The sensitivity of transcriptomics BMD modeling to the methods used for microarray data normalization
This dataset is a project file generated by BMDExpress 2.2 SW (Sciome, Research Triangle Park, NC). It contains gene expression data for livers of rats exposed to 4 chemicals (crude MCHM, neat MCHM, DMPT, p-toluidine) and kidneys of rats exposed to PPH. The project file includes normalized expression data (GeneChip Rat 230 2.0 Array) using 7 different pre-processing methods (RMA, GCRMA, MAS5.0, MAS5.0_noA calls, PLIER, PLIER16, and PLIER16_noA calls); differentially expressed probe-sets detected by William's method (p<0.05, and minimum fold change of 1.5); probeset-level and pathway-level BMD and BMDL values from transcriptomic dose-response modeling.
This dataset is associated with the following publication:
Mezencev, R., and S. Auerbach. The sensitivity of transcriptomics BMD modeling to the methods used for microarray data normalization. PLOS ONE. Public Library of Science, San Francisco, CA, USA, 15(5): e0232955, (2020).
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Mezencev_Auerbach_5_cmpds_7_normalizations_BMDExpress.zip
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Complete Metadata
| @type | dcat:Dataset |
|---|---|
| accessLevel | public |
| bureauCode |
[ "020:00" ] |
| contactPoint |
{ "fn": "Roman Mezencev", "hasEmail": "mailto:mezencev.roman@epa.gov" } |
| describedBy | https://pasteur.epa.gov/uploads/10.23719/1504295/documents/Mezencev_Auerbach_Data_Dictionary.docx |
| describedByType | application/vnd.openxmlformats-officedocument.wordprocessingml.document |
| description | This dataset is a project file generated by BMDExpress 2.2 SW (Sciome, Research Triangle Park, NC). It contains gene expression data for livers of rats exposed to 4 chemicals (crude MCHM, neat MCHM, DMPT, p-toluidine) and kidneys of rats exposed to PPH. The project file includes normalized expression data (GeneChip Rat 230 2.0 Array) using 7 different pre-processing methods (RMA, GCRMA, MAS5.0, MAS5.0_noA calls, PLIER, PLIER16, and PLIER16_noA calls); differentially expressed probe-sets detected by William's method (p<0.05, and minimum fold change of 1.5); probeset-level and pathway-level BMD and BMDL values from transcriptomic dose-response modeling. This dataset is associated with the following publication: Mezencev, R., and S. Auerbach. The sensitivity of transcriptomics BMD modeling to the methods used for microarray data normalization. PLOS ONE. Public Library of Science, San Francisco, CA, USA, 15(5): e0232955, (2020). |
| distribution |
[ { "title": "Mezencev_Auerbach_5_cmpds_7_normalizations_BMDExpress.zip", "mediaType": "application/x-zip-compressed", "downloadURL": "https://pasteur.epa.gov/uploads/10.23719/1504295/Mezencev_Auerbach_5_cmpds_7_normalizations_BMDExpress.zip" } ] |
| identifier | https://doi.org/10.23719/1504295 |
| keyword |
[ "dose-response modeling", "microarray", "toxicogenomics" ] |
| license | https://pasteur.epa.gov/license/sciencehub-license.html |
| modified | 2018-08-30 |
| programCode |
[ "020:062" ] |
| publisher |
{ "name": "U.S. EPA Office of Research and Development (ORD)", "subOrganizationOf": { "name": "U.S. Environmental Protection Agency", "subOrganizationOf": { "name": "U.S. Government" } } } |
| references |
[ "https://doi.org/10.1371/journal.pone.0232955" ] |
| rights |
null
|
| title | The sensitivity of transcriptomics BMD modeling to the methods used for microarray data normalization |
