GEO Logo
   NCBI > GEO > Accession DisplayHelp Not logged in | LoginHelp
GEO help: Mouse over screen elements for information.
Series GSE34573 Query DataSets for GSE34573
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
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.
Overall design Gene expression and DNA copy number of nasopharyngeal carcinoma was compared with those of normal controls.
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
Submission date Dec 20, 2011
Last update date Mar 25, 2019
Contact name Wenbin Wei
Organization name Durham University
Department Biosciences
Street address Stockton Road
City Durham
ZIP/Postal code DH1 3LE
Country United Kingdom
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
Samples (64)
GSM850481 MSTA
GSM850482 MBEZ
GSM850483 MHAU
BioProject PRJNA151019

Download family Format
SOFT formatted family file(s) SOFTHelp
MINiML formatted family file(s) MINiMLHelp
Series Matrix File(s) TXTHelp

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

| NLM | NIH | GEO Help | Disclaimer | Accessibility |
NCBI Home NCBI Search NCBI SiteMap