GEO series

caArray_gray-00298: Genomic and transcriptional aberrations linked to breast cancer pathophysiologies - Genome Copy Number (Scanning and OncoBAC)

GSE69035 Homo sapiens (human) Genome variation profiling by genome tiling array 290 samples Submitted 2015/05/20 Platform GPL20218Platform GPL20217

At a glance

human · 290 samples

Organism: Homo sapiens (human)
Topic: Breast cancerThis series is part of our curated briefing on it.
Samples: 290 samples
Data you can get: A processed table (series matrix) and supplementary files from NCBI.

Summary (written by the submitters)

This study explores the roles of genome copy number abnormalities (CNAs) in breast cancer pathophysiology by identifying associations between recurrent CNAs, gene expression, and clinical outcome in a set of aggressively treated early-stage breast tumors. It shows that the recurrent CNAs differ between tumor subtypes defined by expression pattern and that stratification of patients according to outcome can be improved by measuring both expression and copy number, especially high-level amplification.

Read the full summary ↓

Sixty-six genes deregulated by the high-level amplifications are potential therapeutic targets. Nine of these (FGFR1, IKBKB, ERBB2, PROCC, ADAM9, FNTA, ACACA, PNMT, and NR1D1) are considered druggable. Low-level CNAs appear to contribute to cancer progression by altering RNA and cellular metabolism.

This dataset

Open GSE69035 in finder → Find more human 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 (GSE69035_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 ↓

Also filed as BioProject PRJNA284371. Searching any of these in the dataset finder brings you back here.

NCBI GEO page ↗ Paper (PMID 17157792) ↗

Samples in this study

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+ 290 more — browse all 290 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
GSE69031 caArray_gray-00248: Genomic and transcriptional aberrations linked to breast cancer pathophysiologies 130 samples shares pathophysiologies, aberrations, caarray, linked, breast
GSE232381 RNA-seq of Peripheral Blood Cells Identifies Molecular Network Linked to Lymphocyte Subset Aberrations and Active Lupus Nephritis in SLE 25 samples shares aberrations, linked
GSE37385 Subgroup specific somatic copy number aberrations in the medulloblastoma genome 1382 samples shares aberrations

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