Siftome Phase 3L

GSE213565

Transcriptional Characterization of Early Esophageal Squamous Cell Carcinoma

Not suitable Dataset does not meet the current suitability threshold.
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
2022-09-16
Last update
2023-09-09
Organization
Fudan University
Department
Not available
Public date
2023-09-09
Experiment types
Expression profiling by high throughput sequencing
Platforms
GPL24676 Illumina NovaSeq 6000 (Homo sapiens)
Series type
Series
SubSeries
Not available
BioProject
PRJNA881354
Supplementary files
TXT: GSE213565_All_exp_FPKM.txt.gz
Organism
Homo sapiens
Assay
bulk RNA-seq
Samples
20
Study design
Tumor vs matched 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 matched normal Tissue

Analysis Readiness

Ready after review
94% 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

15/15 pts

All samples are assigned to a case or control group.

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

No readiness blockers detected.

Next Steps

  • Review the sample grouping CSV and contrast CSV before running differential expression.
  • Confirm processed count files and sample identifiers match the exported metadata.

Analysis Preparation Checklist

5/6 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

Ready

No review-needed or unassigned samples are present in the proposed grouping.

Still scan the grouping table for biology-specific ambiguity.

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

Standard analyst review

Proceed only after the analyst confirms grouping, exclusions, and source files.

No expert-review triggers were detected by Siftome.

Why This Is Ranked Here

Patient tissue tumor-vs-normal
Not suitable Dataset does not meet the current suitability threshold.

Score Components

  • relevance 50% Organism normalized. Assay type normalized.
  • comparison suitability 0% Tumor and normal sample groups detected. No excluded sample type flags detected. Matched tumor/normal design boosted for colorectal tumor-vs-normal tissue triage. Patient tissue or biopsy specimens boosted for tissue comparison triage. Non-colorectal cancer context downgraded for colorectal 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 34% 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 tumor/normal grouping is from a non-colorectal cancer context.

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 matched normal Study design remains rule-derived: Tumor vs matched normal.
  • Specimen/source Tissue Specimen/source remains rule-derived: Tissue.
  • Likely case group tumor sample 10 samples
  • Likely control group normal tissue 10 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 matched 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: not a colorectal/GI cancer cohort. Derived from current-intent ranking reasons and warnings.

Applied Review Decisions

No active review decisions affect this ranking.

Ranking Facts

  • Recommendation Not suitable Dataset does not meet the current suitability threshold.
  • Supporting fact Tumor vs matched normal · Tissue · suitability 0%. Contributed to match or upgrade evidence.
  • Supporting fact Prioritized for patient tissue tumor-vs-normal triage. 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: not a colorectal/GI cancer cohort. 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 Non-colorectal cancer context downgraded for colorectal 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 tumor/normal grouping is from a non-colorectal cancer context. Contributed to downgrade or manual-review evidence.
  • Caution fact Downgraded disease context: not a colorectal/GI cancer cohort. 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
GSE213565
Sample records
20 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
GSE213565
  • 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
GSE213565
  • 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
GSE213565
  • 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: GSE213565
dataset_title: Transcriptional Characterization of Early Esophageal Squamous Cell Carcinoma
organism: Homo sapiens
assay_type: bulk RNA-seq
processed_data_available: true
raw_data_available: true
submission_date: 2022-09-16
last_update_date: 2023-09-09
organization_name: Fudan University
department: Not available
public_date: 2023-09-09
experiment_types: Expression profiling by high throughput sequencing
platforms: GPL24676 Illumina NovaSeq 6000 (Homo sapiens)
sub_series: Not available
bioproject: PRJNA881354
supplementary_files: TXT: GSE213565_All_exp_FPKM.txt.gz
series_type: Series

Why It Matched

  • Tumor vs matched normal · Tissue · suitability 0%.
  • Prioritized for patient tissue tumor-vs-normal triage.
  • Prioritized assay: bulk RNA-seq is the active assay expectation.
  • Downgraded disease context: not a colorectal/GI cancer cohort.
  • 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.
  • Non-colorectal cancer context downgraded for colorectal 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 tumor/normal grouping is from a non-colorectal cancer context.
  • Downgraded disease context: not a colorectal/GI cancer cohort.
  • 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

