Unknown,Transcriptomics,Genomics,Proteomics

Dataset Information

A Global View of the Oncogenic Landscape in Nasopharyngeal Carcinoma:An Integrated Analysis at the Genetic and Expression Levels

ABSTRACT: 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. Gene expression and DNA copy number of nasopharyngeal carcinoma was compared with those of normal controls.

ORGANISM(S): Homo sapiens

SUBMITTER: Wenbin Wei

PROVIDER: E-GEOD-34573 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

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Publications

A global view of the oncogenic landscape in nasopharyngeal carcinoma: an integrated analysis at the genetic and expression levels.

Hu Chunfang C Wei Wenbin W Chen Xiaoyi X Woodman Ciaran B CB Yao Yunhong Y Nicholls John M JM Joab Irène I Sihota Sim K SK Shao Jian-Yong JY Derkaoui K Dalia KD Amari Aicha A Maloney Stephanie L SL Bell Andrew I AI Murray Paul G PG Dawson Christopher W CW Young Lawrence S LS Arrand John R JR

PloS one 20120717 7

Previous studies have reported that the tumour cells of nasopharyngeal carcinoma (NPC) exhibit recurrent chromosome abnormalities. These genetic changes are broadly assumed to lead to changes in gene expression which are important for the pathogenesis of this tumour. However, this assumption has yet to be formally tested at a global level. Therefore a genome wide analysis of chromosome copy number and gene expression was performed in tumour cells micro-dissected from the same NPC biopsies. Cellu ...[more]

PMID: 22815911

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Dataset Information

A Global View of the Oncogenic Landscape in Nasopharyngeal Carcinoma:An Integrated Analysis at the Genetic and Expression Levels

Publications

A global view of the oncogenic landscape in nasopharyngeal carcinoma: an integrated analysis at the genetic and expression levels.

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