GEO series

mRNA expression profiling of nasopharyngeal carcinoma

GSE12452 Homo sapiens (human) Expression microarray 41 samples Submitted 2008/08/16 Platform GPL570

At a glance

Expression microarray · human · 41 samples

What it is: Expression microarrayGene activity read on a chip (the older technology that RNA-seq replaced).
Organism: Homo sapiens (human)
Topic: Nasopharyngeal carcinomaThis series is part of our curated briefing on it.
Samples: 41 samples
Data you can get: A processed expression table (series matrix) and the array files, from NCBI.

Summary (written by the submitters)

Nasopharyngeal carcinoma is an Epstein-Barr virus-associated epithelial cancer with high prevalence in Southeast Asia. mRNA expression levels were measured for essentially all human genes and all latent Epstein-Barr virus (EBV) genes in nasopharyngeal carcinoma tissue samples and normal nasopharyngeal tissues. Data were analyzed for differential gene expression between tumor and normal tissue and for correlations with levels of viral gene expression.

Read the full summary ↓

Primary publications: Sengupta et al, 2006, Cancer Research 66(16): 7999-8006. Dodd et al, 2006, Cancer Epidemiology, Biomarkers & Prevention 15(11): 2216-2225. In subsequent studies using the same set of tissue samples, microRNA levels were measured in tumors and normal tissues and analyzed for correlations with differential target gene expression (Sengupta et al, 2008, Proc. Nat. Acad. Sci. USA 105: 5874-5878.) Keywords: mRNA expression profiling

This dataset

Open GSE12452 in finder → Find more human microarray datasets → Nasopharyngeal 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 (GSE12452_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 PRJNA113009. Searching any of these in the dataset finder brings you back here.

NCBI GEO page ↗ Paper (PMID 17119049) ↗

Samples in this study

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

+ 41 more — browse all 41 samples with per-sample file links →

More Nasopharyngeal carcinoma datasets

GSE234440 mRNA expression profiling of nasopharyngeal carcinoma cell line HONE1 upon ARNTL2 knockdown [RNA-seq] 6 samples same disease briefing · shares nasopharyngeal, mrna
GSE305669 Reduced expression of UPF1 promotes tumor progression through stabilizing COX-2 mRNA in nasopharyngeal carcinoma 12 samples same disease briefing · shares nasopharyngeal, mrna
GSE262035 RAN directly binds and stabilizes G3BP1 mRNA in the nucleus to facilitate proliferation and metastasis of nasopharyngeal carcinoma 14 samples same disease briefing · shares nasopharyngeal, mrna
GSE53819 Genome-wide expressing profiling of nasopharyngeal carcinoma primary tumors versus non-cancerous nasopharyngeal tissues. 36 samples same disease briefing · shares nasopharyngeal
GSE102349 Genomic Analysis of Nasopharyngeal Carcinoma Reveals TME-based Subtypes 113 samples same disease briefing · shares nasopharyngeal
GSE293574 Effect of BAY2402234 treatment on gene expression in nasopharyngeal carcinoma C666-1 cells 10 samples same disease briefing · shares nasopharyngeal
GSE231572 Development and validation of a microbiota signature to predict prognosis in nasopharyngeal carcinoma 64 samples same disease briefing · shares nasopharyngeal
GSE120926 Single-cell RNA sequencing defines the interplay between tumor cells, virus and microenvironment in nasopharyngeal carcinoma 56 samples same disease briefing · shares nasopharyngeal

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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.