Siftome Phase 3L

GSE194116

Prognostic value of SPODD1 in esophageal squamous cell carcinoma: a comprehensive study based on bioinformatics and validation

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
2022-01-20
Last update
2022-07-20
Organization
FJNU
Department
Not available
Public date
2022-01-23
Experiment types
Expression profiling by high throughput sequencing
Platforms
GPL16791 Illumina HiSeq 2500 (Homo sapiens)
Series type
Series
SubSeries
Not available
BioProject
PRJNA799125
Supplementary files
TXT: GSE194116_Raw_gene_counts_matrix.txt.gz
Organism
Homo sapiens
Assay
bulk RNA-seq
Samples
12
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 6 samples
  • Likely control group normal tissue 6 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
GSE194116
Sample records
12 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
GSE194116
  • 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
GSE194116
  • 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
GSE194116
  • 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: GSE194116
dataset_title: Prognostic value of SPODD1 in esophageal squamous cell carcinoma: a comprehensive study based on bioinformatics and validation
organism: Homo sapiens
assay_type: bulk RNA-seq
processed_data_available: true
raw_data_available: true
submission_date: 2022-01-20
last_update_date: 2022-07-20
organization_name: FJNU
department: Not available
public_date: 2022-01-23
experiment_types: Expression profiling by high throughput sequencing
platforms: GPL16791 Illumina HiSeq 2500 (Homo sapiens)
sub_series: Not available
bioproject: PRJNA799125
supplementary_files: TXT: GSE194116_Raw_gene_counts_matrix.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

