Siftome Phase 3L

GSE155800

Identification of transcriptional difference between Imatinib-sensitive and resistant patients with gastrointerstinal stromal tumor (GIST)

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
2020-08-06
Last update
2021-08-31
Organization
Shanghai Jiao Tong University School of Medicine
Department
Not available
Public date
2021-07-29
Experiment types
Expression profiling by high throughput sequencing
Platforms
GPL21290 Illumina HiSeq 3000 (Homo sapiens)
Series type
Series
SubSeries
Not available
BioProject
PRJNA655677
Supplementary files
TXT: GSE155800_GIST_gene_TPM_matrix.txt.gz; TXT: GSE155800_GIST_gene_counts_matrix.txt.gz
Organism
Homo sapiens
Assay
bulk RNA-seq
Samples
20
Study design
Tumor vs matched normal
Specimen/source
Tissue
Scoring version
intent-aware-scoring-v15
Ranking batch
b69568dd1e4fe1b9ee2d880bf5495d748a7e4c5c11e4107f02528c3be0e76012
Ranking created
2026-06-05T20:20:27.088676Z
Warning version
intent-aware-warnings-v2

Current Intent Interpretation

Patient tissue tumor-vs-normal

Expectations

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

Rules

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

Study Classification

Tumor vs matched normal Tissue

Analysis Readiness

Ready after review
94% DE readiness

Contrast completeness

25/25 pts

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

Minimum group size

20/20 pts

Each contrast group has at least 2 samples.

Processed data availability

20/20 pts

Processed data is marked available in the GEO index.

Sample decision clarity

15/15 pts

All samples are assigned to a case or control group.

Blocking warnings

7/10 pts

Warnings are present, but none are critical blockers.

Metadata normalization

7/10 pts

Metadata quality is usable, but still deserves review.

Blockers

No readiness blockers detected.

Next Steps

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

Analysis Preparation Checklist

5/6 ready

Group labels reviewed

Needs review

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

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

Minimum sample count met

Ready

Both groups meet the minimum of 2 samples.

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

Processed counts available

Ready

Processed data availability is marked true in the GEO index.

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

Ambiguous samples handled

Ready

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

Still scan the grouping table for biology-specific ambiguity.

Exclusion decisions recorded

Ready

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

Record any manual exclusions in the downstream analysis notes.

Source links preserved

Ready

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

Keep GEO dataset and sample links with exported metadata.

Bioinformatician Review

Standard analyst review

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

No expert-review triggers were detected by Siftome.

Why This Is Ranked Here

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

Score Components

  • relevance 50% Organism normalized. Assay type normalized.
  • comparison suitability 0% Tumor and normal sample groups detected. No excluded sample type flags detected. Matched tumor/normal design boosted for colorectal tumor-vs-normal tissue triage. Patient tissue or biopsy specimens boosted for tissue comparison triage. Non-colorectal cancer context downgraded for colorectal tumor-vs-normal tissue ranking.
  • metadata quality 70% Sample source clarity: All samples have source metadata and clear GSE/GSM accessions. Group clarity: Rule-based grouping found both case and control samples. Disease clarity: Disease or condition metadata was not normalized. Tissue clarity: Tissue metadata was not normalized. Treatment clarity: No unclear treatment split detected in the sample metadata. Replicate clarity: No pooled sample or technical replicate flags detected. Data availability clarity: Dataset-level processed or raw data availability is explicit.
  • data availability 100% Processed data available. Raw data available.
  • overall 34% Weighted score: 30% relevance, 30% comparison suitability, 25% metadata quality, 15% data availability. Overall score capped because comparison suitability is weak for the selected search intent. Overall score capped because tumor/normal grouping is from a non-colorectal cancer context.

