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

Methods Mol Biol. 2020;2063:235-255. doi: 10.1007/978-1-0716-0138-9_17.

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.

Keywords: Anticancer target drugs; Bioinformatics; Gene expression; Intracellular molecular pathways; Proteomics; Response to cancer therapy; Systems biology; Transcriptomics; Tumor biomarkers.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Aged
  • Algorithms
  • Antineoplastic Agents / pharmacology*
  • Biomarkers, Tumor / genetics
  • Clinical Trials as Topic
  • Computational Biology / methods*
  • Drug Delivery Systems
  • Drug Discovery / methods*
  • Female
  • Gene Expression Profiling
  • Gene Expression Regulation, Neoplastic
  • Gene Regulatory Networks
  • Humans
  • Molecular Targeted Therapy / methods*
  • Mutation / genetics
  • Mutation Rate
  • Neoplasms / drug therapy*
  • Neoplasms / genetics
  • Protein Kinase Inhibitors / pharmacology
  • Treatment Outcome

Substances

  • Antineoplastic Agents
  • Biomarkers, Tumor
  • Protein Kinase Inhibitors