Siftome Phase 3L

GSE253906

Enhancer plasticity in endometrial tumorigenesis demarcates non-coding driver mutations and 3D genome alterations to stimulate oncogene expression [RNA-seq_ECa_patients]

Exploratory only Dataset can inform exploration but is not strong enough for primary analysis.
Sample grouping CSV Contrast CSV DESeq2 metadata CSV R handoff notes Handoff report Download instructions Open GEO dataset
Source
GEO
Search intent
Patient tissue tumor-vs-normal
Intent behavior
search-intent-behavior-v1
Submission date
2024-01-22
Last update
2025-05-10
Organization
Netherlands Cancer Institute
Department
Oncogenomics
Public date
2025-03-24
Experiment types
Expression profiling by high throughput sequencing
Platforms
GPL24676 Illumina NovaSeq 6000 (Homo sapiens)
Series type
SubSeries
SubSeries
Not available
BioProject
PRJNA1067833
Supplementary files
TXT: GSE253906_RNAseq_ECa_patients.txt.gz
Organism
Homo sapiens
Assay
bulk RNA-seq
Samples
6
Study design
Tumor vs unmatched normal
Specimen/source
Tissue
Scoring version
intent-aware-scoring-v15
Ranking batch
b69568dd1e4fe1b9ee2d880bf5495d748a7e4c5c11e4107f02528c3be0e76012
Ranking created
2026-06-05T20:20:27.088676Z
Warning version
intent-aware-warnings-v2

Current Intent Interpretation

Patient tissue tumor-vs-normal

Expectations

Organism
Homo sapiens
Assay
bulk RNA-seq
Specimen/source
patient tissue or biopsy
Controls
matched normal, adjacent normal, paired normal, healthy tissue control, or otherwise normal tissue control

Rules

Default filters
Human only; Bulk RNA-seq only; Tumor-normal only; Tissue or biopsy only; Hide biofluid/model systems
Warning rules
missing or unclear control group, unclear disease context, unclear tissue source, mixed sample types, model-system markers, secondary assay context, missing processed data, or small cohort size
Score caps
non-human datasets stay below the primary recommendation band, missing colorectal/colon/rectal/CRC context stays below the primary recommendation band, biofluid and model-system datasets cannot reach Recommended by default, microarray and secondary assays are capped unless explicitly enabled, or small cohorts are capped below high-confidence recommendations
Downgraded contexts
microarray unless explicitly enabled, biofluid-only datasets, cell-line datasets, organoid datasets, xenograft or PDX datasets, non-colorectal disease contexts, or treatment-only experiments

Study Classification

Tumor vs unmatched normal Tissue

Analysis Readiness

Review before analysis
87% DE readiness

Contrast completeness

25/25 pts

Both case and control groups are present in the proposed grouping.

Minimum group size

20/20 pts

Each contrast group has at least 2 samples.

Processed data availability

20/20 pts

Processed data is marked available in the GEO index.

Sample decision clarity

8/15 pts

A small number of samples remain unassigned.

Blocking warnings

7/10 pts

Warnings are present, but none are critical blockers.

Metadata normalization

7/10 pts

Metadata quality is usable, but still deserves review.

Blockers

  • 1 samples are still unassigned.

Next Steps

  • Resolve unassigned or review-needed samples in the grouping table.

Analysis Preparation Checklist

4/6 ready

Group labels reviewed

Needs review

Siftome proposed case and control labels, but no reviewer confirmation is stored yet.

Open the sample grouping CSV and confirm group labels before analysis.

Minimum sample count met

Ready

Both groups meet the minimum of 2 samples.

Confirm whether the cohort is large enough for the intended statistical analysis.

Processed counts available

Ready

Processed data availability is marked true in the GEO index.

Verify that downloaded processed files contain usable count or expression identifiers.

Ambiguous samples handled

Needs review

0 review-needed samples and 1 unassigned samples remain.

Resolve ambiguous and unassigned samples before finalizing the contrast.

Exclusion decisions recorded

Ready

No hard-excluded samples were detected by the current rules.

Record any manual exclusions in the downstream analysis notes.

Source links preserved

Ready

The dataset and sample accessions can be linked back to GEO.

Keep GEO dataset and sample links with exported metadata.

Bioinformatician Review

Bioinformatician review required

Ask a bioinformatician to review grouping, count availability, exclusions, and design before DE.

  • Analysis readiness has blockers that must be resolved before DE.
  • One or more samples are unassigned and need manual grouping decisions.

