Siftome Phase 3L

GSE191334

Bulk RNA-Seq of cutaneous squamous cell carcinomas (cSCC) with paired normal controls

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
2021-12-20
Last update
2022-09-23
Organization
Stanford University School of Medicine
Department
Not available
Public date
2022-06-24
Experiment types
Expression profiling by high throughput sequencing
Platforms
GPL11154 Illumina HiSeq 2000 (Homo sapiens)
Series type
SubSeries
SubSeries
Not available
BioProject
PRJNA790997
Supplementary files
TXT: GSE191334_SCC_Counts.txt.gz
Organism
Homo sapiens
Assay
bulk RNA-seq
Samples
16
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

Ready after review
97% 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

10/10 pts

Metadata quality is high enough to support downstream handoff.

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 60% Organism normalized. Assay type normalized. Tissue metadata normalized.
  • comparison suitability 0% 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. Non-colorectal cancer context downgraded for colorectal tumor-vs-normal tissue ranking.
  • metadata quality 85% 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 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 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 8 samples
  • Likely control group normal tissue 8 samples

Warnings

  • DISEASE_LABEL_UNCLEAR warning Disease or condition label 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 1 active warning 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 Not suitable Dataset does not meet the current suitability threshold.
  • Supporting fact Tumor vs unmatched normal · Tissue · suitability 0%. 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 1 warning 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 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: 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: 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
GSE191334
Sample records
16 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
GSE191334
  • 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
GSE191334
  • 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
GSE191334
  • 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: GSE191334
dataset_title: Bulk RNA-Seq of cutaneous squamous cell carcinomas (cSCC) with paired normal controls
organism: Homo sapiens
assay_type: bulk RNA-seq
processed_data_available: true
raw_data_available: true
submission_date: 2021-12-20
last_update_date: 2022-09-23
organization_name: Stanford University School of Medicine
department: Not available
public_date: 2022-06-24
experiment_types: Expression profiling by high throughput sequencing
platforms: GPL11154 Illumina HiSeq 2000 (Homo sapiens)
sub_series: Not available
bioproject: PRJNA790997
supplementary_files: TXT: GSE191334_SCC_Counts.txt.gz
series_type: SubSeries

Why It Matched

  • Tumor vs unmatched normal · Tissue · suitability 0%.
  • 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.
  • 1 warning require review.

Why It May Not Be Suitable

  • Disease or condition label 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: 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: 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.

