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Algorithm for reducing errors in transcriptome analysis

Date:
August 18, 2014
Source:
Biogerontology Research Foundation
Summary:
Researchers are proposing a new concept for signalome-wide analysis of changes in intracellular pathways, called OncoFinder, which allows for accurate and robust cross-platform analysis of gene expression data. This new technique will allow scientists to derive useful information from and compare the hundreds of thousands of data sets obtained using legacy equipment as well as data sets obtained from biological samples preserved in paraffin blocks and partially-degraded samples.

Scientists from the Biogerontology Research Foundation (BGRF), a UK-based charity founded to support aging research and address the challenges of a rapidly aging population, propose a new concept for signalome-wide analysis of changes in intracellular pathways, called OncoFinder, which allows for accurate and robust cross-platform analysis of gene expression data. This new technique will allow scientists to derive useful information from and compare the hundreds of thousands of data sets obtained using legacy equipment as well as data sets obtained from biological samples preserved in paraffin blocks and partially-degraded samples.

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The original research, published in the journal Frontiers in Molecular Biosciences, shows that the OncoFinder method significantly reduces errors introduced by transcriptome-wide experimental techniques. Scientists compared gene expression data for the same biological samples obtained by both next generation sequencing (NGS) and microarray methods, finding that these different techniques have almost no correlation between the gene expression values for all datasets analysed. In contrast, when the OncoFinder algorithm is applied to the data, a clear correlation between next generation sequencing and microarray gene expression datasets was seen.

"For several years the potential for the use of gene expression data in research and clinical applications has been underappreciated due to the inconsistency of the data coming from the various types of equipment. There is just too much variation and complexity when comparing the massive number of individual genes. But when this complexity is reduced and the gene expression is mapped onto signalling pathways, we can evaluate the pathway activation drift and analyse the changes and transitions much more effectively. The OncoFinder algorithm enables scientists to characterise the functional states of transcriptomes more accurately than before and we hope that this will become a method of choice in genetics, physiology, biomedicine and molecular diagnostics," said Alex Zhavoronkov, PhD, director of the BGRF and co-author of the study.


Story Source:

The above story is based on materials provided by Biogerontology Research Foundation. Note: Materials may be edited for content and length.


Journal Reference:

  1. Anton A. Buzdin, Alex Zhavoronkov, Mikhail Korzinkin, Sergey A Roumiantsev, Alexander M Aliper, Larisa S. Venkova, Philip Smirnov and Nicolay M Borisov. The OncoFinder algorithm for minimizing the errors introduced by the high-throughput methods of transcriptome analysis. Frontiers in Molecular Biosciences, 2014; DOI: 10.3389/fmolb.2014.00008

Cite This Page:

Biogerontology Research Foundation. "Algorithm for reducing errors in transcriptome analysis." ScienceDaily. ScienceDaily, 18 August 2014. <www.sciencedaily.com/releases/2014/08/140818095214.htm>.
Biogerontology Research Foundation. (2014, August 18). Algorithm for reducing errors in transcriptome analysis. ScienceDaily. Retrieved November 28, 2014 from www.sciencedaily.com/releases/2014/08/140818095214.htm
Biogerontology Research Foundation. "Algorithm for reducing errors in transcriptome analysis." ScienceDaily. www.sciencedaily.com/releases/2014/08/140818095214.htm (accessed November 28, 2014).

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