GEO series

Affymetrix 250K StyI SNP array data across multiple human cancer types

GSE19399 Homo sapiens (human) Genome variation profiling by SNP array 826 samples Submitted 2010/02/18 Platform GPL3720

At a glance

human · 826 samples

Organism: Homo sapiens (human)
Samples: 826 samples
Data you can get: A processed table (series matrix) and supplementary files from NCBI.

Summary (written by the submitters)

A powerful way to discover key genes playing causal roles in oncogenesis is to identify genomic regions that undergo frequent alteration in human cancers. We have reported high-resolution analyses of somatic copy-number alterations (SCNAs) from 3131 cancer specimens, belonging largely to 26 histological types. We identify 158 regions of focal SCNA that are altered at significant frequency across multiple cancer types, of which 122 cannot be explained by the presence of a known cancer target gene located within these regions.

Read the full summary ↓

Several candidate genes and families are enriched among these regions of focal SCNA, including members of the BCL2 family of apoptosis regulators and the NF-κΒ pathway. We show that cancer cells harboring amplifications surrounding the MCL1 and BCL2L1 anti-apoptotic genes depend upon expression of these genes for survival. Finally, we demonstrate that a large majority of SCNAs identified in individual cancer types are present in multiple cancer types.

This dataset

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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 (GSE19399_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 PRJNA121763. Searching any of these in the dataset finder brings you back here.

NCBI GEO page ↗ Paper (PMID 20164920) ↗

Samples in this study

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+ 826 more — browse all 826 samples with per-sample file links →

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