Normalized Fields

34 fields
Field Value Source Origin Confidence Evidence Reason
assay_type bulk RNA-seq dataset GSE191334 Runtime Siftome inference GEO:dataset:GSE191334:4666cbb6622a441794d76fea035f39c70cdde11d9bb0e0c889c9f06f557a5bf5 high confidence bulk rna-seq dataset_accession: GSE191334 dataset_title: Bulk RNA-Seq of cutaneous squamous cell carcinomas (cSCC) with paired normal controls organism: Homo sapiens assay_type: bulk RNA-seq... keyword match keyword match: bulk rna-seq
organism Homo sapiens dataset GSE191334 Runtime Siftome inference GEO:dataset:GSE191334:4666cbb6622a441794d76fea035f39c70cdde11d9bb0e0c889c9f06f557a5bf5 high confidence homo sapiens dataset_accession: GSE191334 dataset_title: Bulk RNA-Seq of cutaneous squamous cell carcinomas (cSCC) with paired normal controls organism: Homo sapiens assay_type: bulk RNA-seq... keyword match keyword match: homo sapiens
sample_type normal tissue sample GSM5743952 Runtime Siftome inference GEO:sample:GSM5743952:cd2d408ffcc51c15fcdf4d7c6fb0cfa5169b5665d8e0590ad4482a3a688f9310 low confidence normal sample_accession: GSM5743952 sample_title: P16_Normal_Skin source_name: Skin characteristics: tissue: Skin; condition: Normal Skin P16_Normal_Skin controlled vocabulary controlled vocabulary sample type match: normal
sample_type tumor sample sample GSM5743953 Runtime Siftome inference GEO:sample:GSM5743953:06b2db5d579a2143385568184f85e97c20d9d07ca5072fa8d2c7b0b814ad9698 medium confidence carcinoma sample_accession: GSM5743953 sample_title: P16_SCC source_name: Skin characteristics: tissue: Skin; condition: cutaneous squamous cell carcinomas (cSCC) P16_SCC controlled vocabulary controlled vocabulary sample type match: carcinoma
sample_type normal tissue sample GSM5743954 Runtime Siftome inference GEO:sample:GSM5743954:decc577c45349092b616bb21a4bf4fefa284fcfa8199e505e65984c625f8a7af low confidence normal sample_accession: GSM5743954 sample_title: P24_Normal_Skin source_name: Skin characteristics: tissue: Skin; condition: Normal Skin P24_Normal_Skin controlled vocabulary controlled vocabulary sample type match: normal
sample_type tumor sample sample GSM5743955 Runtime Siftome inference GEO:sample:GSM5743955:cbc1a0e2b16e17a4cf03ba9aa498392ed1e41bed4755b1c808ef3ba852f8dd75 medium confidence carcinoma sample_accession: GSM5743955 sample_title: P24_SCC source_name: Skin characteristics: tissue: Skin; condition: cutaneous squamous cell carcinomas (cSCC) P24_SCC controlled vocabulary controlled vocabulary sample type match: carcinoma
sample_type normal tissue sample GSM5743956 Runtime Siftome inference GEO:sample:GSM5743956:a8024f2bc9fa9782a2a5c0e0e6c844a9dced221dc6b2210c8e7c37a09eb9613f low confidence normal sample_accession: GSM5743956 sample_title: P29_Normal_Skin source_name: Skin characteristics: tissue: Skin; condition: Normal Skin P29_Normal_Skin controlled vocabulary controlled vocabulary sample type match: normal
sample_type tumor sample sample GSM5743957 Runtime Siftome inference GEO:sample:GSM5743957:e27b88d9467178e7a4f6f9fd8f292f8fe990d2462a7ad382dabe03354e9bb435 medium confidence carcinoma sample_accession: GSM5743957 sample_title: P29_SCC source_name: Skin characteristics: tissue: Skin; condition: cutaneous squamous cell carcinomas (cSCC) P29_SCC controlled vocabulary controlled vocabulary sample type match: carcinoma
sample_type normal tissue sample GSM5743958 Runtime Siftome inference GEO:sample:GSM5743958:5e436551fb0202fd6649ea2c0eb2bca9e3f0241845797ac7cc636d92a705d6f1 low confidence normal sample_accession: GSM5743958 sample_title: P32_Normal_Skin source_name: Skin characteristics: tissue: Skin; condition: Normal Skin P32_Normal_Skin controlled vocabulary controlled vocabulary sample type match: normal
sample_type tumor sample sample GSM5743959 Runtime Siftome inference GEO:sample:GSM5743959:212aab18eab9f5799e337e2a7fc3605246a041c5e8dc04dac6c038218d5394df medium confidence carcinoma sample_accession: GSM5743959 sample_title: P32_SCC source_name: Skin characteristics: tissue: Skin; condition: cutaneous squamous cell carcinomas (cSCC) P32_SCC controlled vocabulary controlled vocabulary sample type match: carcinoma
sample_type normal tissue sample GSM5743960 Runtime Siftome inference GEO:sample:GSM5743960:74c874ce56939b4329c55f2c6cce31be47bd7fc5a04567ef754d51e564957ee3 low confidence normal sample_accession: GSM5743960 sample_title: P33_Normal_Skin source_name: Skin characteristics: tissue: Skin; condition: Normal Skin P33_Normal_Skin controlled vocabulary controlled vocabulary sample type match: normal