Derived Classifications

  • Organism Homo sapiens Organism remains rule-derived: Homo sapiens.
  • Assay bulk RNA-seq Assay remains rule-derived: bulk RNA-seq.
  • Study design Tumor vs matched normal Study design remains rule-derived: Tumor vs matched normal.
  • Specimen/source Tissue Specimen/source remains rule-derived: Tissue.
  • Likely case group tumor sample 10 samples
  • Likely control group normal tissue 10 samples

Warnings

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

Intent Interpretation

  • Active intent Patient tissue tumor-vs-normal Ranks human colorectal tissue or biopsy cohorts where tumor samples can be compared with normal controls.
  • Organism expectation Homo sapiens Dataset organism is interpreted as Homo sapiens.
  • Assay expectation bulk RNA-seq Dataset assay is interpreted as bulk RNA-seq.
  • Specimen assumption patient tissue or biopsy Derived specimen/source is Tissue.
  • Control-group assumption matched normal, adjacent normal, paired normal, healthy tissue control, or otherwise normal tissue control Derived study design is Tumor vs matched normal; likely groups are tumor sample vs normal tissue.
  • Score caps Applied when matching conditions are present non-human datasets stay below the primary recommendation band, missing colorectal/colon/rectal/CRC context stays below the primary recommendation band, biofluid and model-system datasets cannot reach Recommended by default, microarray and secondary assays are capped unless explicitly enabled, or small cohorts are capped below high-confidence recommendations
  • Warning rules 2 active warnings missing or unclear control group, unclear disease context, unclear tissue source, mixed sample types, model-system markers, secondary assay context, missing processed data, or small cohort size
  • Downgrade or exclusion reason Downgraded disease context: 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 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: colorectal/GI relevance is unclear. Contributed to match or upgrade evidence.
  • Supporting fact Processed data is available for downstream review. Contributed to match or upgrade evidence.
  • Supporting fact 2 warnings require review. Contributed to match or upgrade evidence.
  • Caution fact Disease or condition label could not be normalized. Contributed to downgrade or manual-review evidence.
  • Caution fact Tissue or cell type could not be normalized. Contributed to downgrade or manual-review evidence.
  • Caution fact 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: 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
GSE155800
Sample records
20 GSM samples
  • GEO has priority for original metadata under the Phase 3J source rules.
  • Processed data: available.
  • Raw data: available.
  • No external source conflict is present in the current runtime data.

recount3

Not imported

Planned trusted source for processed count availability.

GEO accession
GSE155800
  • 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
GSE155800
  • 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
GSE155800
  • 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: GSE155800
dataset_title: Identification of transcriptional difference between Imatinib-sensitive and resistant patients with gastrointerstinal stromal tumor (GIST)
organism: Homo sapiens
assay_type: bulk RNA-seq
processed_data_available: true
raw_data_available: true
submission_date: 2020-08-06
last_update_date: 2021-08-31
organization_name: Shanghai Jiao Tong University School of Medicine
department: Not available
public_date: 2021-07-29
experiment_types: Expression profiling by high throughput sequencing
platforms: GPL21290 Illumina HiSeq 3000 (Homo sapiens)
sub_series: Not available
bioproject: PRJNA655677
supplementary_files: TXT: GSE155800_GIST_gene_TPM_matrix.txt.gz; TXT: GSE155800_GIST_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: colorectal/GI relevance is unclear.
  • Processed data is available for downstream review.
  • 2 warnings require review.

Why It May Not Be Suitable

  • Disease or condition label could not be normalized.
  • Tissue or cell type could not be normalized.
  • 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: colorectal/GI relevance is unclear.
  • Missing or unclear metadata: Downgraded disease context: colorectal/GI relevance is unclear.
  • Comparison suitability score is below the Phase 1 recommended threshold.