20 fields
Field Value Source Origin Confidence Evidence Reason
assay_type bulk RNA-seq dataset GSE194116 Runtime Siftome inference GEO:dataset:GSE194116:32b46501a530bb567a96bfef29720bd5864d6f6c800bfac12865f52c5b25c196 high confidence bulk rna-seq dataset_accession: GSE194116 dataset_title: Prognostic value of SPODD1 in esophageal squamous cell carcinoma: a comprehensive study based on bioinformatics and validation organi... keyword match keyword match: bulk rna-seq
normal_tissue_type adjacent normal sample GSM5828360 Runtime Siftome inference GEO:sample:GSM5828360:9f3ea46af198b0e7bf5d821b4da84a774f03c1512796a00c80d1cc2b2cdccaca high confidence adjacent normal sample_accession: GSM5828360 sample_title: 154836-zhengchang [Normal-1] source_name: esophagus characteristics: subject/sample id: 154836; tissue: esophagus; tissue subtype: adj... controlled vocabulary controlled vocabulary normal tissue type match: adjacent normal
normal_tissue_type adjacent normal sample GSM5828362 Runtime Siftome inference GEO:sample:GSM5828362:49ece4341215a0b31f80e5cf76518bb72977548cf24fde6123a9533042c5814f high confidence adjacent normal sample_accession: GSM5828362 sample_title: 270678-zhengchang [Normal-2] source_name: esophagus characteristics: subject/sample id: 270678; tissue: esophagus; tissue subtype: adj... controlled vocabulary controlled vocabulary normal tissue type match: adjacent normal
normal_tissue_type adjacent normal sample GSM5828364 Runtime Siftome inference GEO:sample:GSM5828364:067ac0b07e2a504c357ecedce1f279850f406769ae4ba472c650503295bc9b82 high confidence adjacent normal sample_accession: GSM5828364 sample_title: 270954-zhengchang [Normal-3] source_name: esophagus characteristics: subject/sample id: 270954; tissue: esophagus; tissue subtype: adj... controlled vocabulary controlled vocabulary normal tissue type match: adjacent normal
normal_tissue_type adjacent normal sample GSM5828366 Runtime Siftome inference GEO:sample:GSM5828366:d3831aef849eb98632dd1d4671f0dcb320554333b9b844942c4211983d5486d7 high confidence adjacent normal sample_accession: GSM5828366 sample_title: 271116-zhengchang [Normal-4] source_name: esophagus characteristics: subject/sample id: 271116; tissue: esophagus; tissue subtype: adj... controlled vocabulary controlled vocabulary normal tissue type match: adjacent normal
normal_tissue_type adjacent normal sample GSM5828368 Runtime Siftome inference GEO:sample:GSM5828368:5b8b31c272725f160bfa120569a2f8318d2ed66470f2ad9b27869de0d4612a52 high confidence adjacent normal sample_accession: GSM5828368 sample_title: 271121-zhengchang [Normal-5] source_name: esophagus characteristics: subject/sample id: 271121; tissue: esophagus; tissue subtype: adj... controlled vocabulary controlled vocabulary normal tissue type match: adjacent normal
normal_tissue_type adjacent normal sample GSM5828370 Runtime Siftome inference GEO:sample:GSM5828370:189a141e9866d39d8909f795e4b7a125803ae9e674ff9c3235bf3f6da1eb45cd high confidence adjacent normal sample_accession: GSM5828370 sample_title: 271364-zhengchang [Normal-6] source_name: esophagus characteristics: subject/sample id: 271364; tissue: esophagus; tissue subtype: adj... controlled vocabulary controlled vocabulary normal tissue type match: adjacent normal
organism Homo sapiens dataset GSE194116 Runtime Siftome inference GEO:dataset:GSE194116:32b46501a530bb567a96bfef29720bd5864d6f6c800bfac12865f52c5b25c196 high confidence homo sapiens dataset_accession: GSE194116 dataset_title: Prognostic value of SPODD1 in esophageal squamous cell carcinoma: a comprehensive study based on bioinformatics and validation organi... keyword match keyword match: homo sapiens
sample_type tumor sample sample GSM5828359 Runtime Siftome inference GEO:sample:GSM5828359:560b5a99e2d01559d4ffcb6f4a9f929b8af74df27d79ade27e8b6fbf479536ad low confidence tumor sample_accession: GSM5828359 sample_title: 154836-ai [ECA-1] source_name: esophagus characteristics: subject/sample id: 154836; tissue: esophagus; tissue subtype: ESCC tumor 154... controlled vocabulary controlled vocabulary sample type match: tumor
sample_type normal tissue sample GSM5828360 Runtime Siftome inference GEO:sample:GSM5828360:9f3ea46af198b0e7bf5d821b4da84a774f03c1512796a00c80d1cc2b2cdccaca high confidence adjacent normal sample_accession: GSM5828360 sample_title: 154836-zhengchang [Normal-1] source_name: esophagus characteristics: subject/sample id: 154836; tissue: esophagus; tissue subtype: adj... controlled vocabulary controlled vocabulary sample type match: adjacent normal