sample_type tumor sample sample GSM5743961 Runtime Siftome inference GEO:sample:GSM5743961:4775ddaacb861ddedcc1e86cb9f38e49933f906733e72dfcce3b355ceccb58e2 medium confidence carcinoma sample_accession: GSM5743961 sample_title: P33_SCC source_name: Skin characteristics: tissue: Skin; condition: cutaneous squamous cell carcinomas (cSCC) P33_SCC controlled vocabulary controlled vocabulary sample type match: carcinoma
sample_type normal tissue sample GSM5743962 Runtime Siftome inference GEO:sample:GSM5743962:e7bf3c55a3a15436c32b532268c1b425709558259e5967c83d38c31617e33845 low confidence normal sample_accession: GSM5743962 sample_title: P34_Normal_Skin source_name: Skin characteristics: tissue: Skin; condition: Normal Skin P34_Normal_Skin controlled vocabulary controlled vocabulary sample type match: normal
sample_type tumor sample sample GSM5743963 Runtime Siftome inference GEO:sample:GSM5743963:122468072d30ff44b0b01cb76f567d9536b1f74ee5a457c3ae1788fbf446e746 medium confidence carcinoma sample_accession: GSM5743963 sample_title: P34_SCC source_name: Skin characteristics: tissue: Skin; condition: cutaneous squamous cell carcinomas (cSCC) P34_SCC controlled vocabulary controlled vocabulary sample type match: carcinoma
sample_type normal tissue sample GSM5743964 Runtime Siftome inference GEO:sample:GSM5743964:75d0ee7bab639f0927355ce20549f7e9d80abec2a9730363be9fb649569e217e low confidence normal sample_accession: GSM5743964 sample_title: P44_Normal_Skin source_name: Skin characteristics: tissue: Skin; condition: Normal Skin P44_Normal_Skin controlled vocabulary controlled vocabulary sample type match: normal
sample_type tumor sample sample GSM5743965 Runtime Siftome inference GEO:sample:GSM5743965:1d3970b56819a4ac62c4ef4dab979a6146e1b2ec68c469636370b411e2667602 medium confidence carcinoma sample_accession: GSM5743965 sample_title: P44_SCC source_name: Skin characteristics: tissue: Skin; condition: cutaneous squamous cell carcinomas (cSCC) P44_SCC controlled vocabulary controlled vocabulary sample type match: carcinoma
sample_type normal tissue sample GSM5743966 Runtime Siftome inference GEO:sample:GSM5743966:c3743ef0fac9e8727b7c69d2b18061a43bdf0dbd9d66396fabb50bb131184a54 low confidence normal sample_accession: GSM5743966 sample_title: P45_Normal_Skin source_name: Skin characteristics: tissue: Skin; condition: Normal Skin P45_Normal_Skin controlled vocabulary controlled vocabulary sample type match: normal
sample_type tumor sample sample GSM5743967 Runtime Siftome inference GEO:sample:GSM5743967:8586a2d2e29d12c826c20e1543c9c6dc3b6be5291b0961ba577d2bf35b3f585c medium confidence carcinoma sample_accession: GSM5743967 sample_title: P45_SCC source_name: Skin characteristics: tissue: Skin; condition: cutaneous squamous cell carcinomas (cSCC) P45_SCC controlled vocabulary controlled vocabulary sample type match: carcinoma
tissue skin sample GSM5743952 Runtime Siftome inference GEO:sample:GSM5743952:cd2d408ffcc51c15fcdf4d7c6fb0cfa5169b5665d8e0590ad4482a3a688f9310 low confidence skin sample_accession: GSM5743952 sample_title: P16_Normal_Skin source_name: Skin characteristics: tissue: Skin; condition: Normal Skin P16_Normal_Skin controlled vocabulary controlled vocabulary tissue match: skin
tissue skin sample GSM5743953 Runtime Siftome inference GEO:sample:GSM5743953:06b2db5d579a2143385568184f85e97c20d9d07ca5072fa8d2c7b0b814ad9698 low confidence skin sample_accession: GSM5743953 sample_title: P16_SCC source_name: Skin characteristics: tissue: Skin; condition: cutaneous squamous cell carcinomas (cSCC) P16_SCC controlled vocabulary controlled vocabulary tissue match: skin
tissue skin sample GSM5743954 Runtime Siftome inference GEO:sample:GSM5743954:decc577c45349092b616bb21a4bf4fefa284fcfa8199e505e65984c625f8a7af low confidence skin sample_accession: GSM5743954 sample_title: P24_Normal_Skin source_name: Skin characteristics: tissue: Skin; condition: Normal Skin P24_Normal_Skin controlled vocabulary controlled vocabulary tissue match: skin
tissue skin sample GSM5743955 Runtime Siftome inference GEO:sample:GSM5743955:cbc1a0e2b16e17a4cf03ba9aa498392ed1e41bed4755b1c808ef3ba852f8dd75 low confidence skin sample_accession: GSM5743955 sample_title: P24_SCC source_name: Skin characteristics: tissue: Skin; condition: cutaneous squamous cell carcinomas (cSCC) P24_SCC controlled vocabulary controlled vocabulary tissue match: skin