Warnings

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

Normalized Fields

32 fields
Field Value Source Origin Confidence Evidence Reason
assay_type bulk RNA-seq dataset GSE155800 Runtime Siftome inference GEO:dataset:GSE155800:3cfa418a74f364f51d221c81ff07399538f0a0668042a196d714fdc6a4fef977 high confidence bulk rna-seq dataset_accession: GSE155800 dataset_title: Identification of transcriptional difference between Imatinib-sensitive and resistant patients with gastrointerstinal stromal tumor (... keyword match keyword match: bulk rna-seq
normal_tissue_type adjacent normal sample GSM4712337 Runtime Siftome inference GEO:sample:GSM4712337:9d0cdf0f01e036acdee1f6ab71577379230225aa46e64c73bac39fdfc60fbe69 high confidence adjacent normal sample_accession: GSM4712337 sample_title: Adjacent normal sample 1 source_name: Gastrointestinal stromal characteristics: tissue: Gastrointestinal stromal; disease: Normal gast... controlled vocabulary controlled vocabulary normal tissue type match: adjacent normal
normal_tissue_type adjacent normal sample GSM4712338 Runtime Siftome inference GEO:sample:GSM4712338:d96ba218372b14219d8f2b8be5585df8047f65b445467f1f98591ee1849b1235 high confidence adjacent normal sample_accession: GSM4712338 sample_title: Adjacent normal sample 2 source_name: Gastrointestinal stromal characteristics: tissue: Gastrointestinal stromal; disease: Normal gast... controlled vocabulary controlled vocabulary normal tissue type match: adjacent normal
normal_tissue_type adjacent normal sample GSM4712339 Runtime Siftome inference GEO:sample:GSM4712339:488349c68adab80164e850b930d2cf138b7e3fdef5cd39d035d5e6b22b9d02d4 high confidence adjacent normal sample_accession: GSM4712339 sample_title: Adjacent normal sample 3 source_name: Gastrointestinal stromal characteristics: tissue: Gastrointestinal stromal; disease: Normal gast... controlled vocabulary controlled vocabulary normal tissue type match: adjacent normal
normal_tissue_type adjacent normal sample GSM4712340 Runtime Siftome inference GEO:sample:GSM4712340:17711f760991ce189457c010dd6c30ee18eb46e053e02988def1fc1aaba688c9 high confidence adjacent normal sample_accession: GSM4712340 sample_title: Adjacent normal sample 4 source_name: Gastrointestinal stromal characteristics: tissue: Gastrointestinal stromal; disease: Normal gast... controlled vocabulary controlled vocabulary normal tissue type match: adjacent normal
normal_tissue_type adjacent normal sample GSM4712341 Runtime Siftome inference GEO:sample:GSM4712341:9c8b196076b1925620bbd82049bfd49514eaa425f9004230255af9e55f95f82c high confidence adjacent normal sample_accession: GSM4712341 sample_title: Adjacent normal sample 5 source_name: Gastrointestinal stromal characteristics: tissue: Gastrointestinal stromal; disease: Normal gast... controlled vocabulary controlled vocabulary normal tissue type match: adjacent normal
normal_tissue_type adjacent normal sample GSM4712347 Runtime Siftome inference GEO:sample:GSM4712347:8550cfb7ab53fc33c267c41a7a003017cb4f31935a2cdb33252a2686600311c6 high confidence adjacent normal sample_accession: GSM4712347 sample_title: Adjacent normal sample 6 source_name: Gastrointestinal stromal characteristics: tissue: Gastrointestinal stromal; disease: Normal gast... controlled vocabulary controlled vocabulary normal tissue type match: adjacent normal
normal_tissue_type adjacent normal sample GSM4712348 Runtime Siftome inference GEO:sample:GSM4712348:41afeda1a63260da6accfe5c4563b009ed4176933e4d00150d2cccf0798d0823 high confidence adjacent normal sample_accession: GSM4712348 sample_title: Adjacent normal sample 7 source_name: Gastrointestinal stromal characteristics: tissue: Gastrointestinal stromal; disease: Normal gast... controlled vocabulary controlled vocabulary normal tissue type match: adjacent normal
normal_tissue_type adjacent normal sample GSM4712349 Runtime Siftome inference GEO:sample:GSM4712349:880f0f600bbabec74b2dd87eeebb5326afdb2ff04c9b1155af46f49a9f27c707 high confidence adjacent normal sample_accession: GSM4712349 sample_title: Adjacent normal sample 8 source_name: Gastrointestinal stromal characteristics: tissue: Gastrointestinal stromal; disease: Normal gast... controlled vocabulary controlled vocabulary normal tissue type match: adjacent normal
normal_tissue_type adjacent normal sample GSM4712350 Runtime Siftome inference GEO:sample:GSM4712350:630d86084b8f47abb931a6854a885d2a41bdea1c350c30aa769a86d818a26c06 high confidence adjacent normal sample_accession: GSM4712350 sample_title: Adjacent normal sample 9 source_name: Gastrointestinal stromal characteristics: tissue: Gastrointestinal stromal; disease: Normal gast... controlled vocabulary controlled vocabulary normal tissue type match: adjacent normal
