Siftome Phase 3L

GSE191139

Comparative transcriptome characterization of paired primary gastric cancer and ovarian metastasis

Exploratory only Dataset can inform exploration but is not strong enough for primary analysis.
Sample grouping CSV Contrast CSV DESeq2 metadata CSV R handoff notes Handoff report Download instructions Open GEO dataset
Source
GEO
Search intent
Patient tissue tumor-vs-normal
Intent behavior
search-intent-behavior-v1
Submission date
2021-12-17
Last update
2021-12-20
Organization
Fudan University
Department
Not available
Public date
2021-12-20
Experiment types
Expression profiling by high throughput sequencing
Platforms
GPL24676 Illumina NovaSeq 6000 (Homo sapiens)
Series type
Series
SubSeries
Not available
BioProject
PRJNA789867
Supplementary files
TXT: GSE191139_All_exp_FPKM.txt.gz
Organism
Homo sapiens
Assay
bulk RNA-seq
Samples
12
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
Exploratory only Dataset can inform exploration but is not strong enough for primary analysis.

Score Components

  • relevance 60% Organism normalized. Assay type normalized. Tissue metadata normalized.
  • comparison suitability 20% 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 gastrointestinal cancer context downgraded for colorectal 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 45% Weighted score: 30% relevance, 30% comparison suitability, 25% metadata quality, 15% data availability. Overall score capped because comparison suitability is weak for the selected search intent. Overall score capped because gastrointestinal context is not explicit colorectal/CRC.

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 4 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: gastrointestinal cancer is present but colorectal metadata is not explicit. Derived from current-intent ranking reasons and warnings.

Applied Review Decisions

No active review decisions affect this ranking.

Ranking Facts

  • Recommendation Exploratory only Dataset can inform exploration but is not strong enough for primary analysis.
  • Supporting fact Tumor vs unmatched normal · Tissue · suitability 20%. 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: gastrointestinal cancer is present but colorectal metadata is not explicit. 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 gastrointestinal cancer context downgraded for colorectal 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 gastrointestinal context is not explicit colorectal/CRC. Contributed to downgrade or manual-review evidence.
  • Caution fact Downgraded disease context: gastrointestinal cancer is present but colorectal metadata is not explicit. 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
GSE191139
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
GSE191139
  • 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
GSE191139
  • 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
GSE191139
  • 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: GSE191139
dataset_title: Comparative transcriptome characterization of paired primary gastric cancer and ovarian metastasis
organism: Homo sapiens
assay_type: bulk RNA-seq
processed_data_available: true
raw_data_available: true
submission_date: 2021-12-17
last_update_date: 2021-12-20
organization_name: Fudan University
department: Not available
public_date: 2021-12-20
experiment_types: Expression profiling by high throughput sequencing
platforms: GPL24676 Illumina NovaSeq 6000 (Homo sapiens)
sub_series: Not available
bioproject: PRJNA789867
supplementary_files: TXT: GSE191139_All_exp_FPKM.txt.gz
series_type: Series

Why It Matched

  • Tumor vs unmatched normal · Tissue · suitability 20%.
  • Prioritized assay: bulk RNA-seq is the active assay expectation.
  • Downgraded disease context: gastrointestinal cancer is present but colorectal metadata is not explicit.
  • 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 gastrointestinal cancer context downgraded for colorectal 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 gastrointestinal context is not explicit colorectal/CRC.
  • Downgraded disease context: gastrointestinal cancer is present but colorectal metadata is not explicit.
  • 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

