Validation of the Predictive Toxicogenomics Space with cell culture data

Pekka Kohonen, Roland Grafström, Egon Willighagen, Juuso Parkkinen, Samuel Kaski & Krister Wennerberg
Cell culture for in vitro cytotoxicity predictions. To validate the predictive performance of the PTGS, a set of CMap instances for 38 compounds that were not included in the NCI-60 data set were assessed. MCF7 (ATCC® HTB22™), PC­3 (ATCC® CRL­1435™) and HL­60 (ATCC® CCL­240™) cell lines were obtained directly from American Type Culture Collection (LGC Promochem AB) and maintained at 37 °C with 5 % CO2 in a humidified incubator according to provider’s instructions. Cell...

4 Related Works

A Transcriptomics Data-Driven Gene Space Accurately Predicts Liver Cytopathology And Drug-Induced Liver Injury

Pekka Kohonen, Juuso Parkkinen, Egon Willighagen, Rebecca Ceder, Krister Wennerberg, Samuel Kaski & Roland Grafström
Predicting unanticipated harmful effects of chemicals and drug molecules is a difficult and costly task. Here we utilize a “big data compacting and data fusion”- concept to capture diverse adverse outcomes on cellular and organismal levels.  The approach generates from transcriptomics data set a “predictive toxicogenomics space” (PTGS) tool composed of 1331 genes distributed over 14 overlapping cytotoxicity-related gene space components. Involving approximately 2.5 x 108 data points and 1300 compounds to construct and validate...

A Transcriptomics Data-Driven Gene Space Accurately Predicts Liver Cytopathology And Drug-Induced Liver Injury

Pekka Kohonen, Juuso Parkkinen, Egon Willighagen, Rebecca Ceder, Krister Wennerberg, Samuel Kaski & Roland Grafström
Predicting unanticipated harmful effects of chemicals and drug molecules is a difficult and costly task. Here we utilize a “big data compacting and data fusion”- concept to capture diverse adverse outcomes on cellular and organismal levels.  The approach generates from transcriptomics data set a “predictive toxicogenomics space” (PTGS) tool composed of 1331 genes distributed over 14 overlapping cytotoxicity-related gene space components. Involving approximately 2.5 x 108 data points and 1300 compounds to construct and validate...

Validation of the Predictive Toxicogenomics Space with cell culture data

Pekka Kohonen, Roland Grafström, Egon Willighagen, Juuso Parkkinen, Samuel Kaski & Krister Wennerberg
Cell culture for in vitro cytotoxicity predictions. To validate the predictive performance of the PTGS, a set of CMap instances for 38 compounds that were not included in the NCI-60 data set were assessed. MCF7 (ATCC® HTB22™), PC­3 (ATCC® CRL­1435™) and HL­60 (ATCC® CCL­240™) cell lines were obtained directly from American Type Culture Collection (LGC Promochem AB) and maintained at 37 °C with 5 % CO2 in a humidified incubator according to provider’s instructions. Cell...

Validation of the Predictive Toxicogenomics Space with cell culture data

Pekka Kohonen, Roland Grafström, Egon Willighagen, Juuso Parkkinen, Samuel Kaski & Krister Wennerberg
Cell culture for in vitro cytotoxicity predictions. To validate the predictive performance of the PTGS, a set of CMap instances for 38 compounds that were not included in the NCI-60 data set were assessed. MCF7 (ATCC® HTB22™), PC­3 (ATCC® CRL­1435™) and HL­60 (ATCC® CCL­240™) cell lines were obtained directly from American Type Culture Collection (LGC Promochem AB) and maintained at 37 °C with 5 % CO2 in a humidified incubator according to provider’s instructions. Cell...

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Publication Year

  • 2017
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  • ZENODO - Research. Shared.
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  • figshare Academic Research System
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