42 fields
Field Value Source Origin Confidence Evidence Reason
assay_type bulk RNA-seq dataset GSE213565 Runtime Siftome inference GEO:dataset:GSE213565:7d2d109185ded5b74fa5f4e4353f4eed68b95b2f58712f6eb041dec0c9744b7b high confidence bulk rna-seq dataset_accession: GSE213565 dataset_title: Transcriptional Characterization of Early Esophageal Squamous Cell Carcinoma organism: Homo sapiens assay_type: bulk RNA-seq processe... keyword match keyword match: bulk rna-seq
normal_tissue_type adjacent normal sample GSM6589221 Runtime Siftome inference GEO:sample:GSM6589221:5f5f17bf46344b2bde07226c00fab6b056b5aa8be741193862d8348242d06e54 high confidence adjacent normal sample_accession: GSM6589221 sample_title: ESCA01N source_name: esophagus tissue characteristics: disease state: Early Esophageal Squamous Cell Carcinoma; tissue: esophagus tiss... controlled vocabulary controlled vocabulary normal tissue type match: adjacent normal
normal_tissue_type adjacent normal sample GSM6589222 Runtime Siftome inference GEO:sample:GSM6589222:c7dd2fd2005838f3240bc1f42d7e0ec35e47e8054e08589a2a9f41089ac40923 high confidence adjacent normal sample_accession: GSM6589222 sample_title: ESCA07N source_name: esophagus tissue characteristics: disease state: Early Esophageal Squamous Cell Carcinoma; tissue: esophagus tiss... controlled vocabulary controlled vocabulary normal tissue type match: adjacent normal
normal_tissue_type adjacent normal sample GSM6589223 Runtime Siftome inference GEO:sample:GSM6589223:c05afeb69c9986983ee96a0c3686640948ed5c89e8838428636e9cb68737f4a8 high confidence adjacent normal sample_accession: GSM6589223 sample_title: ESCA10N source_name: esophagus tissue characteristics: disease state: Early Esophageal Squamous Cell Carcinoma; tissue: esophagus tiss... controlled vocabulary controlled vocabulary normal tissue type match: adjacent normal
normal_tissue_type adjacent normal sample GSM6589224 Runtime Siftome inference GEO:sample:GSM6589224:b77840277dbe5a108254985beb1987ec9be17242ef281d749fc12d8e12315196 high confidence adjacent normal sample_accession: GSM6589224 sample_title: ESCA14N source_name: esophagus tissue characteristics: disease state: Early Esophageal Squamous Cell Carcinoma; tissue: esophagus tiss... controlled vocabulary controlled vocabulary normal tissue type match: adjacent normal
normal_tissue_type adjacent normal sample GSM6589225 Runtime Siftome inference GEO:sample:GSM6589225:d944b8ebc40375c5b3cad646885ef6f3e516f8d246d8c952a0582c4f1058fe2f high confidence adjacent normal sample_accession: GSM6589225 sample_title: ESCA15N source_name: esophagus tissue characteristics: disease state: Early Esophageal Squamous Cell Carcinoma; tissue: esophagus tiss... controlled vocabulary controlled vocabulary normal tissue type match: adjacent normal
normal_tissue_type adjacent normal sample GSM6589226 Runtime Siftome inference GEO:sample:GSM6589226:c7caba841220e641bbc6a7d10e600bc8c38ac8aeae7c58fb75c9ddb886bac815 high confidence adjacent normal sample_accession: GSM6589226 sample_title: ESCA16N source_name: esophagus tissue characteristics: disease state: Early Esophageal Squamous Cell Carcinoma; tissue: esophagus tiss... controlled vocabulary controlled vocabulary normal tissue type match: adjacent normal
normal_tissue_type adjacent normal sample GSM6589227 Runtime Siftome inference GEO:sample:GSM6589227:802e16c7368d483d091d48c02d13993313d78ad8bdf8f411c66dd98db5db2914 high confidence adjacent normal sample_accession: GSM6589227 sample_title: ESCA17N source_name: esophagus tissue characteristics: disease state: Early Esophageal Squamous Cell Carcinoma; tissue: esophagus tiss... controlled vocabulary controlled vocabulary normal tissue type match: adjacent normal
