Siftome Phase 3L

GSE210787

Tumor-specific circRNAs elicit anti-tumor immune response via encoding cryptic peptides [RNA-Seq]

Not suitable Dataset does not meet the current suitability threshold.
Sample grouping CSV Contrast CSV DESeq2 metadata CSV R handoff notes Handoff report Download instructions Open GEO dataset
Source
GEO
Search intent
Patient tissue tumor-vs-normal
Intent behavior
search-intent-behavior-v1
Submission date
2022-08-09
Last update
2024-01-25
Organization
Sun Yat-Sen University
Department
Not available
Public date
2023-10-08
Experiment types
Expression profiling by high throughput sequencing; Non-coding RNA profiling by high throughput sequencing
Platforms
GPL24676 Illumina NovaSeq 6000 (Homo sapiens)
Series type
SubSeries
SubSeries
Not available
BioProject
PRJNA867548
Supplementary files
XLSX: GSE210787_Patients.lncRNA._expression.xlsx
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

Review before analysis
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

  • Secondary RNA assay context should be analyzed separately from ordinary bulk RNA-seq.

Next Steps

  • Review blockers and update sample grouping or dataset selection before analysis.

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

Bioinformatician review required

Ask a bioinformatician to review grouping, count availability, exclusions, and design before DE.

  • Analysis readiness has blockers that must be resolved before DE.
  • Assay context may require expert handling before DESeq2-style analysis.

Why This Is Ranked Here

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

Score Components

  • relevance 100% Disease or condition metadata normalized. 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 100% 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 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 6 samples
  • Likely control group normal tissue 6 samples

Warnings

  • SECONDARY_ASSAY_CONTEXT warning Secondary RNA assay context such as small RNA, miRNA, circRNA, or non-coding RNA was detected.

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: not a colorectal/GI cancer cohort. Derived from current-intent ranking reasons and warnings.

Applied Review Decisions

No active review decisions affect this ranking.

Ranking Facts

  • Recommendation Not suitable Dataset does not meet the current suitability threshold.
  • Supporting fact Tumor vs 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: not a colorectal/GI cancer cohort. Contributed to match or upgrade evidence.
  • Supporting fact Processed data is available for downstream review. Contributed to match or upgrade evidence.
  • Supporting fact 1 warning require review. Contributed to match or upgrade evidence.
  • Caution fact Secondary RNA assay context such as small RNA, miRNA, circRNA, or non-coding RNA was detected. 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: Treatment clarity: No unclear treatment split detected in the sample metadata. Contributed to downgrade or manual-review evidence.
  • Caution fact Overall score capped because comparison suitability is weak for the selected search intent. Contributed to downgrade or manual-review evidence.
  • Caution fact Overall score capped because tumor/normal grouping is from a non-colorectal cancer context. Contributed to downgrade or manual-review evidence.
  • Caution fact Downgraded disease context: not a colorectal/GI cancer cohort. Contributed to downgrade or manual-review evidence.
  • Caution fact Comparison suitability score is below the Phase 1 recommended threshold. Contributed to downgrade or manual-review evidence.

Manual Corrections

0 active

Source Evidence

4 sources

GEO

Primary source

Original dataset metadata, sample metadata, source links, and GEO data availability flags.

Dataset accession
GSE210787
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
GSE210787
  • 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
GSE210787
  • 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
GSE210787
  • 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: GSE210787
dataset_title: Tumor-specific circRNAs elicit anti-tumor immune response via encoding cryptic peptides [RNA-Seq]
organism: Homo sapiens
assay_type: bulk RNA-seq
processed_data_available: true
raw_data_available: true
submission_date: 2022-08-09
last_update_date: 2024-01-25
organization_name: Sun Yat-Sen University
department: Not available
public_date: 2023-10-08
experiment_types: Expression profiling by high throughput sequencing; Non-coding RNA profiling by high throughput sequencing
platforms: GPL24676 Illumina NovaSeq 6000 (Homo sapiens)
sub_series: Not available
bioproject: PRJNA867548
supplementary_files: XLSX: GSE210787_Patients.lncRNA._expression.xlsx
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: not a colorectal/GI cancer cohort.
  • Processed data is available for downstream review.
  • 1 warning require review.