tissue skin sample GSM5743956 Runtime Siftome inference GEO:sample:GSM5743956:a8024f2bc9fa9782a2a5c0e0e6c844a9dced221dc6b2210c8e7c37a09eb9613f low confidence skin sample_accession: GSM5743956 sample_title: P29_Normal_Skin source_name: Skin characteristics: tissue: Skin; condition: Normal Skin P29_Normal_Skin controlled vocabulary controlled vocabulary tissue match: skin
tissue skin sample GSM5743957 Runtime Siftome inference GEO:sample:GSM5743957:e27b88d9467178e7a4f6f9fd8f292f8fe990d2462a7ad382dabe03354e9bb435 low confidence skin sample_accession: GSM5743957 sample_title: P29_SCC source_name: Skin characteristics: tissue: Skin; condition: cutaneous squamous cell carcinomas (cSCC) P29_SCC controlled vocabulary controlled vocabulary tissue match: skin
tissue skin sample GSM5743958 Runtime Siftome inference GEO:sample:GSM5743958:5e436551fb0202fd6649ea2c0eb2bca9e3f0241845797ac7cc636d92a705d6f1 low confidence skin sample_accession: GSM5743958 sample_title: P32_Normal_Skin source_name: Skin characteristics: tissue: Skin; condition: Normal Skin P32_Normal_Skin controlled vocabulary controlled vocabulary tissue match: skin
tissue skin sample GSM5743959 Runtime Siftome inference GEO:sample:GSM5743959:212aab18eab9f5799e337e2a7fc3605246a041c5e8dc04dac6c038218d5394df low confidence skin sample_accession: GSM5743959 sample_title: P32_SCC source_name: Skin characteristics: tissue: Skin; condition: cutaneous squamous cell carcinomas (cSCC) P32_SCC controlled vocabulary controlled vocabulary tissue match: skin
tissue skin sample GSM5743960 Runtime Siftome inference GEO:sample:GSM5743960:74c874ce56939b4329c55f2c6cce31be47bd7fc5a04567ef754d51e564957ee3 low confidence skin sample_accession: GSM5743960 sample_title: P33_Normal_Skin source_name: Skin characteristics: tissue: Skin; condition: Normal Skin P33_Normal_Skin controlled vocabulary controlled vocabulary tissue match: skin
tissue skin sample GSM5743961 Runtime Siftome inference GEO:sample:GSM5743961:4775ddaacb861ddedcc1e86cb9f38e49933f906733e72dfcce3b355ceccb58e2 low confidence skin sample_accession: GSM5743961 sample_title: P33_SCC source_name: Skin characteristics: tissue: Skin; condition: cutaneous squamous cell carcinomas (cSCC) P33_SCC controlled vocabulary controlled vocabulary tissue match: skin
tissue skin sample GSM5743962 Runtime Siftome inference GEO:sample:GSM5743962:e7bf3c55a3a15436c32b532268c1b425709558259e5967c83d38c31617e33845 low confidence skin sample_accession: GSM5743962 sample_title: P34_Normal_Skin source_name: Skin characteristics: tissue: Skin; condition: Normal Skin P34_Normal_Skin controlled vocabulary controlled vocabulary tissue match: skin
tissue skin sample GSM5743963 Runtime Siftome inference GEO:sample:GSM5743963:122468072d30ff44b0b01cb76f567d9536b1f74ee5a457c3ae1788fbf446e746 low confidence skin sample_accession: GSM5743963 sample_title: P34_SCC source_name: Skin characteristics: tissue: Skin; condition: cutaneous squamous cell carcinomas (cSCC) P34_SCC controlled vocabulary controlled vocabulary tissue match: skin
tissue skin sample GSM5743964 Runtime Siftome inference GEO:sample:GSM5743964:75d0ee7bab639f0927355ce20549f7e9d80abec2a9730363be9fb649569e217e low confidence skin sample_accession: GSM5743964 sample_title: P44_Normal_Skin source_name: Skin characteristics: tissue: Skin; condition: Normal Skin P44_Normal_Skin controlled vocabulary controlled vocabulary tissue match: skin
tissue skin sample GSM5743965 Runtime Siftome inference GEO:sample:GSM5743965:1d3970b56819a4ac62c4ef4dab979a6146e1b2ec68c469636370b411e2667602 low confidence skin sample_accession: GSM5743965 sample_title: P44_SCC source_name: Skin characteristics: tissue: Skin; condition: cutaneous squamous cell carcinomas (cSCC) P44_SCC controlled vocabulary controlled vocabulary tissue match: skin
tissue skin sample GSM5743966 Runtime Siftome inference GEO:sample:GSM5743966:c3743ef0fac9e8727b7c69d2b18061a43bdf0dbd9d66396fabb50bb131184a54 low confidence skin sample_accession: GSM5743966 sample_title: P45_Normal_Skin source_name: Skin characteristics: tissue: Skin; condition: Normal Skin P45_Normal_Skin controlled vocabulary controlled vocabulary tissue match: skin
tissue skin sample GSM5743967 Runtime Siftome inference GEO:sample:GSM5743967:8586a2d2e29d12c826c20e1543c9c6dc3b6be5291b0961ba577d2bf35b3f585c low confidence skin sample_accession: GSM5743967 sample_title: P45_SCC source_name: Skin characteristics: tissue: Skin; condition: cutaneous squamous cell carcinomas (cSCC) P45_SCC controlled vocabulary controlled vocabulary tissue match: skin

