IBRI Toxicogenomics Platform
The Starting Point for Early Risk Assessment
The IBRI's ctox platform has been decommissioned.
The platform can still be installed/run from the GitHub repository github.com/IndianaBiosciences/toxapp.
Contact IBRI for assistance
Accelerating Product Discovery and Development
CTox is a new early risk assessment tool using toxicogenomics. CTox is designed to facilitate sharing both private and public sector expertise and processes to enhance the reproducibility of results and catalyze advances in toxicogenomics. CTox data sources include: GEO, TG-GATEs and DrugMatrix.
We believe by making CTox widely available to the broader scientific research community that it will ultimately help accelerate product development by enabling timely decisions on the safety of compounds early in the discovery process. CTox can help do this based on shared data sets, development of new toxicogenomic tools and the collective understanding of the molecule's impact on biological pathways.
Available Data Formats and Analysis Methods
While there are myriad formats in which transcriptomic data can be stored and analyzed, the platform currently handles standard Affymetrix Microarray and RNAseq file formats for upload. Other formats will be added in the future based on user need.
CTox also offers three different analysis methods:
- 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 profile similarity analysis to rate liver reference databases (TG-GATEs, DrugMatrix)
The Creation and Evolution of the CTox Platform
Eli Lilly and Company, Corteva Agriscience (formerly Dow AgroSciences) and the Indiana Biosciences Research Institute(IBRI) partnered to develop a shared data analytics platform for early assessment of the potential effects of different molecules on human health and the environment.
Corteva Agriscience and Eli Lilly and Company both perform predictive safety assessments on a regular basis during discovery research efforts. And, they have engineered their processes in a similar way, despite doing this independently within their respective organizations. This project was an opportunity to work collaboratively to advance the predictive safety science more rapidly.
CTox has currently gone through many releases with multiple deployments maintained by the IBRI, but also deployed at Eli Lilly and Corteva AgriScience. As detailed in the References section, a key paper was published in 2019 and the github repository made publiclly available. The platform is being updated on a regular basis using an agile development process. We are continuing to expand this platform as needed.
The current focus of the collaboration and team is on expanding the user base, improving the useability, and creating training materials.
Indiana Biosciences Research Institute's Role with CTox
The Indiana Biosciences Research Institute (IBRI) is an independent, industry-inspired applied research institute. The IBRI is a catalyst for collaboration and a convener of industry, academia, government and community organizations. It is because of this unique role we play that we can facilitate access and engagement with academic and other research organizations to assist in enhancing CTox.
If you would like to participate as a part of this collaboration and/or become an early adopter. Please email contact the IBRI at Contact Us.