Why It May Not Be Suitable

  • Secondary RNA assay context such as small RNA, miRNA, circRNA, or non-coding RNA was detected.
  • Non-colorectal cancer context downgraded for colorectal tumor-vs-normal tissue ranking.
  • Missing or unclear metadata: Treatment clarity: No unclear treatment split detected in the sample metadata.
  • Overall score capped because comparison suitability is weak for the selected search intent.
  • Overall score capped because tumor/normal grouping is from a non-colorectal cancer context.
  • Downgraded disease context: not a colorectal/GI cancer cohort.
  • Comparison suitability score is below the Phase 1 recommended threshold.

Warnings

  • warning SECONDARY_ASSAY_CONTEXT Secondary RNA assay context such as small RNA, miRNA, circRNA, or non-coding RNA was detected.

Normalized Fields

32 fields
Field Value Source Origin Confidence Evidence Reason
assay_type bulk RNA-seq dataset GSE210787 Runtime Siftome inference GEO:dataset:GSE210787:2469d53c9041c4f96620cbbcab36a4b6e7c9c5ac921f43025729d1b76bc7f2fd high confidence bulk rna-seq dataset_accession: GSE210787 dataset_title: Tumor-specific circRNAs elicit anti-tumor immune response via encoding cryptic peptides [RNA-Seq] organism: Homo sapiens assay_type: ... keyword match keyword match: bulk rna-seq
disease breast cancer sample GSM6437631 Runtime Siftome inference GEO:sample:GSM6437631:6175df02bc462a160a9b67301e1f876668d6235bb262803ca83bb1428cdd5a91 high confidence breast cancer sample_accession: GSM6437631 sample_title: T1 (RNA-seq) source_name: cancer tissue characteristics: Sex: female; age: 46; ethnicity: Han nationality; tumor grade: II; outcome: r... controlled vocabulary controlled vocabulary disease match: breast cancer
disease breast cancer sample GSM6437632 Runtime Siftome inference GEO:sample:GSM6437632:67993f3d6cd9f7052115b0210e1bf781b6e8749876b58f7bf05c6cd6d0ea1fa1 high confidence breast cancer sample_accession: GSM6437632 sample_title: T2 (RNA-seq) source_name: cancer tissue characteristics: Sex: female; age: 52; ethnicity: Han nationality; tumor grade: III; outcome: ... controlled vocabulary controlled vocabulary disease match: breast cancer
disease breast cancer sample GSM6437633 Runtime Siftome inference GEO:sample:GSM6437633:b6eb86f5d0549c424809605eab4b282aefe4ccd7d9d1431cdf87585877e4fad9 high confidence breast cancer sample_accession: GSM6437633 sample_title: T3 (RNA-seq) source_name: cancer tissue characteristics: Sex: female; age: 47; ethnicity: Han nationality; tumor grade: III; outcome: ... controlled vocabulary controlled vocabulary disease match: breast cancer
disease breast cancer sample GSM6437634 Runtime Siftome inference GEO:sample:GSM6437634:0b5881b50d8a6f5a88c5bc7b2329afc18624a0858d09bc0dd4107fe56dd2acff high confidence breast cancer sample_accession: GSM6437634 sample_title: T4 (RNA-seq) source_name: cancer tissue characteristics: Sex: female; age: 56; ethnicity: Han nationality; tumor grade: II; outcome: r... controlled vocabulary controlled vocabulary disease match: breast cancer
disease breast cancer sample GSM6437635 Runtime Siftome inference GEO:sample:GSM6437635:e4876198cc1444035f14eecf2b561f8d14e5c8cfe7aa8d9ad252426fbb199b8d high confidence breast cancer sample_accession: GSM6437635 sample_title: T5 (RNA-seq) source_name: cancer tissue characteristics: Sex: female; age: 49; ethnicity: Han nationality; tumor grade: II; outcome: r... controlled vocabulary controlled vocabulary disease match: breast cancer
disease breast cancer sample GSM6437636 Runtime Siftome inference GEO:sample:GSM6437636:024d0450058635dfe315ee186f60cbdbd67a5557a0a853bbd3ae505f4ef1aaff high confidence breast cancer sample_accession: GSM6437636 sample_title: T6 (RNA-seq) source_name: cancer tissue characteristics: Sex: female; age: 51; ethnicity: Han nationality; tumor grade: II; outcome: r... controlled vocabulary controlled vocabulary disease match: breast cancer
