GEO series

Molecular classification of human cholangiocarcinoma

GSE26566 Homo sapiens (human) Expression microarray 169 samples Submitted 2012/02/25 Platform GPL6104

At a glance

Expression microarray · human · 169 samples

What it is: Expression microarrayGene activity read on a chip (the older technology that RNA-seq replaced).
Organism: Homo sapiens (human)
Topic: CholangiocarcinomaThis series is part of our curated briefing on it.
Samples: 169 samples
Data you can get: A processed expression table (series matrix) and the array files, from NCBI.

Summary (written by the submitters)

Transcriptomic profiling Background Cholangiocarcinoma accounts for 5-10% of primary hepatic cancers. The etiology is unclear and patients are often diagnosed without risk factors. Resection is the only curative treatment although patients frequently remain undiagnosed until advanced stage of disease. Methods To construct molecular classification of cholangiocarcinoma, we profiled the transcriptomes of 104 freshly-frozen tumors and 59 matched non-cancerous livers obtained from Australia, Europe and the United States.

Read the full summary ↓

We also performed mutational analysis of KRAS, EGFR and BRAF, and used laser-capture microdissection to obtain independent gene expression profiles for epithelial and stromal compartments in a subset of tumors. The selected target genes were validated by western blotting and immunohistochemistry. Results Transcriptomic profiling classified cholangiocarcinoma into two distinct subclasses defined by survival (P<0.0007) and early recurrence (P<0.001). Applying leave-one-out cross-validation, we optimized the prognostic classifier to 238 genes which were positively enriched in the epithelial tumor compartment. A deregulated HER2 network was associated with the epithelial compartment which also showed a frequent overexpression of Ki67, EGFR, MET and pRPS6 whereas inflammatory cytokines were enriched in tumor stroma specifically in patients with poor prognosis. KRAS mutations were found in 24.6% of patients with poor disease outcome. Conclusion Our study presents new insights into pathogenesis of cholangiocarcinoma and stratification of the patients according to survival and recurrence. Identification of a subgroup of patients among the poor prognostic cohort characterized by KRAS mutations and oncogenic-addiction may provide a novel therapeutic opportunity for this treatment-refractory malignancy.

This dataset

Open GSE26566 in finder → Find more human microarray datasets → Cholangiocarcinoma 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 (GSE26566_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 PRJNA136231. Searching any of these in the dataset finder brings you back here.

NCBI GEO page ↗ Paper (PMID 22178589) ↗

Samples in this study

The sample list for this study is not cached yet. Press Load samples and it will be fetched from NCBI.

+ 169 more — browse all 169 samples with per-sample file links →

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GSE107943 Integrative molecular and clinical analysis of intrahepatic cholangiocarcinoma reveals two prognostic subclassees 57 samples same disease briefing · shares cholangiocarcinoma
GSE320081 Molecular and cellular consequences of tumor-autonomous IL-6 signaling in intrahepatic cholangiocarcinoma 36 samples same disease briefing · shares cholangiocarcinoma
GSE290614 Comprehensive Molecular Profiling of Combined Hepatocellular Carcinoma and Cholangiocarcinoma reveals Distinct Notch Signaling Subgroups with Prognostic Significance 18 samples same disease briefing · shares cholangiocarcinoma
GSE316441 Transcriptomic profiling of epigenetic regulators and metabolic reprogramming in human cholangiocarcinoma 18 samples same disease briefing · shares cholangiocarcinoma
GSE318388 Anticancer activity of RAS-GTP inhibition in cholangiocarcinoma [Human_Abr24] 12 samples same disease briefing · shares cholangiocarcinoma

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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.