27 fields
Field Value Source Origin Confidence Evidence Reason
assay_type bulk RNA-seq dataset GSE191139 Runtime Siftome inference GEO:dataset:GSE191139:3001add9a272e8448e346d688e632d13876f2db8ea9f2ca39a6e936296b8cdaf high confidence bulk rna-seq dataset_accession: GSE191139 dataset_title: Comparative transcriptome characterization of paired primary gastric cancer and ovarian metastasis organism: Homo sapiens assay_type:... keyword match keyword match: bulk rna-seq
organism Homo sapiens dataset GSE191139 Runtime Siftome inference GEO:dataset:GSE191139:3001add9a272e8448e346d688e632d13876f2db8ea9f2ca39a6e936296b8cdaf high confidence homo sapiens dataset_accession: GSE191139 dataset_title: Comparative transcriptome characterization of paired primary gastric cancer and ovarian metastasis organism: Homo sapiens assay_type:... keyword match keyword match: homo sapiens
sample_type tumor sample sample GSM5739913 Runtime Siftome inference GEO:sample:GSM5739913:df2a80772e0d23f1ad910fa2fe850af7abb810fd4c958c2c3f0821932a770c45 medium confidence carcinoma sample_accession: GSM5739913 sample_title: FDC1P source_name: Stomach characteristics: disease state: gastric adenocarcinoma; pathological types: adenocarcinoma with low differe... controlled vocabulary controlled vocabulary sample type match: carcinoma
sample_type normal tissue sample GSM5739914 Runtime Siftome inference GEO:sample:GSM5739914:7c650a88d90aae3a09facda731d12e3690c82ca4844b14771e4995a6c3fcbf65 low confidence normal sample_accession: GSM5739914 sample_title: FDC1N source_name: Stomach characteristics: disease state: gastric adenocarcinoma; pathological types: adenocarcinoma with low differe... controlled vocabulary controlled vocabulary sample type match: normal
sample_type tumor sample sample GSM5739914 Runtime Siftome inference GEO:sample:GSM5739914:7c650a88d90aae3a09facda731d12e3690c82ca4844b14771e4995a6c3fcbf65 medium confidence carcinoma sample_accession: GSM5739914 sample_title: FDC1N source_name: Stomach characteristics: disease state: gastric adenocarcinoma; pathological types: adenocarcinoma with low differe... controlled vocabulary controlled vocabulary sample type match: carcinoma
sample_type tumor sample sample GSM5739915 Runtime Siftome inference GEO:sample:GSM5739915:24a77d43e775a0e2600f54e039b0aa0acf97112e25279f2050d05a4cb082e103 medium confidence carcinoma sample_accession: GSM5739915 sample_title: FDC1M source_name: Ovary characteristics: disease state: gastric adenocarcinoma; pathological types: adenocarcinoma with low different... controlled vocabulary controlled vocabulary sample type match: carcinoma
sample_type tumor sample sample GSM5739916 Runtime Siftome inference GEO:sample:GSM5739916:584cd1f951d02aa193e7879d9891aba459bd1d18030267b6846f1433df0cdf1c medium confidence carcinoma sample_accession: GSM5739916 sample_title: FDC2P source_name: Stomach characteristics: disease state: gastric adenocarcinoma; pathological types: adenocarcinoma with low differe... controlled vocabulary controlled vocabulary sample type match: carcinoma
sample_type normal tissue sample GSM5739917 Runtime Siftome inference GEO:sample:GSM5739917:ef4e3ad12529cde7de0cc3d3fa89e60e0a6bb6595a0c95ae2429b03c05e79e0c low confidence normal sample_accession: GSM5739917 sample_title: FDC2N source_name: Stomach characteristics: disease state: gastric adenocarcinoma; pathological types: adenocarcinoma with low differe... controlled vocabulary controlled vocabulary sample type match: normal
sample_type tumor sample sample GSM5739917 Runtime Siftome inference GEO:sample:GSM5739917:ef4e3ad12529cde7de0cc3d3fa89e60e0a6bb6595a0c95ae2429b03c05e79e0c medium confidence carcinoma sample_accession: GSM5739917 sample_title: FDC2N source_name: Stomach characteristics: disease state: gastric adenocarcinoma; pathological types: adenocarcinoma with low differe... controlled vocabulary controlled vocabulary sample type match: carcinoma
sample_type tumor sample sample GSM5739918 Runtime Siftome inference GEO:sample:GSM5739918:c045b79d62b9ff8e77dc2e2bed34c5e3d6699f8d222100e112eefe9cd6a3236f medium confidence carcinoma sample_accession: GSM5739918 sample_title: FDC2M source_name: Ovary characteristics: disease state: gastric adenocarcinoma; pathological types: adenocarcinoma with low different... controlled vocabulary controlled vocabulary sample type match: carcinoma
sample_type tumor sample sample GSM5739919 Runtime Siftome inference GEO:sample:GSM5739919:ca1dd3cba345389fe6283e4c1d63d7451e3f047017491f4fcf6fd3446ef9fd3c medium confidence carcinoma sample_accession: GSM5739919 sample_title: FDC3P source_name: Stomach characteristics: disease state: gastric adenocarcinoma; pathological types: adenocarcinoma with low differe... controlled vocabulary controlled vocabulary sample type match: carcinoma
sample_type normal tissue sample GSM5739920 Runtime Siftome inference GEO:sample:GSM5739920:859aaf0d1c13d04ee7c73b67808269d19fb35e77d3c9b856bf3cba386d10bc1d low confidence normal sample_accession: GSM5739920 sample_title: FDC3N source_name: Stomach characteristics: disease state: gastric adenocarcinoma; pathological types: adenocarcinoma with low differe... controlled vocabulary controlled vocabulary sample type match: normal
sample_type tumor sample sample GSM5739920 Runtime Siftome inference GEO:sample:GSM5739920:859aaf0d1c13d04ee7c73b67808269d19fb35e77d3c9b856bf3cba386d10bc1d medium confidence carcinoma sample_accession: GSM5739920 sample_title: FDC3N source_name: Stomach characteristics: disease state: gastric adenocarcinoma; pathological types: adenocarcinoma with low differe... controlled vocabulary controlled vocabulary sample type match: carcinoma
