GEO series

Gene expression patterns in human liver cancers

GSE3500 Homo sapiens (human) Expression microarray 207 samples Submitted 2005/10/25 Platform GPL3009Platform GPL2906Platform GPL2935Platform GPL2938Platform GPL2649Platform GPL3007Platform GPL3010Platform GPL3008Platform GPL2948Platform GPL3011Platform GPL2868Platform GPL2831Platform GPL2648

At a glance

Expression microarray · human · 207 samples

What it is: Expression microarrayGene activity read on a chip (the older technology that RNA-seq replaced).
Organism: Homo sapiens (human)
Topic: Hepatocellular carcinomaThis series is part of our curated briefing on it.
Samples: 207 samples
Data you can get: A processed expression table (series matrix) and the array files, from NCBI.

Summary (written by the submitters)

All the array experiments published in "Gene expression patterns in human liver cancers" by Chen X, et al. Hepatocellular carcinoma (HCC) is a leading cause of death worldwide. Using cDNA microarrays to characterize patterns of gene expression in HCC, we found consistent differences between the expression patterns in HCC compared with those seen in nontumor liver tissues.

Read the full summary ↓

The expression patterns in HCC were also readily distinguished from those associated with tumors metastatic to liver. The global gene expression patterns intrinsic to each tumor were sufficiently distinctive that multiple tumor nodules from the same patient could usually be recognized and distinguished from all the others in the large sample set on the basis of their gene expression patterns alone. The distinctive gene expression patterns are characteristic of the tumors and not the patient; the expression programs seen in clonally independent tumor nodules in the same patient were no more similar than those in tumors from different patients. Moreover, clonally related tumor masses that showed distinct expression profiles were also distinguished by genotypic differences. Some features of the gene expression patterns were associated with specific phenotypic and genotypic characteristics of the tumors, including growth rate, vascular invasion, and p53 overexpression. Set of arrays organized by shared biological context, such as organism, tumors types, processes, etc. Keywords: Logical Set

This dataset

Open GSE3500 in finder → Find more human microarray datasets → Hepatocellular 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 (GSE3500_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 PRJNA93331. Searching any of these in the dataset finder brings you back here.

NCBI GEO page ↗ Paper (PMID 12058060) ↗

Samples in this study

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+ 207 more — browse all 207 samples with per-sample file links →

More Hepatocellular carcinoma datasets

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GSE104580 Using a novel gene signature for predicting the efficacy of the transarterial chemoembolization in patients with hepatocellular carcinoma. 147 samples same disease briefing
GSE10186 Integrative Transcriptome Analysis Reveals Common Molecular Subtypes of Human Hepatocellular Carcinoma 118 samples same disease briefing
GSE107170 Molecular Signature of Hepatitis D Virus-Associated Hepatocellular Carcinoma 307 samples same disease briefing
GSE109211 Molecular predictors of prevention of recurrence in hepatocellular carcinoma with sorafenib as adjuvant treatment in the phase 3 STORM trial 140 samples same disease briefing
GSE114564 Identification of novel serum biomarkers in early-stage HCC patients. 118 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.