normal_tissue_type adjacent normal sample GSM6589228 Runtime Siftome inference GEO:sample:GSM6589228:ebb64d47714122dba73d36e6b3acecfbff6877e7ee6299448fe0715e4808a432 high confidence adjacent normal sample_accession: GSM6589228 sample_title: ESCA18N source_name: esophagus tissue characteristics: disease state: Early Esophageal Squamous Cell Carcinoma; tissue: esophagus tiss... controlled vocabulary controlled vocabulary normal tissue type match: adjacent normal
normal_tissue_type adjacent normal sample GSM6589229 Runtime Siftome inference GEO:sample:GSM6589229:a23131427960050875b3da83bdf1b2c9bf9f334d6f52076383b9bfeafe87db79 high confidence adjacent normal sample_accession: GSM6589229 sample_title: ESCA19N source_name: esophagus tissue characteristics: disease state: Early Esophageal Squamous Cell Carcinoma; tissue: esophagus tiss... controlled vocabulary controlled vocabulary normal tissue type match: adjacent normal
normal_tissue_type adjacent normal sample GSM6589230 Runtime Siftome inference GEO:sample:GSM6589230:a621dd1cfd6edff40c0d974f36626a714efd799a8695023f4aa9fbc0a4f8be1c high confidence adjacent normal sample_accession: GSM6589230 sample_title: ESCA20N source_name: esophagus tissue characteristics: disease state: Early Esophageal Squamous Cell Carcinoma; tissue: esophagus tiss... controlled vocabulary controlled vocabulary normal tissue type match: adjacent normal
organism Homo sapiens dataset GSE213565 Runtime Siftome inference GEO:dataset:GSE213565:7d2d109185ded5b74fa5f4e4353f4eed68b95b2f58712f6eb041dec0c9744b7b high confidence homo sapiens dataset_accession: GSE213565 dataset_title: Transcriptional Characterization of Early Esophageal Squamous Cell Carcinoma organism: Homo sapiens assay_type: bulk RNA-seq processe... keyword match keyword match: homo sapiens
sample_type normal tissue sample GSM6589221 Runtime Siftome inference GEO:sample:GSM6589221:5f5f17bf46344b2bde07226c00fab6b056b5aa8be741193862d8348242d06e54 high confidence adjacent normal sample_accession: GSM6589221 sample_title: ESCA01N source_name: esophagus tissue characteristics: disease state: Early Esophageal Squamous Cell Carcinoma; tissue: esophagus tiss... controlled vocabulary controlled vocabulary sample type match: adjacent normal
sample_type tumor sample sample GSM6589221 Runtime Siftome inference GEO:sample:GSM6589221:5f5f17bf46344b2bde07226c00fab6b056b5aa8be741193862d8348242d06e54 medium confidence carcinoma sample_accession: GSM6589221 sample_title: ESCA01N source_name: esophagus tissue characteristics: disease state: Early Esophageal Squamous Cell Carcinoma; tissue: esophagus tiss... controlled vocabulary controlled vocabulary sample type match: carcinoma
sample_type normal tissue sample GSM6589222 Runtime Siftome inference GEO:sample:GSM6589222:c7dd2fd2005838f3240bc1f42d7e0ec35e47e8054e08589a2a9f41089ac40923 high confidence adjacent normal sample_accession: GSM6589222 sample_title: ESCA07N source_name: esophagus tissue characteristics: disease state: Early Esophageal Squamous Cell Carcinoma; tissue: esophagus tiss... controlled vocabulary controlled vocabulary sample type match: adjacent normal
sample_type tumor sample sample GSM6589222 Runtime Siftome inference GEO:sample:GSM6589222:c7dd2fd2005838f3240bc1f42d7e0ec35e47e8054e08589a2a9f41089ac40923 medium confidence carcinoma sample_accession: GSM6589222 sample_title: ESCA07N source_name: esophagus tissue characteristics: disease state: Early Esophageal Squamous Cell Carcinoma; tissue: esophagus tiss... controlled vocabulary controlled vocabulary sample type match: carcinoma
