GEO series

Distinct gene expression profiles of viral- and non-viral associated Merkel cell carcinoma revealed by transcriptome analysis

GSE39612 Homo sapiens (human) Expression microarray 138 samples Submitted 2012/10/18 Platform GPL570

At a glance

Expression microarray · human · 138 samples

What it is: Expression microarrayGene activity read on a chip (the older technology that RNA-seq replaced).
Organism: Homo sapiens (human)
Topic: Merkel cell carcinomaThis series is part of our curated briefing on it.
Samples: 138 samples
Data you can get: A processed expression table (series matrix) and the array files, from NCBI.

Summary (written by the submitters)

Merkel cell carcinoma (MCC) is an aggressive cutaneous neuroendocrine tumor with high mortality rates. Merkel cell polyomavirus (MCPyV), identified in the majority of MCC, may drive tumorigenesis via viral T antigens. However, mechanisms underlying pathogenesis in MCPyV-negative MCC remain poorly understood. To nominate genes contributing to pathogenesis of MCPyV-negative MCC, we performed DNA microarray analysis on 30 MCCs.

Read the full summary ↓

MCPyV status of MCCs was determined by PCR for viral DNA and RNA. 1593 probe-sets were differentially expressed between MCPyV-negative and -positive MCC, with significant differential expression defined as at least 2-fold change in either direction and p-value of ≤ 0.05. MCPyV-negative tumors showed decreased RB1 expression, whereas MCPyV-positive tumors were enriched for immune response genes. Validation studies included immunohistochemistry demonstration of decreased RB protein expression in MCPyV-negative tumors and increased peritumoral CD8+ T lymphocytes surrounding MCPyV-positive tumors. In conclusion, our data suggest that loss of RB1 expression may play an important role in tumorigenesis of MCPyV-negative MCC. Functional and clinical validation studies are needed to determine whether this tumor suppressor pathway represents an avenue for targeted therapy. We used microarrays to characterize global gene expression patterns related to Merkel cell polyomavirus status in Merkel cell carcinoma. Furthermore, we compared Merkel cell carcinoma to less aggressive primary cutaneous carcinomas.

This dataset

Open GSE39612 in finder → Find more human microarray datasets → Merkel cell carcinoma 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 (GSE39612_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 PRJNA171313. Searching any of these in the dataset finder brings you back here.

NCBI GEO page ↗ Paper (PMID 23223137) ↗

Samples in this study

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

+ 138 more — browse all 138 samples with per-sample file links →

More Merkel cell carcinoma datasets

GSE261681 Interlocking core regulatory circuits enable viral hijacking in Merkel cell carcinoma 43 samples same disease briefing · shares merkel, viral
GSE305197 Targeting an essential viral oncoprotein with an IL-7-enhanced mRNA vaccine induces durable immunity to Merkel cell carcinoma 3 samples same disease briefing · shares merkel, viral
GSE235093 Pre-existing skin-resident CD8 and γδ T cell circuits mediate immune response in Merkel cell carcinoma and Predict immunotherapy efficacy 333 samples same disease briefing · shares merkel
GSE292992 MDM2 degradation overcomes feedback regulation of p53 signaling in Merkel cell carcinoma 66 samples same disease briefing · shares merkel
GSE317774 ATR inhibition induces NF-κB-dependent immunogenicity in Merkel cell carcinoma independent of cGAS-STING 48 samples same disease briefing · shares merkel
GSE154938 Glucose-6-Phosphate Dehydrogenase as a Prognostic Predictor Correlates with the Tumor Immune Activity Including Programmed Death Ligand-1 Expression in Merkel Cell Carcinoma 41 samples same disease briefing · shares merkel
GSE214948 The significance of PAX5 in Merkel cell carcinoma 39 samples same disease briefing · shares merkel
GSE22396 Gene expression analysis of Merkel Cell Carcinoma 35 samples same disease briefing · shares merkel

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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.