GCOD - GeneChip Oncology Database

Overview

Journal BMC Bioinformatics

Publisher Biomed Central

Specialty Biology

Date 2011 Feb 5

PMID 21291543

Citations 7

Authors

Fenglong Liu

Joseph A White

Corina Antonescu

Daniel Gusenleitner

John Quackenbush

Affiliations

Soon will be listed here.

Abstract

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.

Citing Articles

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Oudaert I, Satilmis H, Vlummens P, De Brouwer W, Maes A, Hose D J Exp Clin Cancer Res. 2022; 41(1):45.

PMID: 35105345 PMC: 8805317. DOI: 10.1186/s13046-022-02250-3.

Cancer RNA-Seq Nexus: a database of phenotype-specific transcriptome profiling in cancer cells.

Li J, Sun C, Li W, Chao R, Huang C, Zhou X Nucleic Acids Res. 2015; 44(D1):D944-51.

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Metabolic enzyme expression highlights a key role for MTHFD2 and the mitochondrial folate pathway in cancer.

Nilsson R, Jain M, Madhusudhan N, Gustafsson Sheppard N, Strittmatter L, Kampf C Nat Commun. 2014; 5:3128.

PMID: 24451681 PMC: 4106362. DOI: 10.1038/ncomms4128.

canEvolve: a web portal for integrative oncogenomics.

Samur M, Yan Z, Wang X, Cao Q, Munshi N, Li C PLoS One. 2013; 8(2):e56228.

PMID: 23418540 PMC: 3572035. DOI: 10.1371/journal.pone.0056228.

Reuse of public genome-wide gene expression data.

Rung J, Brazma A Nat Rev Genet. 2012; 14(2):89-99.

PMID: 23269463 DOI: 10.1038/nrg3394.

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