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Series GSE3524 Query DataSets for GSE3524
Status Public on Dec 01, 2005
Title Association b/w gene expression profile & tumor invasion in OSCC
Organism Homo sapiens
Experiment type Expression profiling by array
Summary There are limited studies attempting to correlate the expression changes in oral squamous cell carcinoma with clinically relevant variables. We determined the gene expression profile of 16 tumor and 4 normal tissues from 16 patients by means of Affymetrix Hu133A GeneChips. The hybridized RNA was isolated from cells obtained with laser capture microdissection, then was amplified and labeled using T7 polymerase-based in vitro transcription. The expression of 53 genes was found to differ significantly (33 upregulated, 20 downregulated) in normal versus tumor tissues under two independent statistical methods. The expression changes in four selected genes (LGALS1, MMP1, LAGY, and KRT4) were confirmed with reverse transcriptase polymerase chain reaction. Two-dimensional hierarchical clustering of the 53 genes resulted in the samples clustering according to the extent of tumor infiltration: normal epithelial tissue, tumors less than or equal to 4 cm in dimension, and tumors more than 4 cm in dimension (P=0.0014). The same pattern of clustering was also observed for the 20 downregulated genes. We did not observe any associations with lymph node metastasis (P=0.097).

Keywords: TNM,Tumor-node-metastasis LCM,Laser capture microdissection OSCC,Oral squamous cell Carcinoma
 
Overall design We performed microarray analysis using RNA from OSCC cells obtained with LCM from 16 patients and compared these results with 4 control squamous cell epithelium samples.We identified expression profiles of differentially expressed genes between normal and tumor tissues and found that tumor invasiveness of a tumor is highly correlated with its gene expression profile.
 
Contributor(s) Toruner GA, Ulger C, Alkan M, Galante AT, Rinaggio J, Wilk R, Tian B, Soteropoulos P, Hameed MR, Schwalb MN, Dermody JJ
Citation(s) 15381369
Submission date Oct 28, 2005
Last update date Aug 10, 2018
Contact name Gokce Toruner
E-mail(s) torunega@umdnj.edu
Phone 973-854-3456
Organization name UMDNJ-NJ Medical School
Department Center for Human and Molecular Genetics
Lab Center for Applied Genomics
Street address 225 Warren Street W410Q
City Newark
State/province NJ
ZIP/Postal code 07103
Country USA
 
Platforms (1)
GPL96 [HG-U133A] Affymetrix Human Genome U133A Array
Samples (20)
GSM80460 OSCE-2T
GSM80461 OSCE-4T
GSM80462 OSCE-6T
Relations
BioProject PRJNA93575

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
GSE3524_RAW.tar 67.5 Mb (http)(custom) TAR (of CEL)
Raw data provided as supplementary file

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