The OncoFinder algorithm for minimizing the errors introduced by the high-throughput methods of transcriptome analysis

• Main Authors: Anton A. Buzdin, Alex eZhavoronkov, Mikhail eKorzinkin, Sergey A Roumiantsev, Alexander M Aliper, Larisa S. Venkova, Philip eSmirnov, Nicolay M Borisov
• Format: Article
• Language: English
• Published: Frontiers Media S.A. 2014-08-01
• Series: Frontiers in Molecular Biosciences
• Subjects: Gene Expression; Microarray Analysis; Transcription, Genetic; Cancer; RNA-Seq; data analysis
• Online Access: http://journal.frontiersin.org/Journal/10.3389/fmolb.2014.00008/full

The diversity of the installed sequencing and microarray equipment make it increasingly difficult to compare and analyze the gene expression datasets obtained using the different methods. Many applications requiring high-quality and low error rates can not make use of available data using traditional analytical approaches. Recently, we proposed a new concept of signalome-wide analysis of functional changes in the intracellular pathways termed OncoFinder, a bioinformatic tool for quantitative estimation of the signaling pathway activation (SPA). We also developed methods to compare the gene expression data obtained using multiple platforms and minimizing the error rates by mapping the gene expression data onto the known and custom signaling pathways. This technique for the first time makes it possible to analyze the functional features of intracellular regulation on a mathematical basis. In this study we show that the OncoFinder method significantly reduces the errors introduced by transcriptome-wide experimental techniques. We compared the gene expression data for the same biological samples obtained by both the next generation sequencing (NGS) and microarray methods. For these different techniques we demonstrate that there is virtually no correlation between the gene expression values for all datasets analyzed (R2 < 0.1). In contrast, when the OncoFinder algorithm is applied to the data we observed clear-cut correlations between the NGS and microarray gene expression datasets. The signaling pathway activation profiles obtained using NGS and microarray techniques were almost identical for the same biological samples allowing for the platform-agnostic analytical applications. We conclude that this feature of the OncoFinder enables to characterize the functional states of the transcriptomes and interactomes more accurately as before, which makes OncoFinder a method of choice for many applications including genetics, physiology, biomedicine and molecular diagnostics.