GEO series

Molecular characterization of pancreatic neuroendocrine tumor tissue: characterization of altered pathways and potential non-invasive biomarkers

GSE281039 Homo sapiens (human) RNA-seq (gene expression) 40 samples Submitted 2025/03/12 Platform GPL28038

At a glance

RNA-seq (gene expression) · human · 40 samples

What it is: RNA-seq (gene expression)Gene activity measured by sequencing. The summary does not mention single-cell work, so this is most likely bulk: one average per sample, the usual starting point for comparing groups.
Organism: Homo sapiens (human)
Samples: 40 samples: 36 distinct titles, 4 of them repeatedGroups are read from the sample names, not from the paper. Check the list below.
Data you can get: A processed table (series matrix) and supplementary files from NCBI; the raw sequencing reads from ENA. Which of these hold counts depends on the study, so check the file list.
Paper: Transcriptomic profiling of pancreatic neuroendocrine tumors: dysregulation of WNT, MAPK, PI3K, neddylation pathways and potential non-invasive biomarkersPloS one · 2025

Summary (written by the submitters)

The study aimed to identify potential non-invasive biomarkers for pancreatic neuroendocrine tumours (PanNETs) through transcriptomic profiling of various tissue samples. The analysis encompassed samples from non-functional PanNETs (NF-PanNETs), insulinomas, and adjacent tumour tissues. In tumor vs. tumors adjacent pancreatic tissues differential expression analysis we identified 1210 differentially expressed genes (DEGs).

Read the full summary ↓

Further pathway enrichment analysis revealed a multitude of overrepresented signaling pathways related to cell proliferation, survival and tumorigenesis. Notable findings were Beta-catenin independent and TCF dependent WNT signaling pathways, MAPK1/MAPK3 signaling and PIP3 activates AKT signaling. Amongst the list of DEGs we also identified 28 upregulated genes encoding for cell surface proteins and 24 upregulated genes encoding for cancer associated secretome proteins. Since the products of these genes are found in the bloodstream, there is a potential for further testing of these markers as biomarkers for liquid biopsy assay. Overall, the findings have underscored the promise of transcriptomic landscape analysis in identifying PanNET-specific non-invasive biomarkers and uncovering potential therapeutic targets.

Published in

Transcriptomic profiling of pancreatic neuroendocrine tumors: dysregulation of WNT, MAPK, PI3K, neddylation pathways and potential non-invasive biomarkers

Niedra H, Rogoza O, Saksis R et al. · PloS one 2025 · PMID 40522948 · doi:10.1371/journal.pone.0325672

This dataset

Open GSE281039 in finder → Find more human RNA-seq datasets →

Download · which file do I need?

Direct links to NCBI and ENA, 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, or the whole study as GSE281039_RAW.tar (it can run to tens of gigabytes).

All supplementary files ↗ Whole study · RAW.tar ↓

3 · Start from the raw reads

Raw sequencing reads

The original FASTQ files, straight from the sequencer, held at ENA. Large, and you align them yourself, so only choose this if you need to re-process the study from scratch.

Raw reads on ENA ↗

What the files usually look like: For RNA-seq the counts are usually a table among the supplementary files (look for 'counts', 'expression', 'FPKM' or 'TPM' in the file name). The series matrix of a sequencing study is sometimes nearly empty.

Also filed as BioProject PRJNA1181877 and SRA study SRP543093. Searching any of these in the dataset finder brings you back here.

NCBI GEO page ↗ Paper (PMID 40522948) ↗

Study design

36 distinct titles, 4 of them repeated

NET22,Tumor,Non-functioning, NET22 ×2 NET3,Tumor,Non-functioning, NET3 ×2 NET5,Tumor,Non-functioning, NET5 ×2 NET3,Non-tumor,Tumor adjacent pancreatic tiss… ×2

How we read this: Read from 40 sample titles: 36 distinct titles with little repetition. 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

GSM8609688 NET1,Tumor,Non-functioning
GSM8609689 NET10,Tumor,Non-functioning
GSM8609690 NET11,Tumor,Non-functioning
GSM8609691 NET13,Tumor,Non-functioning
GSM8609692 NET14,Tumor,Non-functioning
GSM8609693 NET17,Tumor,Non-functioning
GSM8609694 NET19,Tumor,Non-functioning
GSM8609695 NET2,Tumor,Non-functioning
GSM8609696 NET20,Tumor,Non-functioning
GSM8609697 NET21,Tumor,Non-functioning
GSM8609698 NET22,Tumor,Non-functioning, NET22_3
GSM8609699 NET22,Tumor,Non-functioning, NET22_4
GSM8609700 NET23,Tumor,Non-functioning
GSM8609701 NET24,Tumor,Non-functioning
GSM8609702 NET25,Tumor,Non-functioning
GSM8609703 NET26,Tumor,Non-functioning
GSM8609704 NET7,Tumor,Non-functioning
GSM8609705 NET12,Tumor,Non-functioning
GSM8609706 NET15,Tumor,Non-functioning
GSM8609707 NET16,Tumor,Non-functioning
GSM8609708 NET18,Tumor,Non-functioning
GSM8609709 NET27,Tumor,Non-functioning
GSM8609710 NET3,Tumor,Non-functioning, NET3_77
GSM8609711 NET3,Tumor,Non-functioning, NET3_78
GSM8609712 NET4,Tumor,Non-functioning
GSM8609713 NET5,Tumor,Non-functioning, NET5_13
GSM8609714 NET5,Tumor,Non-functioning, NET5_14
GSM8609715 NET6,Tumor,Non-functioning
GSM8609716 NET8,Tumor,Non-functioning
GSM8609717 NET9,Tumor,Non-functioning
GSM8609718 NET1,Non-tumor,Tumor adjacent pancreatic tissue
GSM8609719 NET2,Non-tumor,Tumor adjacent pancreatic tissue
GSM8609720 NET3,Non-tumor,Tumor adjacent pancreatic tissue, 4NT_79
GSM8609721 NET3,Non-tumor,Tumor adjacent pancreatic tissue, 4NT_80
GSM8609722 NET61,Non-tumor,Tumor adjacent pancreatic tissue
GSM8609723 NET4,Non-tumor,Tumor adjacent pancreatic tissue
GSM8609724 NET28,Non-tumor,Tumor adjacent pancreatic tissue
GSM8609725 NET29,Tumor,Insulinoma
GSM8609726 NET30,Tumor,Insulinoma
GSM8609727 NET28,Tumor,Insulinoma

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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.