sample_type tumor sample sample GSM5739921 Runtime Siftome inference GEO:sample:GSM5739921:30c618b43518031b8314b53778e3c0bd5b8ed3cb2d47e309278c1b1d75bfc29b medium confidence carcinoma sample_accession: GSM5739921 sample_title: FDC3M source_name: Ovary characteristics: disease state: gastric adenocarcinoma; pathological types: adenocarcinoma with low different... controlled vocabulary controlled vocabulary sample type match: carcinoma
sample_type tumor sample sample GSM5739922 Runtime Siftome inference GEO:sample:GSM5739922:89914c7e5e89e4fb3862de1bdbcf35b61a4de62c08a1387ad1e5ee00952e7cbc medium confidence carcinoma sample_accession: GSM5739922 sample_title: FDC4P source_name: Stomach characteristics: disease state: gastric adenocarcinoma; pathological types: adenocarcinoma with low differe... controlled vocabulary controlled vocabulary sample type match: carcinoma
sample_type normal tissue sample GSM5739923 Runtime Siftome inference GEO:sample:GSM5739923:a72d915407404ac771c44f812ee88369f1df6bba88bc6f42145bccae558b6135 low confidence normal sample_accession: GSM5739923 sample_title: FDC4N source_name: Stomach characteristics: disease state: gastric adenocarcinoma; pathological types: adenocarcinoma with low differe... controlled vocabulary controlled vocabulary sample type match: normal
sample_type tumor sample sample GSM5739923 Runtime Siftome inference GEO:sample:GSM5739923:a72d915407404ac771c44f812ee88369f1df6bba88bc6f42145bccae558b6135 medium confidence carcinoma sample_accession: GSM5739923 sample_title: FDC4N source_name: Stomach characteristics: disease state: gastric adenocarcinoma; pathological types: adenocarcinoma with low differe... controlled vocabulary controlled vocabulary sample type match: carcinoma
sample_type tumor sample sample GSM5739924 Runtime Siftome inference GEO:sample:GSM5739924:8ab4a22750c011ac5b9f4d37a1afc48a1c1ffa93f8b765256b38772ac1a4687b medium confidence carcinoma sample_accession: GSM5739924 sample_title: FDC4M source_name: Ovary characteristics: disease state: gastric adenocarcinoma; pathological types: adenocarcinoma with low different... controlled vocabulary controlled vocabulary sample type match: carcinoma
tissue ovary dataset GSE191139 Runtime Siftome inference GEO:dataset:GSE191139:3001add9a272e8448e346d688e632d13876f2db8ea9f2ca39a6e936296b8cdaf medium confidence ovarian dataset_accession: GSE191139 dataset_title: Comparative transcriptome characterization of paired primary gastric cancer and ovarian metastasis organism: Homo sapiens assay_type:... controlled vocabulary controlled vocabulary tissue match: ovarian
tissue ovary sample GSM5739915 Runtime Siftome inference GEO:sample:GSM5739915:24a77d43e775a0e2600f54e039b0aa0acf97112e25279f2050d05a4cb082e103 low confidence ovary sample_accession: GSM5739915 sample_title: FDC1M source_name: Ovary characteristics: disease state: gastric adenocarcinoma; pathological types: adenocarcinoma with low different... controlled vocabulary controlled vocabulary tissue match: ovary
tissue ovary sample GSM5739918 Runtime Siftome inference GEO:sample:GSM5739918:c045b79d62b9ff8e77dc2e2bed34c5e3d6699f8d222100e112eefe9cd6a3236f low confidence ovary sample_accession: GSM5739918 sample_title: FDC2M source_name: Ovary characteristics: disease state: gastric adenocarcinoma; pathological types: adenocarcinoma with low different... controlled vocabulary controlled vocabulary tissue match: ovary
tissue ovary sample GSM5739921 Runtime Siftome inference GEO:sample:GSM5739921:30c618b43518031b8314b53778e3c0bd5b8ed3cb2d47e309278c1b1d75bfc29b low confidence ovary sample_accession: GSM5739921 sample_title: FDC3M source_name: Ovary characteristics: disease state: gastric adenocarcinoma; pathological types: adenocarcinoma with low different... controlled vocabulary controlled vocabulary tissue match: ovary
tissue ovary sample GSM5739924 Runtime Siftome inference GEO:sample:GSM5739924:8ab4a22750c011ac5b9f4d37a1afc48a1c1ffa93f8b765256b38772ac1a4687b low confidence ovary sample_accession: GSM5739924 sample_title: FDC4M source_name: Ovary characteristics: disease state: gastric adenocarcinoma; pathological types: adenocarcinoma with low different... controlled vocabulary controlled vocabulary tissue match: ovary
tumor_type metastatic tumor sample GSM5739915 Runtime Siftome inference GEO:sample:GSM5739915:24a77d43e775a0e2600f54e039b0aa0acf97112e25279f2050d05a4cb082e103 medium confidence metastasis sample_accession: GSM5739915 sample_title: FDC1M source_name: Ovary characteristics: disease state: gastric adenocarcinoma; pathological types: adenocarcinoma with low different... controlled vocabulary controlled vocabulary tumor type match: metastasis
tumor_type metastatic tumor sample GSM5739918 Runtime Siftome inference GEO:sample:GSM5739918:c045b79d62b9ff8e77dc2e2bed34c5e3d6699f8d222100e112eefe9cd6a3236f medium confidence metastasis sample_accession: GSM5739918 sample_title: FDC2M source_name: Ovary characteristics: disease state: gastric adenocarcinoma; pathological types: adenocarcinoma with low different... controlled vocabulary controlled vocabulary tumor type match: metastasis
tumor_type metastatic tumor sample GSM5739921 Runtime Siftome inference GEO:sample:GSM5739921:30c618b43518031b8314b53778e3c0bd5b8ed3cb2d47e309278c1b1d75bfc29b medium confidence metastasis sample_accession: GSM5739921 sample_title: FDC3M source_name: Ovary characteristics: disease state: gastric adenocarcinoma; pathological types: adenocarcinoma with low different... controlled vocabulary controlled vocabulary tumor type match: metastasis
tumor_type metastatic tumor sample GSM5739924 Runtime Siftome inference GEO:sample:GSM5739924:8ab4a22750c011ac5b9f4d37a1afc48a1c1ffa93f8b765256b38772ac1a4687b medium confidence metastasis sample_accession: GSM5739924 sample_title: FDC4M source_name: Ovary characteristics: disease state: gastric adenocarcinoma; pathological types: adenocarcinoma with low different... controlled vocabulary controlled vocabulary tumor type match: metastasis