sample_type normal tissue sample GSM6589223 Runtime Siftome inference GEO:sample:GSM6589223:c05afeb69c9986983ee96a0c3686640948ed5c89e8838428636e9cb68737f4a8 high confidence adjacent normal sample_accession: GSM6589223 sample_title: ESCA10N source_name: esophagus tissue characteristics: disease state: Early Esophageal Squamous Cell Carcinoma; tissue: esophagus tiss... controlled vocabulary controlled vocabulary sample type match: adjacent normal
sample_type tumor sample sample GSM6589223 Runtime Siftome inference GEO:sample:GSM6589223:c05afeb69c9986983ee96a0c3686640948ed5c89e8838428636e9cb68737f4a8 medium confidence carcinoma sample_accession: GSM6589223 sample_title: ESCA10N source_name: esophagus tissue characteristics: disease state: Early Esophageal Squamous Cell Carcinoma; tissue: esophagus tiss... controlled vocabulary controlled vocabulary sample type match: carcinoma
sample_type normal tissue sample GSM6589224 Runtime Siftome inference GEO:sample:GSM6589224:b77840277dbe5a108254985beb1987ec9be17242ef281d749fc12d8e12315196 high confidence adjacent normal sample_accession: GSM6589224 sample_title: ESCA14N source_name: esophagus tissue characteristics: disease state: Early Esophageal Squamous Cell Carcinoma; tissue: esophagus tiss... controlled vocabulary controlled vocabulary sample type match: adjacent normal
sample_type tumor sample sample GSM6589224 Runtime Siftome inference GEO:sample:GSM6589224:b77840277dbe5a108254985beb1987ec9be17242ef281d749fc12d8e12315196 medium confidence carcinoma sample_accession: GSM6589224 sample_title: ESCA14N source_name: esophagus tissue characteristics: disease state: Early Esophageal Squamous Cell Carcinoma; tissue: esophagus tiss... controlled vocabulary controlled vocabulary sample type match: carcinoma
sample_type normal tissue sample GSM6589225 Runtime Siftome inference GEO:sample:GSM6589225:d944b8ebc40375c5b3cad646885ef6f3e516f8d246d8c952a0582c4f1058fe2f high confidence adjacent normal sample_accession: GSM6589225 sample_title: ESCA15N source_name: esophagus tissue characteristics: disease state: Early Esophageal Squamous Cell Carcinoma; tissue: esophagus tiss... controlled vocabulary controlled vocabulary sample type match: adjacent normal
sample_type tumor sample sample GSM6589225 Runtime Siftome inference GEO:sample:GSM6589225:d944b8ebc40375c5b3cad646885ef6f3e516f8d246d8c952a0582c4f1058fe2f medium confidence carcinoma sample_accession: GSM6589225 sample_title: ESCA15N source_name: esophagus tissue characteristics: disease state: Early Esophageal Squamous Cell Carcinoma; tissue: esophagus tiss... controlled vocabulary controlled vocabulary sample type match: carcinoma
sample_type normal tissue sample GSM6589226 Runtime Siftome inference GEO:sample:GSM6589226:c7caba841220e641bbc6a7d10e600bc8c38ac8aeae7c58fb75c9ddb886bac815 high confidence adjacent normal sample_accession: GSM6589226 sample_title: ESCA16N source_name: esophagus tissue characteristics: disease state: Early Esophageal Squamous Cell Carcinoma; tissue: esophagus tiss... controlled vocabulary controlled vocabulary sample type match: adjacent normal
sample_type tumor sample sample GSM6589226 Runtime Siftome inference GEO:sample:GSM6589226:c7caba841220e641bbc6a7d10e600bc8c38ac8aeae7c58fb75c9ddb886bac815 medium confidence carcinoma sample_accession: GSM6589226 sample_title: ESCA16N source_name: esophagus tissue characteristics: disease state: Early Esophageal Squamous Cell Carcinoma; tissue: esophagus tiss... controlled vocabulary controlled vocabulary sample type match: carcinoma
sample_type normal tissue sample GSM6589227 Runtime Siftome inference GEO:sample:GSM6589227:802e16c7368d483d091d48c02d13993313d78ad8bdf8f411c66dd98db5db2914 high confidence adjacent normal sample_accession: GSM6589227 sample_title: ESCA17N source_name: esophagus tissue characteristics: disease state: Early Esophageal Squamous Cell Carcinoma; tissue: esophagus tiss... controlled vocabulary controlled vocabulary sample type match: adjacent normal
