GEO series

Whole genome landscapes of major melanoma subtypes

GSE80435 Homo sapiens (human) Expression microarray 33 samples Submitted 2017/12/01 Platform GPL6884Platform GPL10558

At a glance

Expression microarray · human · 33 samples

What it is: Expression microarrayGene activity read on a chip (the older technology that RNA-seq replaced).
Organism: Homo sapiens (human)
Topic: MelanomaThis series is part of our curated briefing on it.
Samples: 33 samples
Data you can get: A processed expression table (series matrix) and the array files, from NCBI.

Summary (written by the submitters)

Cutaneous, acral and mucosal subtypes of melanoma were evaluated by whole-genome sequencing, revealing genes affected by novel recurrent mutations to the promoter (TERT, DPH3, OXNAD1, RPL13A, RALY, RPL18A, AP2A1), 5’-UTR (HNRNPUL1, CCDC77, PES1), and 3’-UTR (DYNAP, CHIT1, FUT9, CCDC141, CDH9, PTPRT) regions. TERT promoter mutations had the highest frequency of any mutation, but neither they nor ATRX mutations, associated with the alternative telomere lengthening mechanism, were correlated with greater telomere length.

Read the full summary ↓

Genomic landscapes largely reflected ultraviolet radiation mutagenesis in cutaneous melanoma and provided novel insights into melanoma pathogenesis. In contrast, acral and mucosal melanomas exhibited predominantly structural changes, and mutation signatures of unknown aetiology not previously identified in melanoma. The majority of melanomas had potentially actionable mutations, most of which were in components of the mitogen-activated protein kinase and phosphoinositol kinase pathways.

This dataset

Open GSE80435 in finder → Find more human microarray datasets → Melanoma 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 (GSE80435_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 PRJNA318904. Searching any of these in the dataset finder brings you back here.

NCBI GEO page ↗ Paper (PMID 28467829) ↗

Samples in this study

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

+ 33 more — browse all 33 samples with per-sample file links →

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GSE134459 Genome-wide maps of transcriptomic and epigenomic state in melanoma cell lines 73 samples same disease briefing · shares melanoma
GSE230489 RNA-sequencing of cutaneous melanoma and non-small cell lung cancer biopsies 38 samples same disease briefing · shares melanoma
GSE100797 Mutational and neoantigen load predict clinical benefit of adoptive T cell therapy in melanoma 25 samples same disease briefing · shares melanoma
GSE130956 Investigation of ST8SIA1 expression in icaritin-treated and untreated melanoma cell lines 12 samples same disease briefing · shares melanoma
GSE140150 A rare subpopulation of melanoma cells with low expression of metastasis suppressor NME1 has a neural crest-like phenotype and is highly metastatic in vivo 6 samples same disease briefing · shares melanoma
GSE142751 Genome-wide maps of chromatin state in 142 cancer cell lines [cell line] 855 samples same disease briefing

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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.