sample_type tumor sample sample GSM5828361 Runtime Siftome inference GEO:sample:GSM5828361:f11d2f2570107758792a19863634579cfacb2009e665d33bd216d4298991e424 low confidence tumor sample_accession: GSM5828361 sample_title: 270678-ai [ECA-2] source_name: esophagus characteristics: subject/sample id: 270678; tissue: esophagus; tissue subtype: ESCC tumor 270... controlled vocabulary controlled vocabulary sample type match: tumor
sample_type normal tissue sample GSM5828362 Runtime Siftome inference GEO:sample:GSM5828362:49ece4341215a0b31f80e5cf76518bb72977548cf24fde6123a9533042c5814f high confidence adjacent normal sample_accession: GSM5828362 sample_title: 270678-zhengchang [Normal-2] source_name: esophagus characteristics: subject/sample id: 270678; tissue: esophagus; tissue subtype: adj... controlled vocabulary controlled vocabulary sample type match: adjacent normal
sample_type tumor sample sample GSM5828363 Runtime Siftome inference GEO:sample:GSM5828363:06f442cdaba1da8b443fb01bba019da1946a702318bd4ee3335c37f46ea6d92f low confidence tumor sample_accession: GSM5828363 sample_title: 270954-ai [ECA-3] source_name: esophagus characteristics: subject/sample id: 270954; tissue: esophagus; tissue subtype: ESCC tumor 270... controlled vocabulary controlled vocabulary sample type match: tumor
sample_type normal tissue sample GSM5828364 Runtime Siftome inference GEO:sample:GSM5828364:067ac0b07e2a504c357ecedce1f279850f406769ae4ba472c650503295bc9b82 high confidence adjacent normal sample_accession: GSM5828364 sample_title: 270954-zhengchang [Normal-3] source_name: esophagus characteristics: subject/sample id: 270954; tissue: esophagus; tissue subtype: adj... controlled vocabulary controlled vocabulary sample type match: adjacent normal
sample_type tumor sample sample GSM5828365 Runtime Siftome inference GEO:sample:GSM5828365:03783e1cb45c7a5fc0dccc8429f78ee2ffb003a1d2b0a54acb7f966000535acd low confidence tumor sample_accession: GSM5828365 sample_title: 271116-ai [ECA-4] source_name: esophagus characteristics: subject/sample id: 271116; tissue: esophagus; tissue subtype: ESCC tumor 271... controlled vocabulary controlled vocabulary sample type match: tumor
sample_type normal tissue sample GSM5828366 Runtime Siftome inference GEO:sample:GSM5828366:d3831aef849eb98632dd1d4671f0dcb320554333b9b844942c4211983d5486d7 high confidence adjacent normal sample_accession: GSM5828366 sample_title: 271116-zhengchang [Normal-4] source_name: esophagus characteristics: subject/sample id: 271116; tissue: esophagus; tissue subtype: adj... controlled vocabulary controlled vocabulary sample type match: adjacent normal
sample_type tumor sample sample GSM5828367 Runtime Siftome inference GEO:sample:GSM5828367:307e24861e40f3eb6242ed98962ec1cee46b7965024edf711dab17ea3eef772c low confidence tumor sample_accession: GSM5828367 sample_title: 271121-ai [ECA-5] source_name: esophagus characteristics: subject/sample id: 271121; tissue: esophagus; tissue subtype: ESCC tumor 271... controlled vocabulary controlled vocabulary sample type match: tumor
sample_type normal tissue sample GSM5828368 Runtime Siftome inference GEO:sample:GSM5828368:5b8b31c272725f160bfa120569a2f8318d2ed66470f2ad9b27869de0d4612a52 high confidence adjacent normal sample_accession: GSM5828368 sample_title: 271121-zhengchang [Normal-5] source_name: esophagus characteristics: subject/sample id: 271121; tissue: esophagus; tissue subtype: adj... controlled vocabulary controlled vocabulary sample type match: adjacent normal
sample_type tumor sample sample GSM5828369 Runtime Siftome inference GEO:sample:GSM5828369:230f804a85542ad36c7dc9c07e0b0f8e667cebfce1d737d362e03827e54a952e low confidence tumor sample_accession: GSM5828369 sample_title: 271364-ai [ECA-6] source_name: esophagus characteristics: subject/sample id: 271364; tissue: esophagus; tissue subtype: ESCC tumor 271... controlled vocabulary controlled vocabulary sample type match: tumor
sample_type normal tissue sample GSM5828370 Runtime Siftome inference GEO:sample:GSM5828370:189a141e9866d39d8909f795e4b7a125803ae9e674ff9c3235bf3f6da1eb45cd high confidence adjacent normal sample_accession: GSM5828370 sample_title: 271364-zhengchang [Normal-6] source_name: esophagus characteristics: subject/sample id: 271364; tissue: esophagus; tissue subtype: adj... controlled vocabulary controlled vocabulary sample type match: adjacent normal