sample_type tumor sample sample GSM6589227 Runtime Siftome inference GEO:sample:GSM6589227:802e16c7368d483d091d48c02d13993313d78ad8bdf8f411c66dd98db5db2914 medium confidence carcinoma sample_accession: GSM6589227 sample_title: ESCA17N source_name: esophagus tissue characteristics: disease state: Early Esophageal Squamous Cell Carcinoma; tissue: esophagus tiss... controlled vocabulary controlled vocabulary sample type match: carcinoma
sample_type normal tissue sample GSM6589228 Runtime Siftome inference GEO:sample:GSM6589228:ebb64d47714122dba73d36e6b3acecfbff6877e7ee6299448fe0715e4808a432 high confidence adjacent normal sample_accession: GSM6589228 sample_title: ESCA18N source_name: esophagus tissue characteristics: disease state: Early Esophageal Squamous Cell Carcinoma; tissue: esophagus tiss... controlled vocabulary controlled vocabulary sample type match: adjacent normal
sample_type tumor sample sample GSM6589228 Runtime Siftome inference GEO:sample:GSM6589228:ebb64d47714122dba73d36e6b3acecfbff6877e7ee6299448fe0715e4808a432 medium confidence carcinoma sample_accession: GSM6589228 sample_title: ESCA18N source_name: esophagus tissue characteristics: disease state: Early Esophageal Squamous Cell Carcinoma; tissue: esophagus tiss... controlled vocabulary controlled vocabulary sample type match: carcinoma
sample_type normal tissue sample GSM6589229 Runtime Siftome inference GEO:sample:GSM6589229:a23131427960050875b3da83bdf1b2c9bf9f334d6f52076383b9bfeafe87db79 high confidence adjacent normal sample_accession: GSM6589229 sample_title: ESCA19N source_name: esophagus tissue characteristics: disease state: Early Esophageal Squamous Cell Carcinoma; tissue: esophagus tiss... controlled vocabulary controlled vocabulary sample type match: adjacent normal
sample_type tumor sample sample GSM6589229 Runtime Siftome inference GEO:sample:GSM6589229:a23131427960050875b3da83bdf1b2c9bf9f334d6f52076383b9bfeafe87db79 medium confidence carcinoma sample_accession: GSM6589229 sample_title: ESCA19N source_name: esophagus tissue characteristics: disease state: Early Esophageal Squamous Cell Carcinoma; tissue: esophagus tiss... controlled vocabulary controlled vocabulary sample type match: carcinoma
sample_type normal tissue sample GSM6589230 Runtime Siftome inference GEO:sample:GSM6589230:a621dd1cfd6edff40c0d974f36626a714efd799a8695023f4aa9fbc0a4f8be1c high confidence adjacent normal sample_accession: GSM6589230 sample_title: ESCA20N source_name: esophagus tissue characteristics: disease state: Early Esophageal Squamous Cell Carcinoma; tissue: esophagus tiss... controlled vocabulary controlled vocabulary sample type match: adjacent normal
sample_type tumor sample sample GSM6589230 Runtime Siftome inference GEO:sample:GSM6589230:a621dd1cfd6edff40c0d974f36626a714efd799a8695023f4aa9fbc0a4f8be1c medium confidence carcinoma sample_accession: GSM6589230 sample_title: ESCA20N source_name: esophagus tissue characteristics: disease state: Early Esophageal Squamous Cell Carcinoma; tissue: esophagus tiss... controlled vocabulary controlled vocabulary sample type match: carcinoma
sample_type tumor sample sample GSM6589231 Runtime Siftome inference GEO:sample:GSM6589231:4f0f56bcd48254ba8ebceff8609e57c605748cf797d5c6ca95df2edae03c44b7 low confidence tumor sample_accession: GSM6589231 sample_title: ESCA01T source_name: esophagus tissue characteristics: disease state: Early Esophageal Squamous Cell Carcinoma; tissue: esophagus tiss... controlled vocabulary controlled vocabulary sample type match: tumor
