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Expression data from ALL patients included in the set used to construct a classification signature (COALL cohort)

GSE13425 Homo sapiens (human) Expression microarray 190 samples Submitted 2009/01/26 Platform GPL96
At a glance

Expression microarray · human · 190 samples

What it is
Expression microarrayGene activity read on a chip (the older technology that RNA-seq replaced).
Organism
Homo sapiens (human)
Topic
Acute lymphoblastic leukemiaThis series is part of our curated briefing on it.
Samples
190 samples: 8 conditions, mostly with about 4 replicates eachGroups are read from the sample names, not from the paper. Check the list below.
Data you can get
A processed expression table (series matrix) and the array files, from NCBI.
Summary (written by the submitters)
Childhood acute lymphoblastic leukemia (ALL) comprises a large group of genetic subtypes with a favorable prognosis characterized by a TEL-AML1-fusion, hyperdiploidy (>50 chromosomes) or E2A-PBX1 fusion and a smaller group with unfavorable outcome characterized by either a BCR-ABL-fusion, MLL-rearrangement or T-ALL. About 25% of precursor B-ALL are currently genetically unclassified and have an intermediate prognosis.
Read the full summary ↓
The present study used genome-wide strategies to reveal new biological insights and advance the prognostic classification of childhood ALL. A double-loop cross validation was used to construct a classifier based on gene expression in ALL cells from 190 newly diagnosed cases (COALL cohort, GEO GSE13425) with a prediction accuracy of 90%. T-ALL, TEL-AML1-positive, hyperdiploid and E2A-rearranged cases were identified with 100% sensitivity and ≥94% specificity. The classifier accuracy was confirmed in an independent cohort of 107 cases (87.9%, DCOG cohort, GEO GSE13351). Keywords: gene expression study for classification of ALL subtypes
This dataset
Open GSE13425 in finder → Find more human microarray datasets → Acute lymphoblastic leukemia 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 (GSE13425_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 PRJNA110079. Searching any of these in the dataset finder brings you back here.

NCBI GEO page ↗ Paper (PMID 19138562) ↗
Study design
8 conditions, mostly with about 4 replicates each
bone marrow or peripheral blood, hyperdiploid… ×44 bone marrow or peripheral blood, pre-B ALL, p… ×44 bone marrow or peripheral blood, TEL-AML1, pa… ×43 bone marrow or peripheral blood, T-ALL, patie… ×36 bone marrow or peripheral blood, E2A-rearrang… ×8 bone marrow or peripheral blood, E2A-rearrang… ×4 bone marrow or peripheral blood, BCR-ABL, pat… ×4 bone marrow or peripheral blood, MLL, patient ×4 +3 more

Supports a between-group comparison across 187 samples.

How we read this: 8 replicated groups read from 190 sample titles; they account for 187 of them. These groups are guessed from the sample names, not taken from the paper, so check them against the sample list below before relying on them.

Samples in this study

+ 150 more — browse all 190 samples with per-sample file links →

More Acute lymphoblastic leukemia datasets

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.