Original Research ARTICLE

Front. Mol. Biosci., 26 August 2014 |

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

  • 1Group for Genomic Regulation of Cell Signaling Systems, Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Moscow, Russia
  • 2Laboratory of Bioinformatics, D. Rogachyov Federal Research Center of Pediatric Hematology, Oncology and Immunology, Moscow, Russia
  • 3Pathway Pharmaceuticals, Wan Chai, Hong Kong
  • 4Laboratory of Systems Biology, A.I. Burnasyan Federal Medical Biophysical Center, Moscow, Russia

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 cannot 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 SPA 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.

Keywords: signalome, RNA-Seq, intracellular signaling pathway activation, next generation sequencing, microarray hybridization, gene expression, transcriptome profiling, correction of errors

Citation: Buzdin AA, Zhavoronkov AA, Korzinkin MB, Roumiantsev SA, Aliper AM, Venkova LS, Smirnov PY and Borisov NM (2014) The OncoFinder algorithm for minimizing the errors introduced by the high-throughput methods of transcriptome analysis. Front. Mol. Biosci. 1:8. doi: 10.3389/fmolb.2014.00008

Received: 13 June 2014; Paper pending published: 24 July 2014;
Accepted: 04 August 2014; Published online: 26 August 2014.

Edited by:

John Gregory Marshall, Ryerson University, Canada

Reviewed by:

Nikhil Tyagi, Mitchell Cancer Institute University of South Alabama, USA
Ana Cláudia Coelho, Universidade de Trás-os-Montes e Alto Douro, Portugal

Copyright © 2014 Buzdin, Zhavoronkov, Korzinkin, Roumiantsev, Aliper, Venkova, Smirnov and Borisov. This is an open-access article distributed under the terms of the Creative Commons Attribution License (CC BY). The use, distribution or reproduction in other forums is permitted, provided the original author(s) or licensor are credited and that the original publication in this journal is cited, in accordance with accepted academic practice. No use, distribution or reproduction is permitted which does not comply with these terms.

*Correspondence: Anton A. Buzdin, Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Miklukho-Maklaya 16/10, Moscow 117997, Russia e-mail: