Dataset features

Specifications


Application: Gene expression microarray analysis
Number of samples: 18
Release date: Sep 22 2011
Last update date: Oct 29 2018
Access: Public
Diseases: Glioblastoma, Medulloblastoma, Neoplasms, Rhabdoid Tumor
Dataset link High expression of BMP pathway genes distinguishes a subset of Atypical Teratoid/Rhabdoid Tumors associated with shorter survival

Experimental Protocol


Molecular profiling of 18 AT/RT patient tumor samples was performed using Affymetrix U133 Plus2 GeneChips. Data were background corrected and normalized using gcRMA (as implemented in Bioconductor). Unsupervised agglomerative hierarchical clustering was performed to identify subsets of AT/RTs with similar gene expression. Limma (moderated t-tests; Bioconductor) was used to identify signature genes for each cluster. Bioinformatics web tool DAVID was used to identify enriched biological processes for each cluster. Survival was analyzed using Kaplan-Meier curves and Cox Hazard Ratio. Bioinformatics tools Gene Set Enrichment (GSEA) and Ingenuity Pathways Analysis were also used to gain further insight into cluster differences.

Repositories


GEO

GSE28026

ArrayExpress

E-GEOD-28026

BioProject

PRJNA137973

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Contact


Diane Birks
Diane K Birks