Why This Is Ranked Here

Patient tissue tumor-vs-normal
Exploratory only Dataset can inform exploration but is not strong enough for primary analysis.

Score Components

  • relevance 50% Organism normalized. Assay type normalized.
  • comparison suitability 5% Tumor and normal sample groups detected. No excluded sample type flags detected. Tumor/normal design boosted for colorectal tumor-vs-normal tissue triage. Patient tissue or biopsy specimens boosted for tissue comparison triage. Missing colorectal disease context downgraded for tumor-vs-normal tissue ranking.
  • metadata quality 70% Sample source clarity: All samples have source metadata and clear GSE/GSM accessions. Group clarity: Rule-based grouping found both case and control samples. Disease clarity: Disease or condition metadata was not normalized. Tissue clarity: Tissue metadata was not normalized. Treatment clarity: No unclear treatment split detected in the sample metadata. Replicate clarity: No pooled sample or technical replicate flags detected. Data availability clarity: Dataset-level processed or raw data availability is explicit.
  • data availability 100% Processed data available. Raw data available.
  • overall 45% Weighted score: 30% relevance, 30% comparison suitability, 25% metadata quality, 15% data availability. Overall score capped because comparison suitability is weak for the selected search intent. Overall score capped because fewer than ten samples limit cohort confidence. Overall score capped because colorectal/CRC disease context is not explicit.

Derived Classifications

  • Organism Homo sapiens Organism remains rule-derived: Homo sapiens.
  • Assay bulk RNA-seq Assay remains rule-derived: bulk RNA-seq.
  • Study design Tumor vs unmatched normal Study design remains rule-derived: Tumor vs unmatched normal.
  • Specimen/source Tissue Specimen/source remains rule-derived: Tissue.
  • Likely case group tumor sample 3 samples
  • Likely control group normal tissue 2 samples

Warnings

  • DISEASE_LABEL_UNCLEAR warning Disease or condition label could not be normalized.
  • TISSUE_TYPE_MISSING warning Tissue or cell type could not be normalized.

Intent Interpretation

  • Active intent Patient tissue tumor-vs-normal Ranks human colorectal tissue or biopsy cohorts where tumor samples can be compared with normal controls.
  • Organism expectation Homo sapiens Dataset organism is interpreted as Homo sapiens.
  • Assay expectation bulk RNA-seq Dataset assay is interpreted as bulk RNA-seq.
  • Specimen assumption patient tissue or biopsy Derived specimen/source is Tissue.
  • Control-group assumption matched normal, adjacent normal, paired normal, healthy tissue control, or otherwise normal tissue control Derived study design is Tumor vs unmatched normal; likely groups are tumor sample vs normal tissue.
  • Score caps Applied when matching conditions are present non-human datasets stay below the primary recommendation band, missing colorectal/colon/rectal/CRC context stays below the primary recommendation band, biofluid and model-system datasets cannot reach Recommended by default, microarray and secondary assays are capped unless explicitly enabled, or small cohorts are capped below high-confidence recommendations
  • Warning rules 2 active warnings missing or unclear control group, unclear disease context, unclear tissue source, mixed sample types, model-system markers, secondary assay context, missing processed data, or small cohort size
  • Downgrade or exclusion reason Downgraded disease context: colorectal/GI relevance is unclear. Derived from current-intent ranking reasons and warnings.

Applied Review Decisions

No active review decisions affect this ranking.

