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I-SPY2-990 mRNA/RPPA Data Resource: mRNA component

GSE194040 Homo sapiens (human) Expression microarray 988 samples Submitted 2022/05/25 Platform GPL30493Platform GPL20078
At a glance

Expression microarray · human · 988 samples

What it is
Expression microarrayGene activity read on a chip (the older technology that RNA-seq replaced).
Organism
Homo sapiens (human)
Samples
988 samples: 400 × ISPY2Groups 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.
Paper
Redefining breast cancer subtypes to guide treatment prioritization and maximize response: Predictive biomarkers across 10 cancer therapiesCancer cell · 2022
Summary (written by the submitters)
The I-SPY2-990 mRNA/RPPA Data Resource contains gene expression and clinical data for 987 patients from 10 arms of the neoadjuvant I-SPY2 TRIAL for aggressive early stage breast cancer [210 Control (Ctr); 71 veliparib/carboplatin (VC); 114 neratinib (N); 93 MK2206; 106 ganitumab; 93 ganetespib; 134 trebananib; 52 TDM1/pertuzumab(P); 44 H/P; 69 pembrolizumab (pembro)].
Read the full summary ↓
All 987 patients have pretreatment full transcriptome expression data on over ~19,000 genes assayed on Agilent 44K. Clinical data includes HR, HER2 and MP status, response (pCR or no pCR), and treatment arm. The ISPY2-990 mRNA/RPPA Data Resource also includes normalized pre-treatment LCM-RPPA data for 139 key signaling proteins/phosphoproteins in cancer for 736 patients (see companion GEO record GSE196093 for data and details).
Published in
Redefining breast cancer subtypes to guide treatment prioritization and maximize response: Predictive biomarkers across 10 cancer therapies
Wolf DM, Yau C, Wulfkuhle J et al. · Cancer cell 2022 · PMID 35623341 · doi:10.1016/j.ccell.2022.05.005
This dataset
Open GSE194040 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 (GSE194040_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 PRJNA798787. Searching any of these in the dataset finder brings you back here.

NCBI GEO page ↗ Paper (PMID 35623341) ↗
Study design
400 × ISPY2

Supports a between-group comparison across 400 samples.

How we read this: 1 replicated groups read from the first 400 of 988 sample titles; they account for 400 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

+ 948 more — browse all 988 samples with per-sample file links →

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