Welcome to IBRI's Toxicogenomic Platform

 

This platform provides tools and workflows for early risk assessment using toxicogenomics based on publically available data sources or other data sets that have been released in support of this platform. It is expected that this platform will accelerate the development of the supporting science and increase adoption of new risks assessment tools by the broader research community.

Currently this platform is in the early prototype phase to establish secure collaboration tools for participating organizations and to define the conceptual architecture and framework that leverages and/or integrates with other efforts in toxicogenomics. The first working implementation of this platform delivers a full end-to-end workflow from data to visualizations with to-be-defined research methods based on the best practices of the Sponsor(s).

Available Data Formats Available Analysis Methods
  • Affymetrix Microarray
  • RNAseq
  • Gene Set Enrichment Analysis (GSEA) using Broad Institute MSigDB
  • GSEA using WGCNA (Weighted Gene Co-expression Network Analysis) and transcription factor-centric rat liver gene network modules
  • Transcriptional profil similarity analysis to rate liver reference databases (TG-GATEs, DrugMatrix)
Data Sources
  • GEO
  • TG-GATEs
  • DrugMatrix

 
User Guides and Test Cases
Key Reference (additional available on "About" page)
  • Jeffrey J Sutherland James L Stevens Kamin Johnson Navin Elango Yue W Webster Bradley J Mills Daniel H Robertson, 'A novel open access web portal for integrating mechanistic and toxicogenomic study results', Toxicological Sciences, Advance Online Publication
  • J J Sutherland, Y W Webster, J A Willy, G H Searfoss, K M Goldstein, A R Irizarry, D G Hall, and J L Stevens, 'Toxicogenomic module associations with pathogenesis (TXG-MAP): A network based approach to understanding drug toxicity', The Pharmacogenomics Journal, Advance Online Publication
 
If you would like to participate as a part of this collaboration and/or become an early adopter. Please email the collaborative tox team at ctox@indianabiosciences.org.