Sample Group Preview

Possible case samples

Samples currently treated as the comparison case group.

6
  • GSM5828359 154836-ai [ECA-1] tumor sample Case marker detected. esophagus subject/sample id: 154836; tissue: esophagus; tissue subtype: ESCC tumor
  • GSM5828361 270678-ai [ECA-2] tumor sample Case marker detected. esophagus subject/sample id: 270678; tissue: esophagus; tissue subtype: ESCC tumor
  • GSM5828363 270954-ai [ECA-3] tumor sample Case marker detected. esophagus subject/sample id: 270954; tissue: esophagus; tissue subtype: ESCC tumor
  • GSM5828365 271116-ai [ECA-4] tumor sample Case marker detected. esophagus subject/sample id: 271116; tissue: esophagus; tissue subtype: ESCC tumor
  • GSM5828367 271121-ai [ECA-5] tumor sample Case marker detected. esophagus subject/sample id: 271121; tissue: esophagus; tissue subtype: ESCC tumor
  • GSM5828369 271364-ai [ECA-6] tumor sample Case marker detected. esophagus subject/sample id: 271364; tissue: esophagus; tissue subtype: ESCC tumor

Possible control samples

Samples currently treated as controls or baseline.

6
  • GSM5828360 154836-zhengchang [Normal-1] normal tissue Control marker detected. esophagus subject/sample id: 154836; tissue: esophagus; tissue subtype: adjacent normal tissue
  • GSM5828362 270678-zhengchang [Normal-2] normal tissue Control marker detected. esophagus subject/sample id: 270678; tissue: esophagus; tissue subtype: adjacent normal tissue
  • GSM5828364 270954-zhengchang [Normal-3] normal tissue Control marker detected. esophagus subject/sample id: 270954; tissue: esophagus; tissue subtype: adjacent normal tissue
  • GSM5828366 271116-zhengchang [Normal-4] normal tissue Control marker detected. esophagus subject/sample id: 271116; tissue: esophagus; tissue subtype: adjacent normal tissue
  • GSM5828368 271121-zhengchang [Normal-5] normal tissue Control marker detected. esophagus subject/sample id: 271121; tissue: esophagus; tissue subtype: adjacent normal tissue
  • GSM5828370 271364-zhengchang [Normal-6] normal tissue Control marker detected. esophagus subject/sample id: 271364; tissue: esophagus; tissue subtype: adjacent normal tissue

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

tumor sample

6 samples
  • GSM5828359 154836-ai [ECA-1] esophagus subject/sample id: 154836; tissue: esophagus; tissue subtype: ESCC tumor
  • GSM5828361 270678-ai [ECA-2] esophagus subject/sample id: 270678; tissue: esophagus; tissue subtype: ESCC tumor
  • GSM5828363 270954-ai [ECA-3] esophagus subject/sample id: 270954; tissue: esophagus; tissue subtype: ESCC tumor
  • GSM5828365 271116-ai [ECA-4] esophagus subject/sample id: 271116; tissue: esophagus; tissue subtype: ESCC tumor
  • GSM5828367 271121-ai [ECA-5] esophagus subject/sample id: 271121; tissue: esophagus; tissue subtype: ESCC tumor
  • GSM5828369 271364-ai [ECA-6] esophagus subject/sample id: 271364; tissue: esophagus; tissue subtype: ESCC tumor

normal tissue

6 samples
  • GSM5828360 154836-zhengchang [Normal-1] esophagus subject/sample id: 154836; tissue: esophagus; tissue subtype: adjacent normal tissue
  • GSM5828362 270678-zhengchang [Normal-2] esophagus subject/sample id: 270678; tissue: esophagus; tissue subtype: adjacent normal tissue
  • GSM5828364 270954-zhengchang [Normal-3] esophagus subject/sample id: 270954; tissue: esophagus; tissue subtype: adjacent normal tissue
  • GSM5828366 271116-zhengchang [Normal-4] esophagus subject/sample id: 271116; tissue: esophagus; tissue subtype: adjacent normal tissue
  • GSM5828368 271121-zhengchang [Normal-5] esophagus subject/sample id: 271121; tissue: esophagus; tissue subtype: adjacent normal tissue
  • GSM5828370 271364-zhengchang [Normal-6] esophagus subject/sample id: 271364; tissue: esophagus; tissue subtype: adjacent normal tissue

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

12 samples

Review Audit Trail

0 decisions

No review decisions have been stored for this dataset.