GEO series
Methylation and gene expression patterns in adamantinomatous craniopharyngioma highlight a panel of genes associated with disease progression-free survival
At a glance
DNA methylation · human · 30 samples
- What it is
- DNA methylationChemical marks on DNA that help switch genes on or off.
- Organism
- Homo sapiens (human)
- Samples
- 30 samples: 30 samples, each with a distinct title — no replicated groupsGroups 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
- Methylation and gene expression patterns in adamantinomatous craniopharyngioma highlight a panel of genes associated with disease progression-free survivalFrontiers in endocrinology · 2025
Summary (written by the submitters)
Introduction: Over the past decade, advancements in next-generation sequencing have significantly enhanced our understanding of the molecular pathogenesis of adamantinomatous craniopharyngiomas (ACP). Objective: This study integrated methylome and transcriptome analyses in ACP samples to explore the potential interplay between DNA methylation and RNA expression signatures for diagnostic and prognostic applications in ACP patients.
Read the full summary ↓
Methods: This cross-sectional study evaluated clinicopathological features, DNA methylation, and gene expression profiles in 15 patients with ACP (33% women, age range: 3–55 years, 53% diagnosed before 18 years) treated at Ribeirao Preto Medical School, University of São Paulo. Results: Multidimensional scaling and principal component analysis identified two distinct clusters (ACP-A: n=9, ACP- B: n=6) with consistent composition across DNA methylation and gene expression profiles. While most clinical and histopathological characteristics were similar between clusters, ACP-A exhibited a longer median progression-free survival. ACP-B showed a higher prevalence of hypomethylated probes in CGI sites, with 63% of differentially methylated positions (DMPs) located in gene body regions. Differential methylation patterns were categorized into Methyl-Set1 (hypomethylated in ACP-A and hypermethylated in ACP-B) and Methyl-Set2 (hypermethylated in ACP-A and hypomethylated in ACP-B). Clustering analyses based on the methylation levels of probes and expression levels of the stringently filtered-in 212- and 37-gene sets further confirmed these two distinct ACP subgroups. Functional enrichment analysis highlighted key roles in synaptic modulation, nervous system development, cell adhesion, as well as pathways linked to RAS signaling, GTPase activity, and membrane potential regulation. Conclusion: Although clinical characteristics were largely comparable between the clusters, ACP-B patients exhibited shorter median progression-free survival, suggesting a more aggressive phenotype. The higher prevalence of hypomethylation in ACP-B indicates increased transcriptional activation, potentially driving tumor aggressiveness. The strong concordance between methylation and transcriptomic data in the 212- and 37-gene sets underscores their potential as a clinically relevant molecular biomarker panel. These gene sets demonstrate robustness in distinguishing ACP clusters, making it a promising tool for clinical sample classification.
Published in
Marrero-Gutiérrez J, Bueno AC, Martins CS et al.
· Frontiers in endocrinology 2025
· PMID 40575267
· doi:10.3389/fendo.2025.1585618
This dataset
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.
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 GSE294056_RAW.tar (it can run to tens of gigabytes).
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.
What the files usually look like: Look for beta-value tables or raw IDAT files among the supplementary files.
Also filed as BioProject PRJNA1247970 and SRA study SRP577234. Searching any of these in the dataset finder brings you back here.
Study design
30 samples, each with a distinct title — no replicated groups
Any grouping that defines a comparison lives in the sample characteristics, which GEO records separately from the titles.
