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Nucleic Acid Detection and Structural Investigations pp 189–206Cite as

Quantitation of Molecular Pathway Activation Using RNA Sequencing Data

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

Abstract

Intracellular molecular pathways (IMPs) control all major events in the living cell. IMPs are considered hotspots in biomedical sciences and thousands of IMPs have been discovered for humans and model organisms. Knowledge of IMPs activation is essential for understanding biological functions and differences between the biological objects at the molecular level. Here we describe the Oncobox system for accurate quantitative scoring activities of up to several thousand molecular pathways based on high throughput molecular data. Although initially designed for gene expression and mainly RNA sequencing data, Oncobox is now also applicable for quantitative proteomics, microRNA and transcription factor binding sites mapping data. The Oncobox system includes modules of gene expression data harmonization, aggregation and comparison and a recursive algorithm for automatic annotation of molecular pathways. The universal rationale of Oncobox enables scoring of signaling, metabolic, cytoskeleton, immunity, DNA repair, and other pathways in a multitude of biological objects. The Oncobox system can be helpful to all those working in the fields of genetics, biochemistry, interactomics, and big data analytics in molecular biomedicine.

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Abbreviations

IMP:

Intracellular molecular pathway

miR:

MicroRNA

PAL:

Pathway activation level, calculated using RNA or protein expression data

RNAseq:

RNA sequencing

TFBS:

Transcription factor binding site

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Acknowledgments

This study was supported by the Oncobox research program in oncology and by Russian Science Foundation grants 18-15-00061.

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Authors and Affiliations

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

    Nicolas Borisov, Maxim Sorokin & Anton Buzdin

  2. Omicsway Corp., Walnut, CA, USA

    Nicolas Borisov, Maxim Sorokin, Andrew Garazha & Anton Buzdin

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

    Maxim Sorokin & Anton Buzdin

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  1. Nicolas Borisov
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  2. Maxim Sorokin
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  3. Andrew Garazha
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  4. Anton Buzdin
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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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Borisov, N., Sorokin, M., Garazha, A., Buzdin, A. (2020). Quantitation of Molecular Pathway Activation Using RNA Sequencing 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_15

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  • DOI: https://doi.org/10.1007/978-1-0716-0138-9_15

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