normal_tissue_type adjacent normal sample GSM4712351 Runtime Siftome inference GEO:sample:GSM4712351:89d64d132eda003570c8be5a35d16900f1887c64ce4e55be15e5715c710d26f4 high confidence adjacent normal sample_accession: GSM4712351 sample_title: Adjacent normal sample 10 source_name: Gastrointestinal stromal characteristics: tissue: Gastrointestinal stromal; disease: Normal gas... controlled vocabulary controlled vocabulary normal tissue type match: adjacent normal
organism Homo sapiens dataset GSE155800 Runtime Siftome inference GEO:dataset:GSE155800:3cfa418a74f364f51d221c81ff07399538f0a0668042a196d714fdc6a4fef977 high confidence homo sapiens dataset_accession: GSE155800 dataset_title: Identification of transcriptional difference between Imatinib-sensitive and resistant patients with gastrointerstinal stromal tumor (... keyword match keyword match: homo sapiens
sample_type normal tissue sample GSM4712337 Runtime Siftome inference GEO:sample:GSM4712337:9d0cdf0f01e036acdee1f6ab71577379230225aa46e64c73bac39fdfc60fbe69 high confidence adjacent normal sample_accession: GSM4712337 sample_title: Adjacent normal sample 1 source_name: Gastrointestinal stromal characteristics: tissue: Gastrointestinal stromal; disease: Normal gast... controlled vocabulary controlled vocabulary sample type match: adjacent normal
sample_type normal tissue sample GSM4712338 Runtime Siftome inference GEO:sample:GSM4712338:d96ba218372b14219d8f2b8be5585df8047f65b445467f1f98591ee1849b1235 high confidence adjacent normal sample_accession: GSM4712338 sample_title: Adjacent normal sample 2 source_name: Gastrointestinal stromal characteristics: tissue: Gastrointestinal stromal; disease: Normal gast... controlled vocabulary controlled vocabulary sample type match: adjacent normal
sample_type normal tissue sample GSM4712339 Runtime Siftome inference GEO:sample:GSM4712339:488349c68adab80164e850b930d2cf138b7e3fdef5cd39d035d5e6b22b9d02d4 high confidence adjacent normal sample_accession: GSM4712339 sample_title: Adjacent normal sample 3 source_name: Gastrointestinal stromal characteristics: tissue: Gastrointestinal stromal; disease: Normal gast... controlled vocabulary controlled vocabulary sample type match: adjacent normal
sample_type normal tissue sample GSM4712340 Runtime Siftome inference GEO:sample:GSM4712340:17711f760991ce189457c010dd6c30ee18eb46e053e02988def1fc1aaba688c9 high confidence adjacent normal sample_accession: GSM4712340 sample_title: Adjacent normal sample 4 source_name: Gastrointestinal stromal characteristics: tissue: Gastrointestinal stromal; disease: Normal gast... controlled vocabulary controlled vocabulary sample type match: adjacent normal
sample_type normal tissue sample GSM4712341 Runtime Siftome inference GEO:sample:GSM4712341:9c8b196076b1925620bbd82049bfd49514eaa425f9004230255af9e55f95f82c high confidence adjacent normal sample_accession: GSM4712341 sample_title: Adjacent normal sample 5 source_name: Gastrointestinal stromal characteristics: tissue: Gastrointestinal stromal; disease: Normal gast... controlled vocabulary controlled vocabulary sample type match: adjacent normal
sample_type tumor sample sample GSM4712342 Runtime Siftome inference GEO:sample:GSM4712342:ab0bfa8f5a2ec8103db49cd7662aa6950bb572b541a6141c202cc90046c2b911 low confidence tumor sample_accession: GSM4712342 sample_title: Tumor sample 1 source_name: Gastrointestinal stromal characteristics: tissue: Gastrointestinal stromal; disease: Gastrointestinal stro... controlled vocabulary controlled vocabulary sample type match: tumor
sample_type tumor sample sample GSM4712343 Runtime Siftome inference GEO:sample:GSM4712343:85bb42ef624f26cde58a4b35f92dfecc1abc6a5620c76edd4ff235770971d187 low confidence tumor sample_accession: GSM4712343 sample_title: Tumor sample 2 source_name: Gastrointestinal stromal characteristics: tissue: Gastrointestinal stromal; disease: Gastrointestinal stro... controlled vocabulary controlled vocabulary sample type match: tumor
sample_type tumor sample sample GSM4712344 Runtime Siftome inference GEO:sample:GSM4712344:c1ce3ad30c92ab64bf90551aa2253ffc0a562dea76e248687012707962b30d0b low confidence tumor sample_accession: GSM4712344 sample_title: Tumor sample 3 source_name: Gastrointestinal stromal characteristics: tissue: Gastrointestinal stromal; disease: Gastrointestinal stro... controlled vocabulary controlled vocabulary sample type match: tumor
sample_type tumor sample sample GSM4712345 Runtime Siftome inference GEO:sample:GSM4712345:a46fafb057afc5d8a2a926efa2b8326c93dbbb2eb43af57b233651c57d256ea3 low confidence tumor sample_accession: GSM4712345 sample_title: Tumor sample 4 source_name: Gastrointestinal stromal characteristics: tissue: Gastrointestinal stromal; disease: Gastrointestinal stro... controlled vocabulary controlled vocabulary sample type match: tumor
