E-MTAB-798 - Transcription profiling by array of human hepatocytes treated with approximately 130 chemicals in vitro

Status
Released on 10 February 2012, last updated on 23 July 2013
Organism
Homo sapiens
Samples (2004)
Array (1)
Protocols (6)
Description
The Toxicogenomics Project was a 5-year collaborative project (2002-2007) by a consortium comprising the Japanese government and several pharmaceutical companies. The project produced the 'Toxicogenomics Project-Genomics Assisted Toxicity Evaluation system' (TG-GATEs), a large-scale database of transcriptomics and pathology data potentially useful for predicting the toxicity of new chemical entities. Conventional in vivo toxicology data was collected from single dose and repeat dosing studies on rats, and gene expression measured for the liver (and kidney in some cases). To provide information on species differences, gene expression was also measured in rat and human hepatocytes treated with the chemicals in vitro. Approximately 130 chemicals, primarily medicinal compounds, were tested at multipe doses. Gene expression was analysed using Affymetrix GeneChip arrays. The gene expression data has been submitted in four parts: in vivo single dose (E-MTAB-799), in vivo repeat dosing (E-MTAB-800), in vitro rat (E-MTAB-797) and in vitro human. This submission comprises the in vitro human studies. If publishing results based on this data, please cite the full project name 'Toxicogenomics Project and Toxicogenomics Informatics Project', the database name 'Open TG-GATEs' and the URL 'http://toxico.nibio.go.jp'. Please note that the European Bioinformatics Institute (EBI) was not involved in the Toxicogenomics Project in any way, acting only to submit the transcriptomics data to Array Express. Queries about the project can be addressed to the consortium directly via 'opentggates@nibio.go.jp'.
Experiment types
transcription profiling by array, co-expression, compound treatment, dose response, in vitro
Contacts
Citations
Identification of genomic biomarkers for concurrent diagnosis of drug-induced renal tubular injury using a large-scale toxicogenomics database. Kondo C, Minowa Y, Uehara T, Okuno Y, Nakatsu N, Ono A, Maruyama T, Kato I, Yamate J, Yamada H, Ohno Y, Urushidani T.
The Japanese toxicogenomics project: application of toxicogenomics. Uehara T, Ono A, Maruyama T, Kato I, Yamada H, Ohno Y, Urushidani T.
Species-specific differences in coumarin-induced hepatotoxicity as an example toxicogenomics-based approach to assessing risk of toxicity to humans. Uehara T, Kiyosawa N, Shimizu T, Omura K, Hirode M, Imazawa T, Mizukawa Y, Ono A, Miyagishima T, Nagao T, Urushidani T.
Effect of the difference in vehicles on gene expression in the rat liver--analysis of the control data in the Toxicogenomics Project Database. Takashima K, Mizukawa Y, Morishita K, Okuyama M, Kasahara T, Toritsuka N, Miyagishima T, Nagao T, Urushidani T.
MIAME
PlatformsProtocolsVariablesProcessedRaw
Files
Investigation descriptionE-MTAB-798.idf.txt
Sample and data relationshipE-MTAB-798.sdrf.txt
Raw data (51)Click to browse raw data
Additional data (1)E-MTAB-798.additional.1.zip
Array designA-AFFY-44.adf.txt
Links