Ranking Facts

  • Recommendation Exploratory only Dataset can inform exploration but is not strong enough for primary analysis.
  • Supporting fact Tumor vs unmatched normal · Tissue · suitability 5%. Contributed to match or upgrade evidence.
  • Supporting fact Prioritized assay: bulk RNA-seq is the active assay expectation. Contributed to match or upgrade evidence.
  • Supporting fact Downgraded disease context: colorectal/GI relevance is unclear. Contributed to match or upgrade evidence.
  • Supporting fact Processed data is available for downstream review. Contributed to match or upgrade evidence.
  • Supporting fact 2 warnings require review. Contributed to match or upgrade evidence.
  • Caution fact Disease or condition label could not be normalized. Contributed to downgrade or manual-review evidence.
  • Caution fact Tissue or cell type could not be normalized. Contributed to downgrade or manual-review evidence.
  • Caution fact Missing colorectal disease context downgraded for tumor-vs-normal tissue ranking. Contributed to downgrade or manual-review evidence.
  • Caution fact Missing or unclear metadata: Missing colorectal disease context downgraded for tumor-vs-normal tissue ranking. Contributed to downgrade or manual-review evidence.
  • Caution fact Missing or unclear metadata: Disease clarity: Disease or condition metadata was not normalized. Contributed to downgrade or manual-review evidence.
  • Caution fact Missing or unclear metadata: Tissue clarity: Tissue metadata was not normalized. Contributed to downgrade or manual-review evidence.
  • Caution fact Missing or unclear metadata: Treatment clarity: No unclear treatment split detected in the sample metadata. Contributed to downgrade or manual-review evidence.
  • Caution fact Overall score capped because comparison suitability is weak for the selected search intent. Contributed to downgrade or manual-review evidence.
  • Caution fact Overall score capped because fewer than ten samples limit cohort confidence. Contributed to downgrade or manual-review evidence.
  • Caution fact Overall score capped because colorectal/CRC disease context is not explicit. Contributed to downgrade or manual-review evidence.
  • Caution fact Downgraded disease context: colorectal/GI relevance is unclear. Contributed to downgrade or manual-review evidence.
  • Caution fact Missing or unclear metadata: Downgraded disease context: colorectal/GI relevance is unclear. Contributed to downgrade or manual-review evidence.
  • Caution fact Comparison suitability score is below the Phase 1 recommended threshold. Contributed to downgrade or manual-review evidence.

Manual Corrections

0 active

Source Evidence

4 sources

GEO

Primary source

Original dataset metadata, sample metadata, source links, and GEO data availability flags.

Dataset accession
GSE253906
Sample records
6 GSM samples
  • GEO has priority for original metadata under the Phase 3J source rules.
  • Processed data: available.
  • Raw data: available.
  • No external source conflict is present in the current runtime data.

recount3

Not imported

Planned trusted source for processed count availability.

GEO accession
GSE253906
  • No recount3 project identifier has been imported for this dataset.
  • Once imported, recount3 has priority for processed count availability.
  • The recount3 source filter excludes this dataset until that linkage exists.
No recount3 sync data available.

Expression Atlas

Not imported

Planned source for curated expression experiment links.

GEO accession
GSE253906
  • No Expression Atlas experiment identifier has been imported for this dataset.
  • Once imported, Expression Atlas has priority for curated expression experiment links.
  • The Expression Atlas source filter excludes this dataset until that linkage exists.
No Expression Atlas sync data available.

PubMed

Unavailable

Publication context when PubMed identifiers are already known.

GEO accession
GSE253906
  • No PubMed identifier is present in the current runtime metadata.
  • No live PubMed search is performed from the dataset detail page.
No publication identifier imported.

Dataset Feedback

0 stored

Original GEO Metadata

dataset_accession: GSE253906
dataset_title: Enhancer plasticity in endometrial tumorigenesis demarcates non-coding driver mutations and 3D genome alterations to stimulate oncogene expression [RNA-seq_ECa_patients]
organism: Homo sapiens
assay_type: bulk RNA-seq
processed_data_available: true
raw_data_available: true
submission_date: 2024-01-22
last_update_date: 2025-05-10
organization_name: Netherlands Cancer Institute
department: Oncogenomics
public_date: 2025-03-24
experiment_types: Expression profiling by high throughput sequencing
platforms: GPL24676 Illumina NovaSeq 6000 (Homo sapiens)
sub_series: Not available
bioproject: PRJNA1067833
supplementary_files: TXT: GSE253906_RNAseq_ECa_patients.txt.gz
series_type: SubSeries

Why It Matched

  • Tumor vs unmatched normal · Tissue · suitability 5%.
  • Prioritized assay: bulk RNA-seq is the active assay expectation.
  • Downgraded disease context: colorectal/GI relevance is unclear.
  • Processed data is available for downstream review.
  • 2 warnings require review.

Why It May Not Be Suitable

  • Disease or condition label could not be normalized.
  • Tissue or cell type could not be normalized.
  • Missing colorectal disease context downgraded for tumor-vs-normal tissue ranking.
  • Missing or unclear metadata: Missing colorectal disease context downgraded for tumor-vs-normal tissue ranking.
  • Missing or unclear metadata: Disease clarity: Disease or condition metadata was not normalized.
  • Missing or unclear metadata: Tissue clarity: Tissue metadata was not normalized.
  • Missing or unclear metadata: Treatment clarity: No unclear treatment split detected in the sample metadata.
  • Overall score capped because comparison suitability is weak for the selected search intent.
  • Overall score capped because fewer than ten samples limit cohort confidence.
  • Overall score capped because colorectal/CRC disease context is not explicit.
  • Downgraded disease context: colorectal/GI relevance is unclear.
  • Missing or unclear metadata: Downgraded disease context: colorectal/GI relevance is unclear.
  • Comparison suitability score is below the Phase 1 recommended threshold.