sample_type tumor sample sample GSM4712346 Runtime Siftome inference GEO:sample:GSM4712346:03d1c212f3e9eb5c445a853c7eb42c859eb5fcab47cc0b21bca807c6b83e3fc8 low confidence tumor sample_accession: GSM4712346 sample_title: Tumor sample 5 source_name: Gastrointestinal stromal characteristics: tissue: Gastrointestinal stromal; disease: Gastrointestinal stro... controlled vocabulary controlled vocabulary sample type match: tumor
sample_type normal tissue sample GSM4712347 Runtime Siftome inference GEO:sample:GSM4712347:8550cfb7ab53fc33c267c41a7a003017cb4f31935a2cdb33252a2686600311c6 high confidence adjacent normal sample_accession: GSM4712347 sample_title: Adjacent normal sample 6 source_name: Gastrointestinal stromal characteristics: tissue: Gastrointestinal stromal; disease: Normal gast... controlled vocabulary controlled vocabulary sample type match: adjacent normal
sample_type normal tissue sample GSM4712348 Runtime Siftome inference GEO:sample:GSM4712348:41afeda1a63260da6accfe5c4563b009ed4176933e4d00150d2cccf0798d0823 high confidence adjacent normal sample_accession: GSM4712348 sample_title: Adjacent normal sample 7 source_name: Gastrointestinal stromal characteristics: tissue: Gastrointestinal stromal; disease: Normal gast... controlled vocabulary controlled vocabulary sample type match: adjacent normal
sample_type normal tissue sample GSM4712349 Runtime Siftome inference GEO:sample:GSM4712349:880f0f600bbabec74b2dd87eeebb5326afdb2ff04c9b1155af46f49a9f27c707 high confidence adjacent normal sample_accession: GSM4712349 sample_title: Adjacent normal sample 8 source_name: Gastrointestinal stromal characteristics: tissue: Gastrointestinal stromal; disease: Normal gast... controlled vocabulary controlled vocabulary sample type match: adjacent normal
sample_type normal tissue sample GSM4712350 Runtime Siftome inference GEO:sample:GSM4712350:630d86084b8f47abb931a6854a885d2a41bdea1c350c30aa769a86d818a26c06 high confidence adjacent normal sample_accession: GSM4712350 sample_title: Adjacent normal sample 9 source_name: Gastrointestinal stromal characteristics: tissue: Gastrointestinal stromal; disease: Normal gast... controlled vocabulary controlled vocabulary sample type match: adjacent normal
sample_type normal tissue sample GSM4712351 Runtime Siftome inference GEO:sample:GSM4712351:89d64d132eda003570c8be5a35d16900f1887c64ce4e55be15e5715c710d26f4 high confidence adjacent normal sample_accession: GSM4712351 sample_title: Adjacent normal sample 10 source_name: Gastrointestinal stromal characteristics: tissue: Gastrointestinal stromal; disease: Normal gas... controlled vocabulary controlled vocabulary sample type match: adjacent normal
sample_type tumor sample sample GSM4712352 Runtime Siftome inference GEO:sample:GSM4712352:154b3fe5458f5a9518cfe94ef68dcc49a8377a27578a9d32119194513bd8263a low confidence tumor sample_accession: GSM4712352 sample_title: Tumor sample 6 source_name: Gastrointestinal stromal characteristics: tissue: Gastrointestinal stromal; disease: Gastrointestinal stro... controlled vocabulary controlled vocabulary sample type match: tumor
sample_type tumor sample sample GSM4712353 Runtime Siftome inference GEO:sample:GSM4712353:9a84d11ca4994f4656796de957d92a8f6bfda3584c0abad0a5fd4a2bb60cb30a low confidence tumor sample_accession: GSM4712353 sample_title: Tumor sample 7 source_name: Gastrointestinal stromal characteristics: tissue: Gastrointestinal stromal; disease: Gastrointestinal stro... controlled vocabulary controlled vocabulary sample type match: tumor
sample_type tumor sample sample GSM4712354 Runtime Siftome inference GEO:sample:GSM4712354:b707ceeb22118f335aa6273d81403b5f85fafc1112792a47b8cd552750a12d51 low confidence tumor sample_accession: GSM4712354 sample_title: Tumor sample 8 source_name: Gastrointestinal stromal characteristics: tissue: Gastrointestinal stromal; disease: Gastrointestinal stro... controlled vocabulary controlled vocabulary sample type match: tumor
sample_type tumor sample sample GSM4712355 Runtime Siftome inference GEO:sample:GSM4712355:d42460f62b43101398490782f87f2bef7a31b21d7135a0054e4521b8a3cf5fb9 low confidence tumor sample_accession: GSM4712355 sample_title: Tumor sample 9 source_name: Gastrointestinal stromal characteristics: tissue: Gastrointestinal stromal; disease: Gastrointestinal stro... controlled vocabulary controlled vocabulary sample type match: tumor
sample_type tumor sample sample GSM4712356 Runtime Siftome inference GEO:sample:GSM4712356:28ad84f5c31143c40e249302d5b27121a08c9d25c0d3335825b84dd79185e3bd low confidence tumor sample_accession: GSM4712356 sample_title: Tumor sample 10 source_name: Gastrointestinal stromal characteristics: tissue: Gastrointestinal stromal; disease: Gastrointestinal str... controlled vocabulary controlled vocabulary sample type match: tumor