organism Homo sapiens dataset GSE210787 Runtime Siftome inference GEO:dataset:GSE210787:2469d53c9041c4f96620cbbcab36a4b6e7c9c5ac921f43025729d1b76bc7f2fd high confidence homo sapiens dataset_accession: GSE210787 dataset_title: Tumor-specific circRNAs elicit anti-tumor immune response via encoding cryptic peptides [RNA-Seq] organism: Homo sapiens assay_type: ... keyword match keyword match: homo sapiens
sample_type normal tissue sample GSM6437625 Runtime Siftome inference GEO:sample:GSM6437625:f6bc61dd950146ef40974d846a9a4f3ea5e6f19ed9e02ced5274ed4080c8f052 low confidence normal sample_accession: GSM6437625 sample_title: N1 (RNA-seq) source_name: normal tissue characteristics: Sex: female; age: 46; ethnicity: Han nationality; tumor grade: II; outcome: r... controlled vocabulary controlled vocabulary sample type match: normal
sample_type tumor sample sample GSM6437625 Runtime Siftome inference GEO:sample:GSM6437625:f6bc61dd950146ef40974d846a9a4f3ea5e6f19ed9e02ced5274ed4080c8f052 low confidence tumor sample_accession: GSM6437625 sample_title: N1 (RNA-seq) source_name: normal tissue characteristics: Sex: female; age: 46; ethnicity: Han nationality; tumor grade: II; outcome: r... controlled vocabulary controlled vocabulary sample type match: tumor
sample_type normal tissue sample GSM6437626 Runtime Siftome inference GEO:sample:GSM6437626:37e6fcdf9d7214e8680f737cb68995f60cee56d2f51d47b50a9dd1bff5f3545c low confidence normal sample_accession: GSM6437626 sample_title: N2 (RNA-seq) source_name: normal tissue characteristics: Sex: female; age: 52; ethnicity: Han nationality; tumor grade: III; outcome: ... controlled vocabulary controlled vocabulary sample type match: normal
sample_type tumor sample sample GSM6437626 Runtime Siftome inference GEO:sample:GSM6437626:37e6fcdf9d7214e8680f737cb68995f60cee56d2f51d47b50a9dd1bff5f3545c low confidence tumor sample_accession: GSM6437626 sample_title: N2 (RNA-seq) source_name: normal tissue characteristics: Sex: female; age: 52; ethnicity: Han nationality; tumor grade: III; outcome: ... controlled vocabulary controlled vocabulary sample type match: tumor
sample_type normal tissue sample GSM6437627 Runtime Siftome inference GEO:sample:GSM6437627:da26815abced994e045031a76bef9bf498ae563ff92300b4ed303464684083a1 low confidence normal sample_accession: GSM6437627 sample_title: N3 (RNA-seq) source_name: normal tissue characteristics: Sex: female; age: 47; ethnicity: Han nationality; tumor grade: III; outcome: ... controlled vocabulary controlled vocabulary sample type match: normal
sample_type tumor sample sample GSM6437627 Runtime Siftome inference GEO:sample:GSM6437627:da26815abced994e045031a76bef9bf498ae563ff92300b4ed303464684083a1 low confidence tumor sample_accession: GSM6437627 sample_title: N3 (RNA-seq) source_name: normal tissue characteristics: Sex: female; age: 47; ethnicity: Han nationality; tumor grade: III; outcome: ... controlled vocabulary controlled vocabulary sample type match: tumor
sample_type normal tissue sample GSM6437628 Runtime Siftome inference GEO:sample:GSM6437628:cee1298cceffb060ee480ffe954315a155b23b9398efbdb55f33258de7fba486 low confidence normal sample_accession: GSM6437628 sample_title: N4 (RNA-seq) source_name: normal tissue characteristics: Sex: female; age: 56; ethnicity: Han nationality; tumor grade: II; outcome: r... controlled vocabulary controlled vocabulary sample type match: normal
sample_type tumor sample sample GSM6437628 Runtime Siftome inference GEO:sample:GSM6437628:cee1298cceffb060ee480ffe954315a155b23b9398efbdb55f33258de7fba486 low confidence tumor sample_accession: GSM6437628 sample_title: N4 (RNA-seq) source_name: normal tissue characteristics: Sex: female; age: 56; ethnicity: Han nationality; tumor grade: II; outcome: r... controlled vocabulary controlled vocabulary sample type match: tumor
