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The liver pharmacological and xenobiotic gene response repertoire
We have used a supervised classification approach to systematically mine a large microarray database derived from livers of compound-treated rats. Thirty-four distinct signatures (classifiers) for pharmacological and toxicological end points can be identified. Just 200 genes are sufficient to classi...
Autores principales: | , , , , , , , , , , , |
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Formato: | Texto |
Lenguaje: | English |
Publicado: |
Nature Publishing Group
2008
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Materias: | |
Acceso en línea: | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2290941/ https://www.ncbi.nlm.nih.gov/pubmed/18364709 http://dx.doi.org/10.1038/msb.2008.9 |
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author | Natsoulis, Georges Pearson, Cecelia I Gollub, Jeremy P Eynon, Barrett Ferng, Joe Nair, Ramesh Idury, Radha Lee, May D Fielden, Mark R Brennan, Richard J Roter, Alan H Jarnagin, Kurt |
author_facet | Natsoulis, Georges Pearson, Cecelia I Gollub, Jeremy P Eynon, Barrett Ferng, Joe Nair, Ramesh Idury, Radha Lee, May D Fielden, Mark R Brennan, Richard J Roter, Alan H Jarnagin, Kurt |
author_sort | Natsoulis, Georges |
collection | PubMed |
description | We have used a supervised classification approach to systematically mine a large microarray database derived from livers of compound-treated rats. Thirty-four distinct signatures (classifiers) for pharmacological and toxicological end points can be identified. Just 200 genes are sufficient to classify these end points. Signatures were enriched in xenobiotic and immune response genes and contain un-annotated genes, indicating that not all key genes in the liver xenobiotic responses have been characterized. Many signatures with equal classification capabilities but with no gene in common can be derived for the same phenotypic end point. The analysis of the union of all genes present in these signatures can reveal the underlying biology of that end point as illustrated here using liver fibrosis signatures. Our approach using the whole genome and a diverse set of compounds allows a comprehensive view of most pharmacological and toxicological questions and is applicable to other situations such as disease and development. |
format | Text |
id | pubmed-2290941 |
institution | National Center for Biotechnology Information |
language | English |
publishDate | 2008 |
publisher | Nature Publishing Group |
record_format | MEDLINE/PubMed |
spelling | pubmed-22909412008-04-10 The liver pharmacological and xenobiotic gene response repertoire Natsoulis, Georges Pearson, Cecelia I Gollub, Jeremy P Eynon, Barrett Ferng, Joe Nair, Ramesh Idury, Radha Lee, May D Fielden, Mark R Brennan, Richard J Roter, Alan H Jarnagin, Kurt Mol Syst Biol Article We have used a supervised classification approach to systematically mine a large microarray database derived from livers of compound-treated rats. Thirty-four distinct signatures (classifiers) for pharmacological and toxicological end points can be identified. Just 200 genes are sufficient to classify these end points. Signatures were enriched in xenobiotic and immune response genes and contain un-annotated genes, indicating that not all key genes in the liver xenobiotic responses have been characterized. Many signatures with equal classification capabilities but with no gene in common can be derived for the same phenotypic end point. The analysis of the union of all genes present in these signatures can reveal the underlying biology of that end point as illustrated here using liver fibrosis signatures. Our approach using the whole genome and a diverse set of compounds allows a comprehensive view of most pharmacological and toxicological questions and is applicable to other situations such as disease and development. Nature Publishing Group 2008-03-25 /pmc/articles/PMC2290941/ /pubmed/18364709 http://dx.doi.org/10.1038/msb.2008.9 Text en Copyright © 2008, EMBO and Nature Publishing Group http://creativecommons.org/licenses/by-nc-sa/3.0/ This is an open-access article distributed under the terms of the Creative Commons Attribution Licence, which permits distribution and reproduction in any medium, provided the original author and source are credited. Creation of derivative works is permitted but the resulting work may be distributed only under the same or similar licence to this one. This licence does not permit commercial exploitation without specific permission. |
spellingShingle | Article Natsoulis, Georges Pearson, Cecelia I Gollub, Jeremy P Eynon, Barrett Ferng, Joe Nair, Ramesh Idury, Radha Lee, May D Fielden, Mark R Brennan, Richard J Roter, Alan H Jarnagin, Kurt The liver pharmacological and xenobiotic gene response repertoire |
title | The liver pharmacological and xenobiotic gene response repertoire |
title_full | The liver pharmacological and xenobiotic gene response repertoire |
title_fullStr | The liver pharmacological and xenobiotic gene response repertoire |
title_full_unstemmed | The liver pharmacological and xenobiotic gene response repertoire |
title_short | The liver pharmacological and xenobiotic gene response repertoire |
title_sort | liver pharmacological and xenobiotic gene response repertoire |
topic | Article |
url | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2290941/ https://www.ncbi.nlm.nih.gov/pubmed/18364709 http://dx.doi.org/10.1038/msb.2008.9 |
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