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GCOD - GeneChip Oncology Database
BACKGROUND: DNA microarrays have become a nearly ubiquitous tool for the study of human disease, and nowhere is this more true than in cancer. With hundreds of studies and thousands of expression profiles representing the majority of human cancers completed and in public databases, the challenge has...
Autores principales: | , , , , |
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Formato: | Texto |
Lenguaje: | English |
Publicado: |
BioMed Central
2011
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Materias: | |
Acceso en línea: | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3045303/ https://www.ncbi.nlm.nih.gov/pubmed/21291543 http://dx.doi.org/10.1186/1471-2105-12-46 |
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author | Liu, Fenglong White, Joseph A Antonescu, Corina Gusenleitner, Daniel Quackenbush, John |
author_facet | Liu, Fenglong White, Joseph A Antonescu, Corina Gusenleitner, Daniel Quackenbush, John |
author_sort | Liu, Fenglong |
collection | PubMed |
description | BACKGROUND: DNA microarrays have become a nearly ubiquitous tool for the study of human disease, and nowhere is this more true than in cancer. With hundreds of studies and thousands of expression profiles representing the majority of human cancers completed and in public databases, the challenge has been effectively accessing and using this wealth of data. DESCRIPTION: To address this issue we have collected published human cancer gene expression datasets generated on the Affymetrix GeneChip platform, and carefully annotated those studies with a focus on providing accurate sample annotation. To facilitate comparison between datasets, we implemented a consistent data normalization and transformation protocol and then applied stringent quality control procedures to flag low-quality assays. CONCLUSION: The resulting resource, the GeneChip Oncology Database, is available through a publicly accessible website that provides several query options and analytical tools through an intuitive interface. |
format | Text |
id | pubmed-3045303 |
institution | National Center for Biotechnology Information |
language | English |
publishDate | 2011 |
publisher | BioMed Central |
record_format | MEDLINE/PubMed |
spelling | pubmed-30453032011-02-26 GCOD - GeneChip Oncology Database Liu, Fenglong White, Joseph A Antonescu, Corina Gusenleitner, Daniel Quackenbush, John BMC Bioinformatics Database BACKGROUND: DNA microarrays have become a nearly ubiquitous tool for the study of human disease, and nowhere is this more true than in cancer. With hundreds of studies and thousands of expression profiles representing the majority of human cancers completed and in public databases, the challenge has been effectively accessing and using this wealth of data. DESCRIPTION: To address this issue we have collected published human cancer gene expression datasets generated on the Affymetrix GeneChip platform, and carefully annotated those studies with a focus on providing accurate sample annotation. To facilitate comparison between datasets, we implemented a consistent data normalization and transformation protocol and then applied stringent quality control procedures to flag low-quality assays. CONCLUSION: The resulting resource, the GeneChip Oncology Database, is available through a publicly accessible website that provides several query options and analytical tools through an intuitive interface. BioMed Central 2011-02-03 /pmc/articles/PMC3045303/ /pubmed/21291543 http://dx.doi.org/10.1186/1471-2105-12-46 Text en Copyright ©2011 Liu et al; licensee BioMed Central Ltd. http://creativecommons.org/licenses/by/2.0 This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/2.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited. |
spellingShingle | Database Liu, Fenglong White, Joseph A Antonescu, Corina Gusenleitner, Daniel Quackenbush, John GCOD - GeneChip Oncology Database |
title | GCOD - GeneChip Oncology Database |
title_full | GCOD - GeneChip Oncology Database |
title_fullStr | GCOD - GeneChip Oncology Database |
title_full_unstemmed | GCOD - GeneChip Oncology Database |
title_short | GCOD - GeneChip Oncology Database |
title_sort | gcod - genechip oncology database |
topic | Database |
url | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3045303/ https://www.ncbi.nlm.nih.gov/pubmed/21291543 http://dx.doi.org/10.1186/1471-2105-12-46 |
work_keys_str_mv | AT liufenglong gcodgenechiponcologydatabase AT whitejosepha gcodgenechiponcologydatabase AT antonescucorina gcodgenechiponcologydatabase AT gusenleitnerdaniel gcodgenechiponcologydatabase AT quackenbushjohn gcodgenechiponcologydatabase |