Sample Group Preview

Possible case samples

Samples currently treated as the comparison case group.

10
  • GSM4712342 Tumor sample 1 tumor sample Case marker detected. Gastrointestinal stromal tissue: Gastrointestinal stromal; disease: Gastrointestinal stromal tumor; group: Imatinib sensitive patient
  • GSM4712343 Tumor sample 2 tumor sample Case marker detected. Gastrointestinal stromal tissue: Gastrointestinal stromal; disease: Gastrointestinal stromal tumor; group: Imatinib sensitive patient
  • GSM4712344 Tumor sample 3 tumor sample Case marker detected. Gastrointestinal stromal tissue: Gastrointestinal stromal; disease: Gastrointestinal stromal tumor; group: Imatinib sensitive patient
  • GSM4712345 Tumor sample 4 tumor sample Case marker detected. Gastrointestinal stromal tissue: Gastrointestinal stromal; disease: Gastrointestinal stromal tumor; group: Imatinib sensitive patient
  • GSM4712346 Tumor sample 5 tumor sample Case marker detected. Gastrointestinal stromal tissue: Gastrointestinal stromal; disease: Gastrointestinal stromal tumor; group: Imatinib sensitive patient
  • GSM4712352 Tumor sample 6 tumor sample Case marker detected. Gastrointestinal stromal tissue: Gastrointestinal stromal; disease: Gastrointestinal stromal tumor; group: Imatinib resistant patient
  • GSM4712353 Tumor sample 7 tumor sample Case marker detected. Gastrointestinal stromal tissue: Gastrointestinal stromal; disease: Gastrointestinal stromal tumor; group: Imatinib resistant patient
  • GSM4712354 Tumor sample 8 tumor sample Case marker detected. Gastrointestinal stromal tissue: Gastrointestinal stromal; disease: Gastrointestinal stromal tumor; group: Imatinib resistant patient
  • GSM4712355 Tumor sample 9 tumor sample Case marker detected. Gastrointestinal stromal tissue: Gastrointestinal stromal; disease: Gastrointestinal stromal tumor; group: Imatinib resistant patient
  • GSM4712356 Tumor sample 10 tumor sample Case marker detected. Gastrointestinal stromal tissue: Gastrointestinal stromal; disease: Gastrointestinal stromal tumor; group: Imatinib resistant patient