sample_type tumor sample sample GSM6589232 Runtime Siftome inference GEO:sample:GSM6589232:eacf8edf98e2ae0eba9aabcb88134d55ef7c8a1f7d3a1e7562b01c4acab9bded low confidence tumor sample_accession: GSM6589232 sample_title: ESCA07T source_name: esophagus tissue characteristics: disease state: Early Esophageal Squamous Cell Carcinoma; tissue: esophagus tiss... controlled vocabulary controlled vocabulary sample type match: tumor
sample_type tumor sample sample GSM6589233 Runtime Siftome inference GEO:sample:GSM6589233:65ba86d4f0b08a49d5aad9519adf0995b302fc141a68044cb5401d109ae5a1de low confidence tumor sample_accession: GSM6589233 sample_title: ESCA10T source_name: esophagus tissue characteristics: disease state: Early Esophageal Squamous Cell Carcinoma; tissue: esophagus tiss... controlled vocabulary controlled vocabulary sample type match: tumor
sample_type tumor sample sample GSM6589234 Runtime Siftome inference GEO:sample:GSM6589234:2ec7d3d54fd556ce40d4da7476811c679b0433d3805fc5046236a33a64267f9b low confidence tumor sample_accession: GSM6589234 sample_title: ESCA14T source_name: esophagus tissue characteristics: disease state: Early Esophageal Squamous Cell Carcinoma; tissue: esophagus tiss... controlled vocabulary controlled vocabulary sample type match: tumor
sample_type tumor sample sample GSM6589235 Runtime Siftome inference GEO:sample:GSM6589235:ccb3b0044a44181907e53fc70880a26e3c171d49c64d6b6fc58896bb7f6ad83d low confidence tumor sample_accession: GSM6589235 sample_title: ESCA15T source_name: esophagus tissue characteristics: disease state: Early Esophageal Squamous Cell Carcinoma; tissue: esophagus tiss... controlled vocabulary controlled vocabulary sample type match: tumor
sample_type tumor sample sample GSM6589236 Runtime Siftome inference GEO:sample:GSM6589236:2003ee21b31103d104ccdd22b47e43ef594971b7ab78c2850743767bbabee5f3 low confidence tumor sample_accession: GSM6589236 sample_title: ESCA16T source_name: esophagus tissue characteristics: disease state: Early Esophageal Squamous Cell Carcinoma; tissue: esophagus tiss... controlled vocabulary controlled vocabulary sample type match: tumor
sample_type tumor sample sample GSM6589237 Runtime Siftome inference GEO:sample:GSM6589237:85f12c359170fb99c2b9757d025cbc197cce1e7a8a6c770d3a6168860f6aa46d low confidence tumor sample_accession: GSM6589237 sample_title: ESCA17T source_name: esophagus tissue characteristics: disease state: Early Esophageal Squamous Cell Carcinoma; tissue: esophagus tiss... controlled vocabulary controlled vocabulary sample type match: tumor
sample_type tumor sample sample GSM6589238 Runtime Siftome inference GEO:sample:GSM6589238:8b387b614dff6979cdd0a4c5c53b321818022a9a6ec906839f4460cdac684bbe low confidence tumor sample_accession: GSM6589238 sample_title: ESCA18T source_name: esophagus tissue characteristics: disease state: Early Esophageal Squamous Cell Carcinoma; tissue: esophagus tiss... controlled vocabulary controlled vocabulary sample type match: tumor
sample_type tumor sample sample GSM6589239 Runtime Siftome inference GEO:sample:GSM6589239:741a0b3a2fa52d322a11a53fb9acdca66a20abf969759a09d1ce947cd4bcee7b low confidence tumor sample_accession: GSM6589239 sample_title: ESCA19T source_name: esophagus tissue characteristics: disease state: Early Esophageal Squamous Cell Carcinoma; tissue: esophagus tiss... controlled vocabulary controlled vocabulary sample type match: tumor
sample_type tumor sample sample GSM6589240 Runtime Siftome inference GEO:sample:GSM6589240:66287975a44267b07cbf1ad2429c98e50e8e9e32cc0ebaa9fe36f4bede447883 low confidence tumor sample_accession: GSM6589240 sample_title: ESCA20T source_name: esophagus tissue characteristics: disease state: Early Esophageal Squamous Cell Carcinoma; tissue: esophagus tiss... controlled vocabulary controlled vocabulary sample type match: tumor