Sample Group Preview

Possible case samples

Samples currently treated as the comparison case group.

8
  • GSM5739913 FDC1P tumor sample Case marker detected. Stomach disease state: gastric adenocarcinoma; pathological types: adenocarcinoma with low differentiation; tissue: gastric adenocarcinoma; individual: FDC1
  • GSM5739915 FDC1M tumor sample Case marker detected. Ovary disease state: gastric adenocarcinoma; pathological types: adenocarcinoma with low differentiation; tissue: ovarian metastasis of gastric adenocarcinoma; individual: FDC1
  • GSM5739916 FDC2P tumor sample Case marker detected. Stomach disease state: gastric adenocarcinoma; pathological types: adenocarcinoma with low differentiation; tissue: gastric adenocarcinoma; individual: FDC2
  • GSM5739918 FDC2M tumor sample Case marker detected. Ovary disease state: gastric adenocarcinoma; pathological types: adenocarcinoma with low differentiation; tissue: ovarian metastasis of gastric adenocarcinoma; individual: FDC2
  • GSM5739919 FDC3P tumor sample Case marker detected. Stomach disease state: gastric adenocarcinoma; pathological types: adenocarcinoma with low differentiation; tissue: gastric adenocarcinoma; individual: FDC3
  • GSM5739921 FDC3M tumor sample Case marker detected. Ovary disease state: gastric adenocarcinoma; pathological types: adenocarcinoma with low differentiation; tissue: ovarian metastasis of gastric adenocarcinoma; individual: FDC3
  • GSM5739922 FDC4P tumor sample Case marker detected. Stomach disease state: gastric adenocarcinoma; pathological types: adenocarcinoma with low differentiation; tissue: gastric adenocarcinoma; individual: FDC4
  • GSM5739924 FDC4M tumor sample Case marker detected. Ovary disease state: gastric adenocarcinoma; pathological types: adenocarcinoma with low differentiation; tissue: ovarian metastasis of gastric adenocarcinoma; individual: FDC4

Possible control samples

Samples currently treated as controls or baseline.

