GEO series

Genomics of medulloblastoma identifies four distinct molecular variants

GSE21140 Homo sapiens (human) Expression microarray 103 samples Submitted 2010/09/14 Platform GPL5175

At a glance

Expression microarray · human · 103 samples

What it is: Expression microarrayGene activity read on a chip (the older technology that RNA-seq replaced).
Organism: Homo sapiens (human)
Topic: MedulloblastomaThis series is part of our curated briefing on it.
Samples: 103 samples
Data you can get: A processed expression table (series matrix) and the array files, from NCBI.

Summary (written by the submitters)

Recent genomic approaches have suggested the existence of multiple distinct subtypes of medulloblastoma. We studied a large cohort of medulloblastomas to determine how many subgroups of the disease exist, how they differ, and the extent of overlap between subgroups. We determined gene expression profiles and DNA copy number aberrations for 103 primary medulloblastomas.

Read the full summary ↓

Bioinformatic tools were used for class discovery of medulloblastoma subgroups based on the most informative genes in the dataset. Immunohistochemistry for subgroup-specific ‘signature’ genes was used to determine subgroup affiliation for 294 non-overlapping medulloblastomas on two independent tissue microarrays (TMAs). Multiple unsupervised analyses of transcriptional profiles identified four distinct, non-overlapping molecular variants: WNT, SHH, Group C, and Group D. Supervised analysis of these four subgroups revealed significant subgroup-specific demographics, histology, metastatic status, and DNA copy number aberrations. Immunohistochemistry for DKK1 (WNT), SFRP1 (SHH), NPR3 (Group C), and KCNA1 (Group D) could reliably and uniquely classify formalin fixed medulloblastomas in ~98% of cases. Group C patients (NPR3 +ve tumors) exhibited a significantly diminished progression free and overall survival irrespective of their metastatic status. Our integrative genomics approach to a large cohort of medulloblastomas has identified four disparate subgroups with distinct demographics, clinical presentation, transcriptional profiles, genetic abnormalities, and clinical outcome. Medulloblastomas can be reliably assigned to subgroups through immunohistochemistry, thereby making medulloblastoma sub-classification widely available. Future research on medulloblastoma and the development of clinical trials should take into consideration these four distinct types of medulloblastoma.

This dataset

Open GSE21140 in finder → Find more human microarray datasets → Medulloblastoma landscape →

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 (GSE21140_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 arrays the series matrix is normally the normalised expression table you want; the raw array files (CEL and similar) are in the RAW.tar.

Also filed as BioProject PRJNA126659. Searching any of these in the dataset finder brings you back here.

NCBI GEO page ↗ Paper (PMID 20823417) ↗

Samples in this study

The sample list for this study is not cached yet. Press Load samples and it will be fetched from NCBI.

+ 103 more — browse all 103 samples with per-sample file links →

More Medulloblastoma datasets

GSE37418 Novel mutations target distinct subgroups of medulloblastoma. 76 samples same disease briefing · shares medulloblastoma, distinct
GSE283621 Single-cell multi-omics analysis identifies metabolism-linked epigenetic reprogramming as a driver of therapy-resistant medulloblastoma 79 samples same disease briefing · shares medulloblastoma, identifies
GSE10327 mRNA expression data of 62 human medulloblastoma tumors 62 samples same disease briefing · shares medulloblastoma
GSE37385 Subgroup specific somatic copy number aberrations in the medulloblastoma genome 1382 samples same disease briefing · shares medulloblastoma
GSE246125 3D genome topology distinguishes molecular subgroups of medulloblastoma 55 samples same disease briefing · shares medulloblastoma
GSE270126 Divergent medulloblastoma chromatin states disclose KDM2B as a selective dependency. 219 samples same disease briefing · shares medulloblastoma
GSE270125 Divergent medulloblastoma chromatin states disclose KDM2B as a selective dependency [CUT&Run] 169 samples same disease briefing · shares medulloblastoma
GSE243796 Multiomic profiling of medulloblastoma reveals subtype-specific targetable alterations at the proteome and N-glycan level 90 samples same disease briefing · shares medulloblastoma

Search all human microarray datasets in GEO →

Share this dataset

Metadata from NCBI GEO, cached and refreshed periodically — the NCBI page above is authoritative. Downloads link straight to NCBI/ENA; nothing is proxied through BioTransfer.