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| Status |
Public on Dec 10, 2012 |
| Title |
A Global View of the Oncogenic Landscape in Nasopharyngeal Carcinoma:An Integrated Analysis at the Genetic and Expression Levels |
| Organism |
Homo sapiens |
| Experiment type |
Expression profiling by array
SNP genotyping by SNP array
Genome variation profiling by SNP array
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| Summary |
Previous studies have reported that the tumour cells of nasopharyngeal carcinoma (NPC) exhibit both recurrent chromosome abnormalities and changes in the expression of numerous genes. However, it is not known to what extent changes in the copy number of individual genes are associated with the observed expression changes. To address this, a genome wide analysis of chromosome copy number and gene expression was performed in tumour cells micro-dissected from the same NPC biopsies. Significant gene expression changes were identified in tumour suppressor genes (TSGs) and in tumour-promoting genes (TPGs) but almost 60% of these can be either upregulated or downregulated in different types of cancer. This suggests that the simplistic classification of genes as TSGs or TPGs may not be entirely appropriate and that the concept of onco-suppressors may be more extensive than previously recognised. Several genomic regions showing frequent copy number gain or loss were identified. Whereas TSGs were significantly enriched within regions of frequent loss, no significant enrichment of TPGs was observed in regions of frequent gain. However, on a gene by gene basis little correlation was found between DNA copy number and alterations in gene expression except for loss of expression from homozygous deletions and a single highly amplified segment which showed enhanced gene expression.
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| Overall design |
Gene expression and DNA copy number of nasopharyngeal carcinoma was compared with those of normal controls.
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| Contributor(s) |
Hu C, Wei W, Chen X, Woodman CB, Yao Y, Nicholls J, Joab I, Sihota SK, Shao J, Derkaoui D, Amari A, Maloney SL, Bell AI, Murray PG, Dawson CW, Young LS, Arrand JR |
| Citation(s) |
22815911 |
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| Submission date |
Dec 20, 2011 |
| Last update date |
Mar 25, 2019 |
| Contact name |
Wenbin Wei |
| E-mail(s) |
Wenbin.Wei2@durham.ac.uk
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| Organization name |
Durham University
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| Department |
Biosciences
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| Street address |
Stockton Road
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| City |
Durham |
| ZIP/Postal code |
DH1 3LE |
| Country |
United Kingdom |
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| Platforms (3) |
| GPL570 |
[HG-U133_Plus_2] Affymetrix Human Genome U133 Plus 2.0 Array |
| GPL3718 |
[Mapping250K_Nsp] Affymetrix Mapping 250K Nsp SNP Array |
| GPL3720 |
[Mapping250K_Sty] Affymetrix Mapping 250K Sty2 SNP Array |
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| Samples (64)
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| Relations |
| BioProject |
PRJNA151019 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSE34573_RAW.tar |
1.4 Gb |
(http)(custom) |
TAR (of CEL, CHP) |
| Processed data included within Sample table |
| Processed data provided as supplementary file |
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