Warnings

  • warning DISEASE_LABEL_UNCLEAR Disease or condition label could not be normalized.
  • warning TISSUE_TYPE_MISSING Tissue or cell type could not be normalized.

Normalized Fields

7 fields
Field Value Source Origin Confidence Evidence Reason
assay_type bulk RNA-seq dataset GSE253906 Runtime Siftome inference GEO:dataset:GSE253906:9b2784f34de555bf0b5afe18b0981fa5432c012b4227d89c4dc7c2d93e098d81 high confidence bulk rna-seq dataset_accession: GSE253906 dataset_title: Enhancer plasticity in endometrial tumorigenesis demarcates non-coding driver mutations and 3D genome alterations to stimulate oncoge... keyword match keyword match: bulk rna-seq
organism Homo sapiens dataset GSE253906 Runtime Siftome inference GEO:dataset:GSE253906:9b2784f34de555bf0b5afe18b0981fa5432c012b4227d89c4dc7c2d93e098d81 high confidence homo sapiens dataset_accession: GSE253906 dataset_title: Enhancer plasticity in endometrial tumorigenesis demarcates non-coding driver mutations and 3D genome alterations to stimulate oncoge... keyword match keyword match: homo sapiens
sample_type normal tissue sample GSM8029980 Runtime Siftome inference GEO:sample:GSM8029980:d648bf753871df265bc9cced29e8dcfda7385e8388cdc8869afc926a8092521d low confidence normal sample_accession: GSM8029980 sample_title: RNAseq_H.005.A2 source_name: Healthy Endometrium characteristics: tissue: Healthy Endometrium; cell type: Healthy Endometrium; genotyp... controlled vocabulary controlled vocabulary sample type match: normal
sample_type tumor sample sample GSM8029981 Runtime Siftome inference GEO:sample:GSM8029981:43aca42369da919597032fd170595cb46056d46f90104afb5856350e3fd8f0e2 low confidence tumor sample_accession: GSM8029981 sample_title: RNAseq_T.039.II1 source_name: Endometrial cancer characteristics: tissue: Endometrial cancer; cell type: Endometrial cancer; genotype:... controlled vocabulary controlled vocabulary sample type match: tumor
sample_type tumor sample sample GSM8029982 Runtime Siftome inference GEO:sample:GSM8029982:07d6c9e8e40ba8e0f6084fdf2e3b6803895022d0637e832d28084b3b17ce4838 low confidence tumor sample_accession: GSM8029982 sample_title: RNAseq_T.081.A1 source_name: Endometrial cancer characteristics: tissue: Endometrial cancer; cell type: Endometrial cancer; genotype: ... controlled vocabulary controlled vocabulary sample type match: tumor
sample_type tumor sample sample GSM8029984 Runtime Siftome inference GEO:sample:GSM8029984:7061ae7b3b43c4e20491e45087e44f657027824b9f80d6f9cf18b9408d3138f2 low confidence tumor sample_accession: GSM8029984 sample_title: RNAseq_T.001.A1 source_name: Endometrial cancer characteristics: tissue: Endometrial cancer; cell type: Endometrial cancer; genotype: ... controlled vocabulary controlled vocabulary sample type match: tumor
sample_type normal tissue sample GSM8029985 Runtime Siftome inference GEO:sample:GSM8029985:6e8377ebfeece9e545060004c88fd782c4ae6fccb8b325d93391d982e0e7892e low confidence normal sample_accession: GSM8029985 sample_title: RNAseq_H.081.A2 source_name: Healthy Endometrium characteristics: tissue: Healthy Endometrium; cell type: Healthy Endometrium; genotyp... controlled vocabulary controlled vocabulary sample type match: normal

Sample Group Preview

Possible case samples

Samples currently treated as the comparison case group.

