GEO series
Gene expression analysis of lung adenocarcinoma and matched adjacent non-tumor lung tissue
GSE32863
Homo sapiens (human)
Expression microarray
116 samples
Submitted 2012/03/21
Platform GPL6884
At a glance
Expression microarray · human · 116 samples
- What it is
- Expression microarrayGene activity read on a chip (the older technology that RNA-seq replaced).
- Organism
- Homo sapiens (human)
- Samples
- 116 samples: 116 samples, each with a distinct title — no replicated groupsGroups 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)
Gene expression profiling of 60 lung adenocarcinoma tumors and their matched histologically normal adjacent lung tissue samples were analyzed using Illumina HumanWG-6 v3.0 expression beadchip. We integrated these data with DNA methylation profiles of the same samples to identify potential DNA methylation regulated genes. Lung cancer is the leading cause of cancer death worldwide and adenocarcinoma is its most common histological subtype.
Read the full summary ↓
Clinical and molecular evidence indicates that lung adenocarcinoma is a heterogeneous disease, which has important implications for treatment. Here we performed genome-scale DNA methylation profiling using the Illumina Infinium HumanMethylation27 platform on 59 matched lung adenocarcinoma/non-tumor lung samples, with genome-scale verification on an independent set of tissues. We identified 766 genes showing altered DNA methylation between tumors and non-tumor lung. By integrating DNA methylation and mRNA expression data, we identified 164 hypermethylated genes showing concurrent downregulation, and 57 hypomethylated genes showing increased expression. Integrated pathways analysis indicates that these genes are involved in cell differentiation, epithelial to mesenchymal transition, RAS and WNT signaling pathways and cell cycle regulation, among others. Comparison of DNA methylation profiles between lung adenocarcinomas of current and never-smokers showed modest differences, identifying only LGALS4 as significantly hypermethylated and downregulated in smokers. LGALS4, encoding a galactoside-binding protein involved in cell-cell and cell-matrix interactions, was recently shown to be a tumor-suppressor in colorectal cancer. Unsupervised analysis of the DNA methylation data identified two tumor subgroups, one of which showed increased DNA methylation and was significantly associated with KRAS mutation and to a lesser extent, with smoking. Our analysis lays the groundwork for further molecular studies of lung adenocarcinoma by providing new candidate DNA methylation biomarkers for early detection, identifying novel molecular alterations potentially involved in lung adenocarcinoma development/progression, and describing an epigenetic subgroup of lung adenocarcinoma associated with KRAS mutation.
This dataset
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.
2 · Re-analyse it
Supplementary files
The count tables and other files the authors uploaded. Take only the samples you need.
3 · The original raw files
Whole study · RAW.tar
Everything the authors deposited as one archive (GSE32863_RAW.tar), including the raw array or instrument files. Can be large; the picker in step 2 takes just the samples you need.
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 PRJNA154393. Searching any of these in the dataset finder brings you back here.
Study design
116 samples, each with a distinct title — no replicated groups
Any grouping that defines a comparison lives in the sample characteristics, which GEO records separately from the titles.
How we read this: Read from 116 sample titles: 116 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
- GSM813411 Adjacent non-tumor lung tissue 05L12_N (expression)
- GSM813412 Lung adenocarcinoma 05L12_T (expression)
- GSM813413 Adjacent non-tumor lung tissue 05L13_N (expression)
- GSM813414 Lung adenocarcinoma 05L13_T (expression)
- GSM813415 Adjacent non-tumor lung tissue 05L19_N (expression)
- GSM813416 Lung adenocarcinoma 05L19_T (expression)
- GSM813417 Adjacent non-tumor lung tissue 05L27_N (expression)
- GSM813418 Lung adenocarcinoma 05L27_T (expression)
- GSM813419 Adjacent non-tumor lung tissue 05L32_N (expression)
- GSM813420 Lung adenocarcinoma 05L32_T (expression)
- GSM813421 Adjacent non-tumor lung tissue 05L34_N (expression)
- GSM813422 Lung adenocarcinoma 05L34_T (expression)
- GSM813423 Adjacent non-tumor lung tissue 05L39_N (expression)
- GSM813424 Lung adenocarcinoma 05L39_T (expression)
- GSM813425 Adjacent non-tumor lung tissue 05L4_N (expression)
- GSM813426 Lung adenocarcinoma 05L4_T (expression)
- GSM813427 Adjacent non-tumor lung tissue 05L40_N (expression)
- GSM813428 Lung adenocarcinoma 05L40_T (expression)
- GSM813429 Adjacent non-tumor lung tissue 05L43_N (expression)
- GSM813430 Lung adenocarcinoma 05L43_T (expression)
- GSM813431 Adjacent non-tumor lung tissue 05L45_N (expression)
- GSM813432 Lung adenocarcinoma 05L45_T (expression)
- GSM813433 Adjacent non-tumor lung tissue 05L47_N (expression)
- GSM813434 Lung adenocarcinoma 05L47_T (expression)
- GSM813435 Adjacent non-tumor lung tissue 05L49_N (expression)
- GSM813436 Lung adenocarcinoma 05L49_T (expression)
- GSM813437 Adjacent non-tumor lung tissue 05L54_N (expression)
- GSM813438 Lung adenocarcinoma 05L54_T (expression)
- GSM813439 Adjacent non-tumor lung tissue 05L6_N (expression)
- GSM813440 Lung adenocarcinoma 05L6_T (expression)
- GSM813441 Adjacent non-tumor lung tissue 05L7_N (expression)
- GSM813442 Lung adenocarcinoma 05L7_T (expression)
- GSM813443 Adjacent non-tumor lung tissue 05L9_N (expression)
- GSM813444 Lung adenocarcinoma 05L9_T (expression)
- GSM813445 Adjacent non-tumor lung tissue 06L10_N (expression)
- GSM813446 Lung adenocarcinoma 06L10_T (expression)
- GSM813447 Adjacent non-tumor lung tissue 06L11_N (expression)
- GSM813448 Lung adenocarcinoma 06L11_T (expression)
- GSM813449 Adjacent non-tumor lung tissue 06L14_N (expression)
- GSM813450 Lung adenocarcinoma 06L14_T (expression)
+ 76 more — browse all 116 samples with per-sample file links →
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- GSE288479 Multiomics analysis of lung adenocarcinoma manifesting as radiological part-solid features in female never-smokers 38 samples shares adenocarcinoma, lung
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.