Possible control samples

Samples currently treated as controls or baseline.

10
  • GSM4712337 Adjacent normal sample 1 normal tissue Control marker detected. Gastrointestinal stromal tissue: Gastrointestinal stromal; disease: Normal gastrointestinal stromal; group: Imatinib sensitive patient
  • GSM4712338 Adjacent normal sample 2 normal tissue Control marker detected. Gastrointestinal stromal tissue: Gastrointestinal stromal; disease: Normal gastrointestinal stromal; group: Imatinib sensitive patient
  • GSM4712339 Adjacent normal sample 3 normal tissue Control marker detected. Gastrointestinal stromal tissue: Gastrointestinal stromal; disease: Normal gastrointestinal stromal; group: Imatinib sensitive patient
  • GSM4712340 Adjacent normal sample 4 normal tissue Control marker detected. Gastrointestinal stromal tissue: Gastrointestinal stromal; disease: Normal gastrointestinal stromal; group: Imatinib sensitive patient
  • GSM4712341 Adjacent normal sample 5 normal tissue Control marker detected. Gastrointestinal stromal tissue: Gastrointestinal stromal; disease: Normal gastrointestinal stromal; group: Imatinib sensitive patient
  • GSM4712347 Adjacent normal sample 6 normal tissue Control marker detected. Gastrointestinal stromal tissue: Gastrointestinal stromal; disease: Normal gastrointestinal stromal; group: Imatinib resistant patient
  • GSM4712348 Adjacent normal sample 7 normal tissue Control marker detected. Gastrointestinal stromal tissue: Gastrointestinal stromal; disease: Normal gastrointestinal stromal; group: Imatinib resistant patient
  • GSM4712349 Adjacent normal sample 8 normal tissue Control marker detected. Gastrointestinal stromal tissue: Gastrointestinal stromal; disease: Normal gastrointestinal stromal; group: Imatinib resistant patient
  • GSM4712350 Adjacent normal sample 9 normal tissue Control marker detected. Gastrointestinal stromal tissue: Gastrointestinal stromal; disease: Normal gastrointestinal stromal; group: Imatinib resistant patient
  • GSM4712351 Adjacent normal sample 10 normal tissue Control marker detected. Gastrointestinal stromal tissue: Gastrointestinal stromal; disease: Normal gastrointestinal stromal; group: Imatinib resistant patient

Unassigned samples

Samples with no explicit case or control marker.

0

No samples

Excluded samples

Samples excluded from grouping by hard exclusion rules.

0

No samples

Ambiguous samples

Samples that need manual review before trusting grouping.

