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Norway/Stanford Breast Tumors

GSE4335 Homo sapiens (human) Expression microarray 122 samples Submitted 2006/03/07 Platform GPL180Platform GPL2777Platform GPL3147Platform GPL3047Platform GPL2778Platform GPL3045Platform GPL2776
At a glance

Expression microarray · human · 122 samples

What it is
Expression microarrayGene activity read on a chip (the older technology that RNA-seq replaced).
Organism
Homo sapiens (human)
Samples
122 samples
Data you can get
A processed expression table (series matrix) and the array files, from NCBI.
Summary (written by the submitters)
Characterization of patterns of gene expression measured by cDNA microarrays to subclassify tumors into clinically relevant subgroups. In this study, we have refined the previously defined subtypes of breast tumors that could be distinguished by their distinct patterns of gene expression. A total of 115 malignant breast tumors and 7 benign tissues were analyzed by hierarchical clustering based on patterns of expression of 534 "intrinsic" genes and shown to subdivide into a basal epithelial-like, an ERBB2-overexpressing, two luminal epithelial-like and a normal breast tissue-like subgroup.
Read the full summary ↓
The genes used for classification were selected based on their similar expression levels between pairs of consecutive samples taken from the same tumor separated by 15 weeks of neoadjuvant treatment. A disease state experiment design type is where the state of some disease such as infection, pathology, syndrome, etc is studied. Keywords: disease_state_design
This dataset
Open GSE4335 in finder → Find more human microarray datasets →
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 (GSE4335_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 PRJNA104655. Searching any of these in the dataset finder brings you back here.

NCBI GEO page ↗ Paper (PMID 12829800) ↗
Samples in this study

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