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Oncobox Method for Scoring Efficiencies of Anticancer Drugs Based on Gene Expression Data

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Nucleic Acid Detection and Structural Investigations

Part of the book series: Methods in Molecular Biology ((MIMB,volume 2063))

Abstract

We describe here the Oncobox method for scoring efficiencies of anticancer target drugs (ATDs) using high throughput gene expression data. The method rationale, design, and validation are given along with the examples of its practical applications in biomedicine. The method is based on the analysis of intracellular molecular pathways activation and measuring expressions of molecular target genes for every ATD under consideration. Using Oncobox method requires collection of normal (control) expression profiles and annotated databases of molecular pathways and drug target genes. Both microarray and RNA sequencing profiles are acceptable, although the latter type of data prevails in the most recent applications of this technique.

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Abbreviations

ATD:

Anticancer target drug

IMP:

Intracellular molecular pathway

NGS:

Next generation sequencing

PAL:

Pathway activation level, calculated using mRNA or protein expression data

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Acknowledgments

This study was supported by the Russian Science Foundation grant 18-15-00061.

Author information

Authors and Affiliations

  1. Omicsway Corp., Walnut, CA, USA

    Victor Tkachev, Maxim Sorokin, Andrew Garazha, Nicolas Borisov & Anton Buzdin

  2. Laboratory of Clinical Bioinformatics, I.M. Sechenov First Moscow State Medical University, Moscow, Russia

    Maxim Sorokin, Nicolas Borisov & Anton Buzdin

  3. Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Moscow, Russia

    Anton Buzdin

Authors
  1. Victor Tkachev
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  2. Maxim Sorokin
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  3. Andrew Garazha
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  4. Nicolas Borisov
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  5. Anton Buzdin
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Corresponding author

Correspondence to Anton Buzdin .

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Editors and Affiliations

  1. Department of Chemistry, Technical University of Denmark, Kongens Lyngby, Denmark

    Kira Astakhova

  2. Department of Chemistry, Technical University of Denmark, Kongens Lyngby, Denmark

    Syeda Atia Bukhari

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Tkachev, V., Sorokin, M., Garazha, A., Borisov, N., Buzdin, A. (2020). Oncobox Method for Scoring Efficiencies of Anticancer Drugs Based on Gene Expression Data. In: Astakhova, K., Bukhari, S. (eds) Nucleic Acid Detection and Structural Investigations. Methods in Molecular Biology, vol 2063. Humana, New York, NY. https://doi.org/10.1007/978-1-0716-0138-9_17

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  • DOI: https://doi.org/10.1007/978-1-0716-0138-9_17

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  • Publisher Name: Humana, New York, NY

  • Print ISBN: 978-1-0716-0137-2

  • Online ISBN: 978-1-0716-0138-9

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