, modern microarray technology produces signals aggregated over a random number of individual cells, a "nitty-gritty" aspect of such arrays, thereby causing a random effect that distorts the correlation structure of intra-cellular gene expression levels. This paper provides a theoretical consideration of the random effect of signal aggregation and its implications for correlation analysis and network inference. An attempt is made to quantitatively assess the magnitude of this effect from real data. Some preliminary ideas are offered to mitigate the consequences of random signal aggregation in the analysis of gene expression data. Resulting from the summation of expression intensities over a random number of individual cells, the observed signals may not adequately reflect the true dependence structure of intra-cellular gene expression levels needed as a source of information for network reconstruction. Whether the reported effect ...Continue Reading

References

Jun 28, 2002·Cancer Cell·Dinesh SinghWilliam R Sellers
Jun 17, 2003·Proceedings of the National Academy of Sciences of the United States of America·G A HeldY Tu
Mar 22, 2005·Nature Genetics·Katia BassoAndrea Califano
May 21, 2005·BMC Bioinformatics·Xing QiuNdrei Yakovlev
Apr 13, 2007·Biology Direct·Lev Klebanov, Andrei Yakovlev
Oct 3, 2007·PLoS Genetics·Jeffrey T Leek, John D Storey
May 9, 2008·Journal of Bioinformatics and Computational Biology·Lev KlebanovAndrei Yakovlev

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Citations

Feb 18, 2014·BMC Systems Biology·Gabriel N TekuMauno Vihinen
Oct 20, 2009·Molecular and Cellular Probes·Adrian E PlattsStephen A Krawetz

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