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E-GEOD-53084 - Cross-platform toxicogenomics for the prediction of nongenotoxic hepatocarcinogenesis in rat (protein)

Released on 18 August 2014, last updated on 26 August 2014
Rattus norvegicus
Samples (63)
Array (1)
Protocols (7)
In this study we performed microarray-based molecular profiling of liver samples from Wistar rats exposed to genotoxic carcinogens (GC), nongenotoxic carcinogens (NGC) or non-hepatocarcinogens (NC) for up to 14 days. In contrast to previous toxicogenomics studies aimed at the inference of molecular signatures for assessing the potential and mode of compound carcinogenicity, we considered multi-level omics data. Besides evaluating the predictive power of signatures observed on individual biological levels, such as mRNA, miRNA and protein expression, we also introduced novel feature representations which capture putative molecular interactions or pathway alterations by integrating expression profiles across platforms interrogating different biological levels. Male Wistar rats were treated by oral gavage with the eight nongenotoxic hepatocarcinogens Phenobarbital sodium (PB), Piperonylbutoxide (PBO), Dehydroepiandrosterone (DHEA), Acetamide (AA), Methapyrilene HCl (MPy), Methylcarbamate (Mcarb), Diethylstilbestrol (DES) and Ethionine (ETH), the two genotoxic carcinogens C.I Direct Black (CIDB) and dimethylnitrosamine (DMN), the two non-hepatocarcinogens Cefuroxime (CFX) and Nifedipine (Nif), and the three compounds with undefined carcinogenic class Cyproterone acetate (CPA), Thioacetamid (TAA) and Wy-14643 (Wy). Depending on the administered compound, livers were taken after 3, 7, or 14 days for histopathological evaluation. From the five animals per treatment group three animals were selected based on the histopathological findings and subjected to molecular profiling using Affymetrix RG-230A arrays (mRNA expression), Agilent G4473A arrays (miRNA expression) and Zeptosens ZeptoMARK reverse arrays (protein expression).
Experiment type
proteomic profiling by array 
Johannes Eichner <>, Heidrun Ellinger-Ziegelbauer, Michael Römer
Cross-platform toxicogenomics for the prediction of non-genotoxic hepatocarcinogenesis in rat. R�mer M, Eichner J, Metzger U, Templin MF, Plummer S, Ellinger-Ziegelbauer H, Zell A. , PMID:24830643
Investigation descriptionE-GEOD-53084.idf.txt
Sample and data relationshipE-GEOD-53084.sdrf.txt
Raw data (1)
Processed data (1)
Array designA-GEOD-17787.adf.txt