Dataset features

Specifications


Application: Gene expression microarray analysis
Number of samples: 39
Release date: Dec 22 2009
Last update date: Aug 10 2018
Access: Public
Diseases: Neoplasms, Wilms Tumor
Dataset link Subsets of very low risk Wilms Tumors show distinctive gene expression, histologic, and clinical features

Experimental Protocol


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.

Repositories


GEO

GSE14767

ArrayExpress

E-GEOD-14767

BioProject

PRJNA112147

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Contact


Elizabeth Perlman