Sample Group Preview

Possible case samples

Samples currently treated as the comparison case group.

8
  • GSM5743953 P16_SCC tumor sample Case marker detected. Skin tissue: Skin; condition: cutaneous squamous cell carcinomas (cSCC)
  • GSM5743955 P24_SCC tumor sample Case marker detected. Skin tissue: Skin; condition: cutaneous squamous cell carcinomas (cSCC)
  • GSM5743957 P29_SCC tumor sample Case marker detected. Skin tissue: Skin; condition: cutaneous squamous cell carcinomas (cSCC)
  • GSM5743959 P32_SCC tumor sample Case marker detected. Skin tissue: Skin; condition: cutaneous squamous cell carcinomas (cSCC)
  • GSM5743961 P33_SCC tumor sample Case marker detected. Skin tissue: Skin; condition: cutaneous squamous cell carcinomas (cSCC)
  • GSM5743963 P34_SCC tumor sample Case marker detected. Skin tissue: Skin; condition: cutaneous squamous cell carcinomas (cSCC)
  • GSM5743965 P44_SCC tumor sample Case marker detected. Skin tissue: Skin; condition: cutaneous squamous cell carcinomas (cSCC)
  • GSM5743967 P45_SCC tumor sample Case marker detected. Skin tissue: Skin; condition: cutaneous squamous cell carcinomas (cSCC)

Possible control samples

Samples currently treated as controls or baseline.

8
  • GSM5743952 P16_Normal_Skin normal tissue Control marker detected. Skin tissue: Skin; condition: Normal Skin
  • GSM5743954 P24_Normal_Skin normal tissue Control marker detected. Skin tissue: Skin; condition: Normal Skin
  • GSM5743956 P29_Normal_Skin normal tissue Control marker detected. Skin tissue: Skin; condition: Normal Skin
  • GSM5743958 P32_Normal_Skin normal tissue Control marker detected. Skin tissue: Skin; condition: Normal Skin
  • GSM5743960 P33_Normal_Skin normal tissue Control marker detected. Skin tissue: Skin; condition: Normal Skin
  • GSM5743962 P34_Normal_Skin normal tissue Control marker detected. Skin tissue: Skin; condition: Normal Skin
  • GSM5743964 P44_Normal_Skin normal tissue Control marker detected. Skin tissue: Skin; condition: Normal Skin
  • GSM5743966 P45_Normal_Skin normal tissue Control marker detected. Skin tissue: Skin; condition: Normal Skin

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

85 pts
Clarity
85%
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 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

8 samples
  • GSM5743952 P16_Normal_Skin Skin tissue: Skin; condition: Normal Skin
  • GSM5743954 P24_Normal_Skin Skin tissue: Skin; condition: Normal Skin
  • GSM5743956 P29_Normal_Skin Skin tissue: Skin; condition: Normal Skin
  • GSM5743958 P32_Normal_Skin Skin tissue: Skin; condition: Normal Skin
  • GSM5743960 P33_Normal_Skin Skin tissue: Skin; condition: Normal Skin
  • GSM5743962 P34_Normal_Skin Skin tissue: Skin; condition: Normal Skin
  • GSM5743964 P44_Normal_Skin Skin tissue: Skin; condition: Normal Skin
  • GSM5743966 P45_Normal_Skin Skin tissue: Skin; condition: Normal Skin

tumor sample

8 samples
  • GSM5743953 P16_SCC Skin tissue: Skin; condition: cutaneous squamous cell carcinomas (cSCC)
  • GSM5743955 P24_SCC Skin tissue: Skin; condition: cutaneous squamous cell carcinomas (cSCC)
  • GSM5743957 P29_SCC Skin tissue: Skin; condition: cutaneous squamous cell carcinomas (cSCC)
  • GSM5743959 P32_SCC Skin tissue: Skin; condition: cutaneous squamous cell carcinomas (cSCC)
  • GSM5743961 P33_SCC Skin tissue: Skin; condition: cutaneous squamous cell carcinomas (cSCC)
  • GSM5743963 P34_SCC Skin tissue: Skin; condition: cutaneous squamous cell carcinomas (cSCC)
  • GSM5743965 P44_SCC Skin tissue: Skin; condition: cutaneous squamous cell carcinomas (cSCC)
  • GSM5743967 P45_SCC Skin tissue: Skin; condition: cutaneous squamous cell carcinomas (cSCC)

Score Breakdown

60%

relevance

  • Organism normalized.
  • Assay type normalized.
  • Tissue metadata normalized.
0%

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.
  • Non-colorectal cancer context downgraded for colorectal tumor-vs-normal tissue ranking.
85%

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 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

16 samples

Review Audit Trail

0 decisions

No review decisions have been stored for this dataset.