GEO series

Integrative Genome-wide Analysis of Glioblastoma.

GSE10878 Homo sapiens (human) Gene expression profiling 60 samples Submitted 2008/10/30 Platform GPL2879Platform GPL6480

At a glance

Gene expression profiling · human · 60 samples

What it is: Gene expression profilingGene activity measured per sample, the usual starting point for comparing groups.
Organism: Homo sapiens (human)
Topic: GlioblastomaThis series is part of our curated briefing on it.
Samples: 60 samples
Data you can get: A processed table (series matrix) and supplementary files from NCBI.

Summary (written by the submitters)

Glioblastoma multiforme shows multiple chromosomal aberrations, the impact of which on gene expression remains unclear. To investigate this relationship and to identify putative initiating genomic events, we integrated a paired copy number and gene expression survey in glioblastoma using whole human genome arrays. Loci of recurrent copy number alterations were combined with gene expression profiles obtained on the same tumor samples.

Read the full summary ↓

We identified a set of 406 ‘cis-acting DNA targeted genes’ corresponding to genomic aberrations with direct copy-number-driving changes in gene expression, defined as genes with either significantly concordant or correlated changes in DNA copy number and expression. Functional annotation revealed that these genes participate in key processes of cancer cell biology, providing insights into the genetic mechanisms driving glioblastoma. The robustness of the gene selection was validated on an external microarray data set including 81 glioblastomas and 23 non-neoplastic brain samples. The integration of array CGH and gene expression data highlights a robust ‘cis-acting DNA targeted genes’ signature that may be critical for glioblastoma progression, with two tumor suppressor genes PCDH9 and STARD13 that could be involved in tumor invasiveness and resistance to etoposide. Keywords: Glioblastoma Multiforme, array CGH, microarray, data integration

This dataset

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Download · which file do I need?

Direct links to NCBI, no account and no request form. Pick by what you want to do: take the small processed table to look, the supplementary files to re-analyse, or the original raw data to start over.

1 · Just have a look

Processed table

The series matrix: one table of values per sample as the submitters processed it. The smallest download, and it opens in Excel or R. Start here to see what the data look like.

Series matrix ↓

2 · Re-analyse it

Supplementary files

The count tables and other files the authors uploaded. Take only the samples you need.

All supplementary files ↗

3 · The original raw files

Whole study · RAW.tar

Everything the authors deposited as one archive (GSE10878_RAW.tar), including the raw array or instrument files. Can be large; the picker in step 2 takes just the samples you need.

Whole study · RAW.tar ↓

What the files usually look like: For RNA-seq the counts are usually a table among the supplementary files (look for 'counts', 'expression', 'FPKM' or 'TPM' in the file name). The series matrix of a sequencing study is sometimes nearly empty.

Also filed as BioProject PRJNA107267. Searching any of these in the dataset finder brings you back here.

NCBI GEO page ↗ Paper (PMID 18828157) ↗

Samples in this study

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+ 60 more — browse all 60 samples with per-sample file links →

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GSE11233 The Cancer Genome Atlas (TCGA) Consortium Integrated DNA Methylation Analysis 8 samples same disease briefing

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