GEO series

Validation cohort for genomic predictor of response and survival following neoadjuvant taxane-anthracycline chemotherapy in breast cancer

GSE25065 Homo sapiens (human) Expression microarray 198 samples Submitted 2011/05/11 Platform GPL96

At a glance

Expression microarray · human · 198 samples

What it is: Expression microarrayGene activity read on a chip (the older technology that RNA-seq replaced).
Organism: Homo sapiens (human)
Samples: 198 samples: 130 distinct titles, 4 of them repeatedGroups 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)

PURPOSE: To develop a predictive test for response and survival following neoadjuvant taxane-anthracycline chemotherapy for HER2-negative invasive breast cancer. METHODS: We developed a microarray-based gene expression test from pre-treatment tumor biopsies (310 patients) to predict favorable outcome based on estrogen receptor (ER) status,pathologic response to chemotherapy, 3-year disease outcomes, and sensitivity to endocrine therapy.

Read the full summary ↓

Tumors were classified as treatment-sensitive if predicted to have pathologic response (and not resistance) to chemotherapy, or sensitive to endocrine therapy. We tested predictive accuracy, with 95% confidence interval (CI), for pathologic response (PPV, positive predictive value), distant relapse-free survival (DRFS), and absolute risk reduction at median follow-up in 198 other patients. Independence from clinical-pathologic factors was assessed in a multivariate Cox regression analysis based on the likelihood ratio test. Other evaluable, published response predictors (genomic grade index (GGI), intrinsic subtype (PAM50), pCR predictor (DLDA30)) were compared.

This dataset

Open GSE25065 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 (GSE25065_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 PRJNA142731. Searching any of these in the dataset finder brings you back here.

NCBI GEO page ↗ Paper (PMID 21558518) ↗

Study design

130 distinct titles, 4 of them repeated

PERU ×24 LBJ ×17 Spain ×16 MDA ×15

How we read this: Read from 198 sample titles: 130 distinct titles with little repetition. 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

GSM615631 1
GSM615632 5
GSM615633 12
GSM615634 13
GSM615635 18
GSM615636 20
GSM615637 23
GSM615638 24
GSM615639 30
GSM615640 31
GSM615641 32
GSM615642 35
GSM615643 36
GSM615644 45
GSM615645 46
GSM615646 48
GSM615647 51
GSM615648 52
GSM615649 67
GSM615650 68
GSM615651 70
GSM615652 76
GSM615653 77
GSM615654 80
GSM615655 85
GSM615656 86
GSM615657 87
GSM615658 88
GSM615659 94
GSM615660 95
GSM615661 96
GSM615662 97
GSM615663 100
GSM615664 101
GSM615665 103
GSM615666 104
GSM615667 106
GSM615668 110
GSM615669 111
GSM615670 112

+ 158 more — browse all 198 samples with per-sample file links →

Datasets on a similar topic

GSE25055 Discovery cohort for genomic predictor of response and survival following neoadjuvant taxane-anthracycline chemotherapy in breast cancer 310 samples shares taxane-anthracycline, chemotherapy, neoadjuvant, predictor, following, survival, cohort
GSE25066 Genomic predictor of response and survival following neoadjuvant taxane-anthracycline chemotherapy in breast cancer 508 samples shares taxane-anthracycline, chemotherapy, neoadjuvant, predictor, following, survival
GSE247185 Impact of immune repertoire in Muscle – Invasive Bladder Cancer (MIBC) on predicting response and survival after neoadjuvant cisplatin-based chemotherapy (NAC) 13 samples shares chemotherapy, neoadjuvant, survival
GSE290327 RNA-seq Profiling of Response to Cisplatin and Gemcitabine Chemotherapy in Advanced Urothelial Carcinoma: An External Validation Cohort 10 samples shares chemotherapy, validation, cohort
GSE4779 A stroma-related gene signature predicts sensitivity to epirubicin-containing neoadjuvant chemotherapy in breast cancer. 102 samples shares chemotherapy, neoadjuvant
GSE279390 Basal/squamous and mixed subtype bladder cancers present poor outcomes after neoadjuvant chemotherapy in the VESPER trial 540 samples shares chemotherapy, neoadjuvant
GSE222557 Neoadjuvant PARPi or Chemotherapy in Ovarian Cancer Informs Targeting Effector Treg Cells for Homologous-Recombination-Deficient Tumors 148 samples shares chemotherapy, neoadjuvant
GSE294705 High-frequency recurrence index for predicting multiple recurrences in non-muscle-invasive bladder cancer (Validation cohort) 94 samples shares validation, cohort

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.