0

No samples

Metadata Quality Components

Persisted metadata quality

70 pts
Clarity
70%
Weight
100 pts

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

Detected Sample Groups

normal tissue

10 samples
  • GSM4712337 Adjacent normal sample 1 Gastrointestinal stromal tissue: Gastrointestinal stromal; disease: Normal gastrointestinal stromal; group: Imatinib sensitive patient
  • GSM4712338 Adjacent normal sample 2 Gastrointestinal stromal tissue: Gastrointestinal stromal; disease: Normal gastrointestinal stromal; group: Imatinib sensitive patient
  • GSM4712339 Adjacent normal sample 3 Gastrointestinal stromal tissue: Gastrointestinal stromal; disease: Normal gastrointestinal stromal; group: Imatinib sensitive patient
  • GSM4712340 Adjacent normal sample 4 Gastrointestinal stromal tissue: Gastrointestinal stromal; disease: Normal gastrointestinal stromal; group: Imatinib sensitive patient
  • GSM4712341 Adjacent normal sample 5 Gastrointestinal stromal tissue: Gastrointestinal stromal; disease: Normal gastrointestinal stromal; group: Imatinib sensitive patient
  • GSM4712347 Adjacent normal sample 6 Gastrointestinal stromal tissue: Gastrointestinal stromal; disease: Normal gastrointestinal stromal; group: Imatinib resistant patient
  • GSM4712348 Adjacent normal sample 7 Gastrointestinal stromal tissue: Gastrointestinal stromal; disease: Normal gastrointestinal stromal; group: Imatinib resistant patient
  • GSM4712349 Adjacent normal sample 8 Gastrointestinal stromal tissue: Gastrointestinal stromal; disease: Normal gastrointestinal stromal; group: Imatinib resistant patient
  • GSM4712350 Adjacent normal sample 9 Gastrointestinal stromal tissue: Gastrointestinal stromal; disease: Normal gastrointestinal stromal; group: Imatinib resistant patient
  • GSM4712351 Adjacent normal sample 10 Gastrointestinal stromal tissue: Gastrointestinal stromal; disease: Normal gastrointestinal stromal; group: Imatinib resistant patient

tumor sample

10 samples
  • GSM4712342 Tumor sample 1 Gastrointestinal stromal tissue: Gastrointestinal stromal; disease: Gastrointestinal stromal tumor; group: Imatinib sensitive patient
  • GSM4712343 Tumor sample 2 Gastrointestinal stromal tissue: Gastrointestinal stromal; disease: Gastrointestinal stromal tumor; group: Imatinib sensitive patient
  • GSM4712344 Tumor sample 3 Gastrointestinal stromal tissue: Gastrointestinal stromal; disease: Gastrointestinal stromal tumor; group: Imatinib sensitive patient
  • GSM4712345 Tumor sample 4 Gastrointestinal stromal tissue: Gastrointestinal stromal; disease: Gastrointestinal stromal tumor; group: Imatinib sensitive patient
  • GSM4712346 Tumor sample 5 Gastrointestinal stromal tissue: Gastrointestinal stromal; disease: Gastrointestinal stromal tumor; group: Imatinib sensitive patient
  • GSM4712352 Tumor sample 6 Gastrointestinal stromal tissue: Gastrointestinal stromal; disease: Gastrointestinal stromal tumor; group: Imatinib resistant patient
  • GSM4712353 Tumor sample 7 Gastrointestinal stromal tissue: Gastrointestinal stromal; disease: Gastrointestinal stromal tumor; group: Imatinib resistant patient
  • GSM4712354 Tumor sample 8 Gastrointestinal stromal tissue: Gastrointestinal stromal; disease: Gastrointestinal stromal tumor; group: Imatinib resistant patient
  • GSM4712355 Tumor sample 9 Gastrointestinal stromal tissue: Gastrointestinal stromal; disease: Gastrointestinal stromal tumor; group: Imatinib resistant patient
  • GSM4712356 Tumor sample 10 Gastrointestinal stromal tissue: Gastrointestinal stromal; disease: Gastrointestinal stromal tumor; group: Imatinib resistant patient

Score Breakdown

50%

relevance

  • Organism normalized.
  • Assay type normalized.
0%

comparison suitability

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

metadata quality

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

data availability

  • Processed data available.
  • Raw data available.
34%

overall

  • Weighted score: 30% relevance, 30% comparison suitability, 25% metadata quality, 15% data availability.
  • Overall score capped because comparison suitability is weak for the selected search intent.
  • Overall score capped because tumor/normal grouping is from a non-colorectal cancer context.

Sample Links

20 samples

Review Audit Trail

0 decisions

No review decisions have been stored for this dataset.