3
  • GSM8029981 RNAseq_T.039.II1 tumor sample Case marker detected. Endometrial cancer tissue: Endometrial cancer; cell type: Endometrial cancer; genotype: Tumor
  • GSM8029982 RNAseq_T.081.A1 tumor sample Case marker detected. Endometrial cancer tissue: Endometrial cancer; cell type: Endometrial cancer; genotype: Tumor
  • GSM8029984 RNAseq_T.001.A1 tumor sample Case marker detected. Endometrial cancer tissue: Endometrial cancer; cell type: Endometrial cancer; genotype: Tumor

Possible control samples

Samples currently treated as controls or baseline.

2
  • GSM8029980 RNAseq_H.005.A2 normal tissue Control marker detected. Healthy Endometrium tissue: Healthy Endometrium; cell type: Healthy Endometrium; genotype: Normal
  • GSM8029985 RNAseq_H.081.A2 normal tissue Control marker detected. Healthy Endometrium tissue: Healthy Endometrium; cell type: Healthy Endometrium; genotype: Normal

Unassigned samples

Samples with no explicit case or control marker.

1
  • GSM8029983 RNAseq_H.069.C2 unassigned No explicit case or control marker detected. Healthy Endometrium tissue: Healthy Endometrium; cell type: Healthy Endometrium; genotype: N ormal

Excluded samples

Samples excluded from grouping by hard exclusion rules.

0

No samples

Ambiguous samples

Samples that need manual review before trusting grouping.

0

No samples

Metadata Quality Components

Persisted metadata quality

70 pts
Clarity
70%
Weight
100 pts

Sample source clarity: All samples have source metadata and clear GSE/GSM accessions. Group clarity: Rule-based grouping found both case and control samples. Disease clarity: Disease or condition metadata was not normalized. Tissue clarity: Tissue metadata was not normalized. Treatment clarity: No unclear treatment split detected in the sample metadata. Replicate clarity: No pooled sample or technical replicate flags detected. Data availability clarity: Dataset-level processed or raw data availability is explicit.

Detected Sample Groups

normal tissue

2 samples
  • GSM8029980 RNAseq_H.005.A2 Healthy Endometrium tissue: Healthy Endometrium; cell type: Healthy Endometrium; genotype: Normal
  • GSM8029985 RNAseq_H.081.A2 Healthy Endometrium tissue: Healthy Endometrium; cell type: Healthy Endometrium; genotype: Normal

tumor sample

3 samples
  • GSM8029981 RNAseq_T.039.II1 Endometrial cancer tissue: Endometrial cancer; cell type: Endometrial cancer; genotype: Tumor
  • GSM8029982 RNAseq_T.081.A1 Endometrial cancer tissue: Endometrial cancer; cell type: Endometrial cancer; genotype: Tumor
  • GSM8029984 RNAseq_T.001.A1 Endometrial cancer tissue: Endometrial cancer; cell type: Endometrial cancer; genotype: Tumor

unassigned

1 sample
  • GSM8029983 RNAseq_H.069.C2 Healthy Endometrium tissue: Healthy Endometrium; cell type: Healthy Endometrium; genotype: N ormal

Score Breakdown

50%

relevance

  • Organism normalized.
  • Assay type normalized.
5%

comparison suitability

  • Tumor and normal sample groups detected.
  • No excluded sample type flags detected.
  • Tumor/normal design boosted for colorectal tumor-vs-normal tissue triage.
  • Patient tissue or biopsy specimens boosted for tissue comparison triage.
  • Missing colorectal disease context downgraded for tumor-vs-normal tissue ranking.
70%

metadata quality

  • Sample source clarity: All samples have source metadata and clear GSE/GSM accessions.
  • Group clarity: Rule-based grouping found both case and control samples.
  • Disease clarity: Disease or condition metadata was not normalized.
  • Tissue clarity: Tissue metadata was not normalized.
  • Treatment clarity: No unclear treatment split detected in the sample metadata.
  • Replicate clarity: No pooled sample or technical replicate flags detected.
  • Data availability clarity: Dataset-level processed or raw data availability is explicit.
100%

data availability

  • Processed data available.
  • Raw data available.
45%

overall

  • Weighted score: 30% relevance, 30% comparison suitability, 25% metadata quality, 15% data availability.
  • Overall score capped because comparison suitability is weak for the selected search intent.
  • Overall score capped because fewer than ten samples limit cohort confidence.
  • Overall score capped because colorectal/CRC disease context is not explicit.

Sample Links

6 samples

Review Audit Trail

0 decisions

No review decisions have been stored for this dataset.