GEO series

Gene expression-based prediction of neodjuvant chemotherapy response in early breast cancer

GSE140494 Homo sapiens (human) Expression microarray 91 samples Submitted 2020/11/15 Platform GPL570

At a glance

Expression microarray · human · 91 samples

What it is: Expression microarrayGene activity read on a chip (the older technology that RNA-seq replaced).
Organism: Homo sapiens (human)
Topic: Breast cancerThis series is part of our curated briefing on it.
Samples: 91 samples
Data you can get: A processed expression table (series matrix) and the array files, from NCBI.

Summary (written by the submitters)

Prospective, non-comparative Phase II multicenter trial (EXPRESSION EudraCT: 2008-006381-29) where the patients received three 3-week cycles of docetaxel (100 mg/m2) followed by three 3-week cycles of 5-fluorouracil (500 mg/m2), epirubicin (100 mg/m2), and cyclophosphamide (500 mg/m2) (FEC). The primary end point was the identification of a gene expression signature predictive of pathological complete response (pCR).

Read the full summary ↓

In this trial, pCR was defined as absence of invasive or non-invasive cancer in the breast. External validation of the predictive performance was performed using publicly available data.

This dataset

Open GSE140494 in finder → Find more human microarray datasets → Breast cancer 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 (GSE140494_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 PRJNA589890. Searching any of these in the dataset finder brings you back here.

NCBI GEO page ↗ Paper (PMID 33542080) ↗

Samples in this study

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

+ 91 more — browse all 91 samples with per-sample file links →

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GSE104675 Role for the Transcriptional Activator ZRF1 in Breast Cancer Progression and Endocrine Resistance 6 samples same disease briefing · shares breast
GSE10885 An integromic analysis reveals that metaplastic carcinomas are distinct from basal-like tumors. 244 samples same disease briefing
GSE25066 Genomic predictor of response and survival following neoadjuvant taxane-anthracycline chemotherapy in breast cancer 508 samples shares chemotherapy, breast
GSE25055 Discovery cohort for genomic predictor of response and survival following neoadjuvant taxane-anthracycline chemotherapy in breast cancer 310 samples shares chemotherapy, breast
GSE25065 Validation cohort for genomic predictor of response and survival following neoadjuvant taxane-anthracycline chemotherapy in breast cancer 198 samples shares chemotherapy, breast

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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.