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Series GSE14767 Query DataSets for GSE14767
Status Public on Dec 22, 2009
Title Subsets of very low risk Wilms Tumors show distinctive gene expression, histologic, and clinical features
Organism Homo sapiens
Experiment type Expression profiling by array
Summary The goal of this study is to define biologically distinct subsets of Very Low Risk Wilms Tumors (VLRWT) using oligonucleotide arrays.

Description: 52 tumors from the original case:cohort of 600 tumors from NWTS-5 met the criteria for VLRWT. Thirteen tumors were excluded for quality control reasons, resulting in 39 tumors for analysis. Global gene expression analysis was performed on these 39 tumors. A total of 4,000 probesets representing the greatest variability according to coefficient of variation was utilized for hierarchical clustering, and three clusters were identified. Two subsets within VLRWT are identified that have pathogenetic and molecular differences and apparent differences in risk for relapse. If these predictors can be prospectively validated, this would enable future clinical stratification and broadening the definition of VLRWT.

Keywords: Classification by microarray analysis
 
Overall design Global gene expression analysis was performed on 39 tumors that met the criteria of VLRWT and passed quality control parameters in order to define biologically distinct subsets.

Hierarchical clustering identified three tumor clusters (C1, C2 and C3). The top differentially expressed genes were identified by first filtering out probesets with a maximum expression of less than 6.5 in all 39 tumors. Using the remaining 14,452 probesets, the expression of each cluster was compared with the expression in the remaining tumors, and those genes with a p-value <0.00001 and positive or negative fold-change (FC) of greater than 2.5 were identified. This resulted in 161 probesets from the comparison of C1 with C2+C3, 43 probesets from the comparison of C2 with C1+C3, and 71 probesets from the comparison of C3 with C1+C2. The false discovery rates were 0.02%, 0.06% and 0.05% for C1, C2, and C3, respectively. These three lists were combined, resulting in 239 probesets (161 genes) which are provided in Supplemental Table 1, linked below.
 
Contributor(s) Gadd S, Perlman EJ
Citation(s) 19903788
Submission date Feb 09, 2009
Last update date Aug 10, 2018
Contact name Elizabeth J Perlman
E-mail(s) eperlman@childrensmemorial.org
Organization name Children's Memorial Research Center
Department Pathology
Street address 2373 North Lincoln Avenue, Room A.204
City Chicago
State/province IL
ZIP/Postal code 60614
Country USA
 
Platforms (1)
GPL96 [HG-U133A] Affymetrix Human Genome U133A Array
Samples (39)
GSM368771 Favorable Histology Wilms Tumor (WT00-002)
GSM368772 Favorable Histology Wilms Tumor (WT00-015)
GSM368773 Favorable Histology Wilms Tumor (WT00-026)
Relations
BioProject PRJNA112147

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
GSE14767_RAW.tar 97.2 Mb (http)(custom) TAR (of CEL)
GSE14767_Supplemental_Table_1.xls.gz 27.7 Kb (ftp)(http) XLS
GSE14767_summary.pdf 82.0 Kb (ftp)(http) PDF
Processed data included within Sample table
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