Sample Group Preview

Possible case samples

Samples currently treated as the comparison case group.

10
  • GSM6589231 ESCA01T tumor sample Case marker detected. esophagus tissue disease state: Early Esophageal Squamous Cell Carcinoma; tissue: esophagus tissue; cell type: tumor
  • GSM6589232 ESCA07T tumor sample Case marker detected. esophagus tissue disease state: Early Esophageal Squamous Cell Carcinoma; tissue: esophagus tissue; cell type: tumor
  • GSM6589233 ESCA10T tumor sample Case marker detected. esophagus tissue disease state: Early Esophageal Squamous Cell Carcinoma; tissue: esophagus tissue; cell type: tumor
  • GSM6589234 ESCA14T tumor sample Case marker detected. esophagus tissue disease state: Early Esophageal Squamous Cell Carcinoma; tissue: esophagus tissue; cell type: tumor
  • GSM6589235 ESCA15T tumor sample Case marker detected. esophagus tissue disease state: Early Esophageal Squamous Cell Carcinoma; tissue: esophagus tissue; cell type: tumor
  • GSM6589236 ESCA16T tumor sample Case marker detected. esophagus tissue disease state: Early Esophageal Squamous Cell Carcinoma; tissue: esophagus tissue; cell type: tumor
  • GSM6589237 ESCA17T tumor sample Case marker detected. esophagus tissue disease state: Early Esophageal Squamous Cell Carcinoma; tissue: esophagus tissue; cell type: tumor
  • GSM6589238 ESCA18T tumor sample Case marker detected. esophagus tissue disease state: Early Esophageal Squamous Cell Carcinoma; tissue: esophagus tissue; cell type: tumor
  • GSM6589239 ESCA19T tumor sample Case marker detected. esophagus tissue disease state: Early Esophageal Squamous Cell Carcinoma; tissue: esophagus tissue; cell type: tumor
  • GSM6589240 ESCA20T tumor sample Case marker detected. esophagus tissue disease state: Early Esophageal Squamous Cell Carcinoma; tissue: esophagus tissue; cell type: tumor

Possible control samples

Samples currently treated as controls or baseline.

10
  • GSM6589221 ESCA01N normal tissue Control marker detected. esophagus tissue disease state: Early Esophageal Squamous Cell Carcinoma; tissue: esophagus tissue; cell type: adjacent normal
  • GSM6589222 ESCA07N normal tissue Control marker detected. esophagus tissue disease state: Early Esophageal Squamous Cell Carcinoma; tissue: esophagus tissue; cell type: adjacent normal
  • GSM6589223 ESCA10N normal tissue Control marker detected. esophagus tissue disease state: Early Esophageal Squamous Cell Carcinoma; tissue: esophagus tissue; cell type: adjacent normal
  • GSM6589224 ESCA14N normal tissue Control marker detected. esophagus tissue disease state: Early Esophageal Squamous Cell Carcinoma; tissue: esophagus tissue; cell type: adjacent normal
  • GSM6589225 ESCA15N normal tissue Control marker detected. esophagus tissue disease state: Early Esophageal Squamous Cell Carcinoma; tissue: esophagus tissue; cell type: adjacent normal
  • GSM6589226 ESCA16N normal tissue Control marker detected. esophagus tissue disease state: Early Esophageal Squamous Cell Carcinoma; tissue: esophagus tissue; cell type: adjacent normal
  • GSM6589227 ESCA17N normal tissue Control marker detected. esophagus tissue disease state: Early Esophageal Squamous Cell Carcinoma; tissue: esophagus tissue; cell type: adjacent normal
  • GSM6589228 ESCA18N normal tissue Control marker detected. esophagus tissue disease state: Early Esophageal Squamous Cell Carcinoma; tissue: esophagus tissue; cell type: adjacent normal
  • GSM6589229 ESCA19N normal tissue Control marker detected. esophagus tissue disease state: Early Esophageal Squamous Cell Carcinoma; tissue: esophagus tissue; cell type: adjacent normal
  • GSM6589230 ESCA20N normal tissue Control marker detected. esophagus tissue disease state: Early Esophageal Squamous Cell Carcinoma; tissue: esophagus tissue; cell type: adjacent normal

Unassigned samples

Samples with no explicit case or control marker.

