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OncoboxPD: human 51 672 molecular pathways database with tools for activity calculating and visualization.

Marianna A Zolotovskaia1,2,3, Victor S Tkachev1, Anastasia A Guryanova1,4

  • 1Omicsway Corp., Walnut, CA 91789, USA.

Computational and Structural Biotechnology Journal
|May 26, 2022
PubMed
Summary

OncoboxPD is a comprehensive human molecular pathway database. It enables pathway activation level (PAL) calculations and visualization of molecular interactions for biological research.

Keywords:
ARR, activation/repressor role coefficientBEL, Biological Expression LanguageInteractomicsKEGG, Kyoto Encyclopedia of Genes and GenomesMetabolomicsMolecular pathway databasePAL, pathway activation levelPathway activation levelPathway visualizationProtein–protein interactionsSPIKE, Signaling Pathways Integrated Knowledge EngineSPOKE, Scalable Precision Medicine Open Knowledge EngineVM, virtual machine

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Area of Science:

  • Bioinformatics
  • Systems Biology
  • Molecular Biology

Background:

  • Human molecular pathways are crucial for understanding cellular functions.
  • Existing pathway databases often lack uniform processing and functional annotation.
  • A unified resource for pathway analysis is needed to advance biological research.

Purpose of the Study:

  • To introduce OncoboxPD, a novel human molecular pathway databank.
  • To provide a platform for calculating statistically supported pathway activation levels (PALs).
  • To enable visualization of molecular interactions and differential gene expression within pathways.

Main Methods:

  • Compiled 51,672 uniformly processed human molecular pathways.
  • Constructed an interactome graph of protein-protein interactions and metabolic reactions.
  • Developed algorithmic functional annotation for pathway node roles (activator/repressor).
  • Integrated a bioinformatic tool for online PAL calculation using expression data.
  • Implemented static and dynamic graph visualization for pathways and differential expression.

Main Results:

  • OncoboxPD contains 51,672 human molecular pathways.
  • The interactome graph comprises 361,654 interactions and 64,095 molecular participants.
  • Pathway Activation Levels (PALs) can be calculated and statistically supported.
  • Interactive pathway visualizations, including differential expression, are available.
  • Summaries of top up- and downregulated pathways are generated for comparisons.

Conclusions:

  • OncoboxPD offers a valuable, uniformly processed resource for pathway analysis.
  • The platform facilitates the calculation and interpretation of pathway activation.
  • OncoboxPD supports systems biology approaches through interactome visualization and analysis.
  • This databank empowers researchers to explore molecular mechanisms and gene expression patterns.