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A Knowledge Graph Approach to Elucidate the Role of Organellar Pathways in Disease via Biomedical Reports
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BrainProt v3.0: An Integrative and Simplified Omics-Based Knowledge-Base About the Human Brain and Its Associated

Deeptarup Biswas1, Sanjyot Vinayak Shenoy2, Aparna Chauhan1

  • 1Department of Biosciences and Bioengineering, Indian Institute of Technology Bombay, Powai, Mumbai 400076, India.

Journal of Proteome Research
|September 26, 2025
PubMed
Summary

BrainProt v3.0 is a new knowledge base for human brain diseases, integrating omics data to identify disease markers and drug targets. This resource aids neuroscience research by consolidating scattered data, advancing the Human Brain Proteome Project.

Keywords:
biomarkersbrain tumorsclinical trialshuman brainneurodegenerative diseasesproteomicstranscriptomics

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Area of Science:

  • Neuroscience
  • Bioinformatics
  • Genomics
  • Proteomics

Background:

  • Neuroscience research generates vast amounts of data on brain diseases, often fragmented across repositories.
  • This data fragmentation hinders global efforts to understand and treat neurological disorders.
  • Omics technologies provide deep biological insights but require integrated platforms for effective analysis.

Purpose of the Study:

  • To introduce BrainProt v3.0, an omics-driven knowledge base for human brain diseases.
  • To integrate diverse datasets including genes, chemical interactions, clinical trials, and multiomics data.
  • To facilitate the exploration of biological cross-talk and identify critical disease markers.

Main Methods:

  • Development and integration of the Human Brain Disease Atlas (HBDA), Brain Disease Marker Curator (BDMC), and Brain Disease Drug Finder (BDDF).
  • Collation of multiomics data (transcriptomics and proteomics) for significant brain diseases via the Brain Disease Transcriptome Map (BDTM) and Brain Disease Proteome Map (BDPM).
  • Analysis of 52 datasets and 1,868 samples to display expression profiles and identify correlations.

Main Results:

  • BrainProt v3.0 incorporates 20,202 disease-associated genes and 136,557 chemical target interactions.
  • The platform includes 2,145 clinical trial details and collates multiomics data from major brain diseases.
  • Facilitates exploration of transcriptomic and proteomic data correlations to identify disease markers.

Conclusions:

  • BrainProt v3.0 advances the Human Brain Proteome Project (HBPP) by enhancing data integration for brain diseases.
  • The platform aids in elucidating the complexities of brain diseases and their associated markers.
  • Supports research on the interplay between brain tumors and neurodegenerative disorders.