GEO series

Affymetrix SNP array data for 47 lung squamous cell carcinoma and 40 esophageal squamous cell carcinoma samples.

GSE17958 Homo sapiens (human) Genome variation profiling by SNP array 87 samples Submitted 2009/10/04 Platform GPL3720

At a glance

human · 87 samples

Organism: Homo sapiens (human)
Topic: Lung cancerThis series is part of our curated briefing on it.
Samples: 87 samples
Data you can get: A processed table (series matrix) and supplementary files from NCBI.

Summary (written by the submitters)

Lineage-survival oncogenes are targeted by gene amplification in cancers arising from the tissues where these genes play a role in normal development. Here we show that the transcription factor SOX2—previously known to be mutated in hereditary human esophageal malformations, to be necessary for normal esophageal squamous development, to promote proliferation of basal tracheal cells and to co-operate in induction of pluripotent stem cells -- acts as an amplified oncogene in squamous cell carcinomas (SCC) of the lung and esophagus.

Read the full summary ↓

We identified SOX2 at a peak of genomic amplification on chromosome 3q26.33 in SCCs of both the lung and esophagus but did not find it to be significantly amplified in adenocarcinomas from these tissues. Tumors with SOX2 amplification showed higher SOX2 mRNA expression, and suppression of SOX2 by RNAi in lung and esophageal SCC cell lines revealed that SOX2 expression is required for proliferation and anchorage-independent growth. Furthermore, ectopic expression of SOX2 cooperated with FOXE1 or FGFR2 to transform immortalized tracheobronchial epithelial cells. SOX2-driven tumors showed expression of markers of both squamous differentiation and pluripotency. These observations identify SOX2 as a novel lineage survival oncogene in lung and esophageal SCC and suggest novel connections between development, pluripotency and carcinogenesis.

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 (GSE17958_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 PRJNA119921. Searching any of these in the dataset finder brings you back here.

NCBI GEO page ↗ Paper (PMID 19801978) ↗

Samples in this study

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+ 87 more — browse all 87 samples with per-sample file links →

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