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Genome-wide molecular profiles of HCV-induced dysplasia and hepatocellular carcinoma

GSE6764 Homo sapiens (human) Expression microarray 75 samples Submitted 2007/06/21 Platform GPL570
At a glance

Expression microarray · human · 75 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
75 samples: 13 conditions, mostly in duplicateGroups are read from the sample names, not from the paper. Check the list below.
Data you can get
A processed expression table (series matrix) and the array files, from NCBI.
Summary (written by the submitters)
Gene expression profiles of 75 tissue samples were analyzed representing the stepwise carcinogenic process from pre-neoplastic lesions (cirrhosis and dysplasia) to HCC, including four neoplastic stages (very early HCC to metastatic tumors) from patients with HCV infection. Gene signatures that accurately reflect the pathological progression of disease at each stage were identified and potential molecular markers for early diagnosis uncovered.
Read the full summary ↓
Pathway analysis revealed dysregulation of the Notch and Toll-like receptor pathways in cirrhosis, followed by deregulation of several components of the Jak/STAT pathway in early carcinogenesis, then up-regulation of genes involved in DNA replication and repair and cell cycle in late cancerous stages. Keywords: 8 pathological stages of HCV-induced HCC
This dataset
Open GSE6764 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 (GSE6764_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 PRJNA98935. Searching any of these in the dataset finder brings you back here.

NCBI GEO page ↗ Paper (PMID 17393520) ↗
Study design
13 conditions, mostly in duplicate
ci_NY ×10 lg_NY ×10 aa_NY ×10 hg_NY ×7 c_NY ×5 a_NY ×5 e_NY ×4 ve_NY ×3 +16 more

Supports a between-group comparison across 64 samples.

How we read this: 13 replicated groups read from 75 sample titles; they account for 64 of them. These groups are guessed from the sample names, not taken from the paper, so check them against the sample list below before relying on them.

Samples in this study

+ 35 more — browse all 75 samples with per-sample file links →

More Hepatocellular carcinoma datasets

Search all human microarray datasets in GEO →

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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.