Related Experiment Video
Updated: Feb 14, 2026

Project-Based Learning Guidelines for Health Sciences Students: An Analysis with Data Mining and Qualitative Techniques
Published on: December 9, 2022
Release of (and lessons learned from mining) a pioneering large toxicogenomics database
Komal S Sandhu1, Vamsi Veeramachaneni1, Xiang Yao2
1Strand Life Sciences Pvt Ltd, Bangalore, India.
Aim:
We release the Janssen Toxicogenomics database. This rat liver gene-expression database was generated using Codelink microarrays, and has been used over the past years within Janssen to derive signatures for multiple end points and to classify proprietary compounds.
Materials & Methods:
The release consists of gene-expression responses to 124 compounds, selected to give a broad coverage of liver-active compounds. A selection of the compounds were also analyzed on Affymetrix microarrays.
Results:
The release includes results of an in-house reannotation pipeline to Entrez gene annotations, to classify probes into different confidence classes. High confidence unambiguously annotated probes were used to create gene-level data which served as starting point for cross-platform comparisons. Connectivity map-based similarity methods show excellent agreement between Codelink and Affymetrix runs of the same samples. We also compared our dataset with the Japanese Toxicogenomics Project and observed reasonable agreement, especially for compounds with stronger gene signatures. We describe an R-package containing the gene-level data and show how it can be used for expression-based similarity searches.
Conclusion:
Comparing the same biological samples run on the Affymetrix and the Codelink platform, good correspondence is observed using connectivity mapping approaches. As expected, this correspondence is smaller when the data are compared with an independent dataset such as TG-GATE. We hope that this collection of gene-expression profiles will be incorporated in toxicogenomics pipelines of users.
More Related Videos
10:43Eye-tracking Technology and Data-mining Techniques used for a Behavioral Analysis of Adults engaged in Learning Processes
Published on: June 10, 2021
07:41Performing Data Mining And Integrative Analysis Of Biomarker in Breast Cancer Using Multiple Publicly Accessible Databases
Published on: May 17, 2019
Related Concept Videos
Learning Disabilities
Dyslexia
Dyslexia is a...
Avoidance Learning and Learned Helplessness
Avoidance learning occurs when an organism learns that a specific behavior can prevent an unpleasant outcome. For example, a student who receives a bad grade may start studying harder to avoid future poor grades. This behavior persists even when the negative outcome is no longer present. Avoidance learning is powerful because it maintains behavior in the absence of the...
Energy-releasing Steps of Glycolysis
The first energy-releasing step—the 6th step of glycolysis...
Associative Learning
Classical conditioning, also known...
Purposive Learning
Observational Learning