How we read this: Read from 30 sample titles: 30 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
- GSM8898106 Tumor RNA from adamantinomatous craniopharyngioma Tumor 002 [KBRZUSPRA_0078_S67_L001]
- GSM8898107 Tumor RNA from adamantinomatous craniopharyngioma Tumor 002 [KBRZUSPRA_0078_S67_L002]
- GSM8898108 Tumor RNA from adamantinomatous craniopharyngioma Tumor 003 [KBRZUSPRA_0079_S68_L001]
- GSM8898109 Tumor RNA from adamantinomatous craniopharyngioma Tumor 003 [KBRZUSPRA_0079_S68_L002]
- GSM8898110 Tumor RNA from adamantinomatous craniopharyngioma Tumor 004 [KBRZUSPRA_0080_S69_L001]
- GSM8898111 Tumor RNA from adamantinomatous craniopharyngioma Tumor 004 [KBRZUSPRA_0080_S69_L002]
- GSM8898112 Tumor RNA from adamantinomatous craniopharyngioma Tumor 008 [KBRZUSPRA_0081_S70_L001]
- GSM8898113 Tumor RNA from adamantinomatous craniopharyngioma Tumor 008 [KBRZUSPRA_0081_S70_L002]
- GSM8898114 Tumor RNA from adamantinomatous craniopharyngioma Tumor 010 [KBRZUSPRA_0082_S71_L001]
- GSM8898115 Tumor RNA from adamantinomatous craniopharyngioma Tumor 010 [KBRZUSPRA_0082_S71_L002]
- GSM8898116 Tumor RNA from adamantinomatous craniopharyngioma Tumor 012 [KBRZUSPRA_0090_S12_L001]
- GSM8898117 Tumor RNA from adamantinomatous craniopharyngioma Tumor 012 [KBRZUSPRA_0090_S12_L002]
- GSM8898118 Tumor RNA from adamantinomatous craniopharyngioma Tumor 015 [KBRZUSPRA_0101_S18_L001]
- GSM8898119 Tumor RNA from adamantinomatous craniopharyngioma Tumor 015 [KBRZUSPRA_0101_S18_L002]
- GSM8898120 Tumor RNA from adamantinomatous craniopharyngioma Tumor 019 [KBRZUSPRA_0103_S7_L001]
- GSM8898121 Tumor RNA from adamantinomatous craniopharyngioma Tumor 019 [KBRZUSPRA_0103_S7_L002]
- GSM8898122 Tumor RNA from adamantinomatous craniopharyngioma Tumor 023 [KBRZUSPRA_0112_S14_L001]
- GSM8898123 Tumor RNA from adamantinomatous craniopharyngioma Tumor 023 [KBRZUSPRA_0112_S14_L002]
- GSM8898124 Tumor RNA from adamantinomatous craniopharyngioma Tumor 024 [KBRZUSPRA_0113_S15_L001]
- GSM8898125 Tumor RNA from adamantinomatous craniopharyngioma Tumor 024 [KBRZUSPRA_0113_S15_L002]
- GSM8898126 Tumor RNA from adamantinomatous craniopharyngioma Tumor 027 [KBRZUSPRA_0114_S16_L001]
- GSM8898127 Tumor RNA from adamantinomatous craniopharyngioma Tumor 027 [KBRZUSPRA_0114_S16_L002]
- GSM8898128 Tumor RNA from adamantinomatous craniopharyngioma Tumor 028 [KBRZUSPRA_0115_S10_L001]
- GSM8898129 Tumor RNA from adamantinomatous craniopharyngioma Tumor 028 [KBRZUSPRA_0115_S10_L002]
- GSM8898130 Tumor RNA from adamantinomatous craniopharyngioma Tumor 031 [KBRZUSPRA_0117_S11_L001]
- GSM8898131 Tumor RNA from adamantinomatous craniopharyngioma Tumor 031 [KBRZUSPRA_0117_S11_L002]
- GSM8898132 Tumor RNA from adamantinomatous craniopharyngioma Tumor 033 [KBRZUSPRA_0118_S18_L001]
- GSM8898133 Tumor RNA from adamantinomatous craniopharyngioma Tumor 033 [KBRZUSPRA_0118_S18_L002]
- GSM8898134 Tumor RNA from adamantinomatous craniopharyngioma Tumor 034 [KBRZUSPRA_0119_S19_L001]
- GSM8898135 Tumor RNA from adamantinomatous craniopharyngioma Tumor 034 [KBRZUSPRA_0119_S19_L002]
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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.