GEO series

HCC Gene Expression Profile

GSE4024 Homo sapiens (human) Expression microarray 98 samples Submitted 2006/01/26 Platform GPL1528

At a glance

Expression microarray · human · 98 samples

What it is: Expression microarrayGene activity read on a chip (the older technology that RNA-seq replaced).
Organism: Homo sapiens (human)
Samples: 98 samples
Data you can get: A processed expression table (series matrix) and the array files, from NCBI.

Summary (written by the submitters)

The variability in the prognosis of hepatocellular carcinoma (HCC) patients suggests that HCC may comprise several distinctive biological phenotypes. These phenotypes may result from different neoplastic pathways during the tumorigenesis and/or from a different cell of origin. Here we address if the transcriptional characteristics of the HCC would provide insight into the cellular origin of the tumors.

Read the full summary ↓

We integrated gene expression data from rat fetal hepatoblasts and adult hepatocytes, HCC from mouse models, and human HCC. The HCC patients who shared gene expression patterns with fetal hepatoblasts showed extremely poor prognosis when compared with those lacking the hepatoblast signature. The gene expression program that distinguishes this novel subtype from the rest of HCC includes well known markers of hepatic oval cells, suggesting that HCC in this subtype may arise from hepatic progenitor cells. Two independent gene network analyses of the gene expression signature characteristic for the tumors sharing the hepatoblast expression patterns revealed that activation of AP-1 transcription factors might play key roles in tumor development in the newly identified HCC subtype. In addition, by applying hepatoblast-specific and genome-wide global signatures, HCC patients were further stratified into three distinct subgroups with a significant association with overall survival and recurrence. Keywords: individual genetic characteristic design

This dataset

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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 (GSE4024_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 PRJNA95127. Searching any of these in the dataset finder brings you back here.

NCBI GEO page ↗ Paper (PMID 16532004) ↗

Samples in this study

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+ 98 more — browse all 98 samples with per-sample file links →

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GSE66529 Expression data from CSC and Non-CSC of three HCC cell lines 6 samples shares hcc
GSE5093 Comparison of metastasis-inclined microenvironment (MIM) and metastasis-averse microenvironment (MAM) HCC patients 20 samples shares hcc
GSE54238 lncRNAs and mRNAs expression profile in liver diseases including HCC 56 samples shares hcc
GSE208036 Next Generation Sequencing facilitates to identify the differential expression genes between tumor (T1-8) and non-tumor tissue (NT1-8) from HBV-infected hepatocellular cacinoma (HCC) patients. 15 samples shares hcc
GSE203625 Effect of knockdown of CENPU on gene expression of Huh-7 and MHCC-97H hepatoma cells 12 samples shares hcc

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