4
  • GSM5739914 FDC1N normal tissue Control marker detected. Stomach disease state: gastric adenocarcinoma; pathological types: adenocarcinoma with low differentiation; tissue: normal gastric mucosa; individual: FDC1
  • GSM5739917 FDC2N normal tissue Control marker detected. Stomach disease state: gastric adenocarcinoma; pathological types: adenocarcinoma with low differentiation; tissue: normal gastric mucosa; individual: FDC2
  • GSM5739920 FDC3N normal tissue Control marker detected. Stomach disease state: gastric adenocarcinoma; pathological types: adenocarcinoma with low differentiation; tissue: normal gastric mucosa; individual: FDC3
  • GSM5739923 FDC4N normal tissue Control marker detected. Stomach disease state: gastric adenocarcinoma; pathological types: adenocarcinoma with low differentiation; tissue: normal gastric mucosa; individual: FDC4

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

tumor sample

8 samples
  • GSM5739913 FDC1P Stomach disease state: gastric adenocarcinoma; pathological types: adenocarcinoma with low differentiation; tissue: gastric adenocarcinoma; individual: FDC1
  • GSM5739915 FDC1M Ovary disease state: gastric adenocarcinoma; pathological types: adenocarcinoma with low differentiation; tissue: ovarian metastasis of gastric adenocarcinoma; individual: FDC1
  • GSM5739916 FDC2P Stomach disease state: gastric adenocarcinoma; pathological types: adenocarcinoma with low differentiation; tissue: gastric adenocarcinoma; individual: FDC2
  • GSM5739918 FDC2M Ovary disease state: gastric adenocarcinoma; pathological types: adenocarcinoma with low differentiation; tissue: ovarian metastasis of gastric adenocarcinoma; individual: FDC2
  • GSM5739919 FDC3P Stomach disease state: gastric adenocarcinoma; pathological types: adenocarcinoma with low differentiation; tissue: gastric adenocarcinoma; individual: FDC3
  • GSM5739921 FDC3M Ovary disease state: gastric adenocarcinoma; pathological types: adenocarcinoma with low differentiation; tissue: ovarian metastasis of gastric adenocarcinoma; individual: FDC3
  • GSM5739922 FDC4P Stomach disease state: gastric adenocarcinoma; pathological types: adenocarcinoma with low differentiation; tissue: gastric adenocarcinoma; individual: FDC4
  • GSM5739924 FDC4M Ovary disease state: gastric adenocarcinoma; pathological types: adenocarcinoma with low differentiation; tissue: ovarian metastasis of gastric adenocarcinoma; individual: FDC4

normal tissue

4 samples
  • GSM5739914 FDC1N Stomach disease state: gastric adenocarcinoma; pathological types: adenocarcinoma with low differentiation; tissue: normal gastric mucosa; individual: FDC1
  • GSM5739917 FDC2N Stomach disease state: gastric adenocarcinoma; pathological types: adenocarcinoma with low differentiation; tissue: normal gastric mucosa; individual: FDC2
  • GSM5739920 FDC3N Stomach disease state: gastric adenocarcinoma; pathological types: adenocarcinoma with low differentiation; tissue: normal gastric mucosa; individual: FDC3
  • GSM5739923 FDC4N Stomach disease state: gastric adenocarcinoma; pathological types: adenocarcinoma with low differentiation; tissue: normal gastric mucosa; individual: FDC4

Score Breakdown

60%

relevance

  • Organism normalized.
  • Assay type normalized.
  • Tissue metadata normalized.
20%

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 gastrointestinal cancer context downgraded for colorectal 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.
45%

overall

  • Weighted score: 30% relevance, 30% comparison suitability, 25% metadata quality, 15% data availability.
  • Overall score capped because comparison suitability is weak for the selected search intent.
  • Overall score capped because gastrointestinal context is not explicit colorectal/CRC.

Sample Links

12 samples

Review Audit Trail

0 decisions

No review decisions have been stored for this dataset.