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Whole genome profiling of liver biopsies discloses potential biomarkers for diagnosis of idiopathic non-cirrhotic portal hypertension

GSE77627 Homo sapiens (human) Expression microarray 54 samples Submitted 2018/03/31 Platform GPL14951
At a glance

Expression microarray · human · 54 samples

What it is
Expression microarrayGene activity read on a chip (the older technology that RNA-seq replaced).
Organism
Homo sapiens (human)
Samples
54 samples: 10 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)
Background. Idiopathic non-cirrhotic portal hypertension (INCPH) is a frequently misdiagnosed cause of portal hypertension. It also lacks a specific test for its diagnosis. This study evaluates whether using new immunohistochemistry makers derived from whole genome analysis improves the diagnosis of INCPH. Methods. We analyzed formalin-fixed, paraffin embedded (FFPE) liver tissue from 18 INCPH and 22 patients with cirrhosis (LC) as well as from 14 histologically normal livers (HNL) as controls.
Read the full summary ↓
Microarray experiments were performed using Illumina Whole-Genome DASL HT BeadChip arrays. Selected genes showing differential expression at Illumina were confirmed using quantitative real-time PCR (qRT-PCR) gene expression performed with Fluidigm Biomark HD system in a subgroup of samples. Immunohistochemistry was used to confirm the qRT-PCR results. Results. At Illumina, a total of 292 genes were differentially expressed (FC>+2/-2 and p-value <0.05) in INCPH compared to the control group (LC and HNL) (202 up-regulated and 90 down-regulated).
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 (GSE77627_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 PRJNA311050. Searching any of these in the dataset finder brings you back here.

NCBI GEO page ↗
Study design
10 conditions, mostly in duplicate
formalin-fixed paraffin-embedded liver tissue… ×9 formalin-fixed paraffin-embedded liver tissue… ×8 formalin-fixed paraffin-embedded liver tissue… ×6 formalin-fixed paraffin-embedded liver tissue… ×4 formalin-fixed paraffin-embedded liver tissue… ×4 formalin-fixed paraffin-embedded liver tissue… ×3 formalin-fixed paraffin-embedded liver tissue… ×3 formalin-fixed paraffin-embedded liver tissue… ×2 +13 more

Supports a between-group comparison across 43 samples.

How we read this: 10 replicated groups read from 54 sample titles; they account for 43 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

+ 14 more — browse all 54 samples with per-sample file links →

Datasets on a similar topic

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