0

No samples

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

10 samples
  • GSM6589221 ESCA01N esophagus tissue disease state: Early Esophageal Squamous Cell Carcinoma; tissue: esophagus tissue; cell type: adjacent normal
  • GSM6589222 ESCA07N esophagus tissue disease state: Early Esophageal Squamous Cell Carcinoma; tissue: esophagus tissue; cell type: adjacent normal
  • GSM6589223 ESCA10N esophagus tissue disease state: Early Esophageal Squamous Cell Carcinoma; tissue: esophagus tissue; cell type: adjacent normal
  • GSM6589224 ESCA14N esophagus tissue disease state: Early Esophageal Squamous Cell Carcinoma; tissue: esophagus tissue; cell type: adjacent normal
  • GSM6589225 ESCA15N esophagus tissue disease state: Early Esophageal Squamous Cell Carcinoma; tissue: esophagus tissue; cell type: adjacent normal
  • GSM6589226 ESCA16N esophagus tissue disease state: Early Esophageal Squamous Cell Carcinoma; tissue: esophagus tissue; cell type: adjacent normal
  • GSM6589227 ESCA17N esophagus tissue disease state: Early Esophageal Squamous Cell Carcinoma; tissue: esophagus tissue; cell type: adjacent normal
  • GSM6589228 ESCA18N esophagus tissue disease state: Early Esophageal Squamous Cell Carcinoma; tissue: esophagus tissue; cell type: adjacent normal
  • GSM6589229 ESCA19N esophagus tissue disease state: Early Esophageal Squamous Cell Carcinoma; tissue: esophagus tissue; cell type: adjacent normal
  • GSM6589230 ESCA20N esophagus tissue disease state: Early Esophageal Squamous Cell Carcinoma; tissue: esophagus tissue; cell type: adjacent normal

tumor sample

10 samples
  • GSM6589231 ESCA01T esophagus tissue disease state: Early Esophageal Squamous Cell Carcinoma; tissue: esophagus tissue; cell type: tumor
  • GSM6589232 ESCA07T esophagus tissue disease state: Early Esophageal Squamous Cell Carcinoma; tissue: esophagus tissue; cell type: tumor
  • GSM6589233 ESCA10T esophagus tissue disease state: Early Esophageal Squamous Cell Carcinoma; tissue: esophagus tissue; cell type: tumor
  • GSM6589234 ESCA14T esophagus tissue disease state: Early Esophageal Squamous Cell Carcinoma; tissue: esophagus tissue; cell type: tumor
  • GSM6589235 ESCA15T esophagus tissue disease state: Early Esophageal Squamous Cell Carcinoma; tissue: esophagus tissue; cell type: tumor
  • GSM6589236 ESCA16T esophagus tissue disease state: Early Esophageal Squamous Cell Carcinoma; tissue: esophagus tissue; cell type: tumor
  • GSM6589237 ESCA17T esophagus tissue disease state: Early Esophageal Squamous Cell Carcinoma; tissue: esophagus tissue; cell type: tumor
  • GSM6589238 ESCA18T esophagus tissue disease state: Early Esophageal Squamous Cell Carcinoma; tissue: esophagus tissue; cell type: tumor
  • GSM6589239 ESCA19T esophagus tissue disease state: Early Esophageal Squamous Cell Carcinoma; tissue: esophagus tissue; cell type: tumor
  • GSM6589240 ESCA20T esophagus tissue disease state: Early Esophageal Squamous Cell Carcinoma; tissue: esophagus tissue; cell type: tumor

Score Breakdown

50%

relevance

  • Organism normalized.
  • Assay type normalized.
0%

comparison suitability

  • Tumor and normal sample groups detected.
  • No excluded sample type flags detected.
  • Matched tumor/normal design boosted for colorectal tumor-vs-normal tissue triage.
  • Patient tissue or biopsy specimens boosted for tissue comparison triage.
  • Non-colorectal cancer context downgraded for colorectal 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.
34%

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 tumor/normal grouping is from a non-colorectal cancer context.

Sample Links

20 samples

Review Audit Trail

0 decisions

No review decisions have been stored for this dataset.