sample_type normal tissue sample GSM6437629 Runtime Siftome inference GEO:sample:GSM6437629:a219096265d2c52002b31f8e6aceb32c92fd49bc53e07f04bbc3010952bf88dc low confidence normal sample_accession: GSM6437629 sample_title: N5 (RNA-seq) source_name: normal tissue characteristics: Sex: female; age: 49; ethnicity: Han nationality; tumor grade: II; outcome: r... controlled vocabulary controlled vocabulary sample type match: normal
sample_type tumor sample sample GSM6437629 Runtime Siftome inference GEO:sample:GSM6437629:a219096265d2c52002b31f8e6aceb32c92fd49bc53e07f04bbc3010952bf88dc low confidence tumor sample_accession: GSM6437629 sample_title: N5 (RNA-seq) source_name: normal tissue characteristics: Sex: female; age: 49; ethnicity: Han nationality; tumor grade: II; outcome: r... controlled vocabulary controlled vocabulary sample type match: tumor
sample_type normal tissue sample GSM6437630 Runtime Siftome inference GEO:sample:GSM6437630:707aa06eb1834c124a1c08eb8566b8609012a92c72f7e5acf18a1027c4e35049 low confidence normal sample_accession: GSM6437630 sample_title: N6 (RNA-seq) source_name: normal tissue characteristics: Sex: female; age: 51; ethnicity: Han nationality; tumor grade: II; outcome: r... controlled vocabulary controlled vocabulary sample type match: normal
sample_type tumor sample sample GSM6437630 Runtime Siftome inference GEO:sample:GSM6437630:707aa06eb1834c124a1c08eb8566b8609012a92c72f7e5acf18a1027c4e35049 low confidence tumor sample_accession: GSM6437630 sample_title: N6 (RNA-seq) source_name: normal tissue characteristics: Sex: female; age: 51; ethnicity: Han nationality; tumor grade: II; outcome: r... controlled vocabulary controlled vocabulary sample type match: tumor
sample_type tumor sample sample GSM6437631 Runtime Siftome inference GEO:sample:GSM6437631:6175df02bc462a160a9b67301e1f876668d6235bb262803ca83bb1428cdd5a91 low confidence tumor sample_accession: GSM6437631 sample_title: T1 (RNA-seq) source_name: cancer tissue characteristics: Sex: female; age: 46; ethnicity: Han nationality; tumor grade: II; outcome: r... controlled vocabulary controlled vocabulary sample type match: tumor
sample_type tumor sample sample GSM6437632 Runtime Siftome inference GEO:sample:GSM6437632:67993f3d6cd9f7052115b0210e1bf781b6e8749876b58f7bf05c6cd6d0ea1fa1 low confidence tumor sample_accession: GSM6437632 sample_title: T2 (RNA-seq) source_name: cancer tissue characteristics: Sex: female; age: 52; ethnicity: Han nationality; tumor grade: III; outcome: ... controlled vocabulary controlled vocabulary sample type match: tumor
sample_type tumor sample sample GSM6437633 Runtime Siftome inference GEO:sample:GSM6437633:b6eb86f5d0549c424809605eab4b282aefe4ccd7d9d1431cdf87585877e4fad9 low confidence tumor sample_accession: GSM6437633 sample_title: T3 (RNA-seq) source_name: cancer tissue characteristics: Sex: female; age: 47; ethnicity: Han nationality; tumor grade: III; outcome: ... controlled vocabulary controlled vocabulary sample type match: tumor
sample_type tumor sample sample GSM6437634 Runtime Siftome inference GEO:sample:GSM6437634:0b5881b50d8a6f5a88c5bc7b2329afc18624a0858d09bc0dd4107fe56dd2acff low confidence tumor sample_accession: GSM6437634 sample_title: T4 (RNA-seq) source_name: cancer tissue characteristics: Sex: female; age: 56; ethnicity: Han nationality; tumor grade: II; outcome: r... controlled vocabulary controlled vocabulary sample type match: tumor
sample_type tumor sample sample GSM6437635 Runtime Siftome inference GEO:sample:GSM6437635:e4876198cc1444035f14eecf2b561f8d14e5c8cfe7aa8d9ad252426fbb199b8d low confidence tumor sample_accession: GSM6437635 sample_title: T5 (RNA-seq) source_name: cancer tissue characteristics: Sex: female; age: 49; ethnicity: Han nationality; tumor grade: II; outcome: r... controlled vocabulary controlled vocabulary sample type match: tumor
sample_type tumor sample sample GSM6437636 Runtime Siftome inference GEO:sample:GSM6437636:024d0450058635dfe315ee186f60cbdbd67a5557a0a853bbd3ae505f4ef1aaff low confidence tumor sample_accession: GSM6437636 sample_title: T6 (RNA-seq) source_name: cancer tissue characteristics: Sex: female; age: 51; ethnicity: Han nationality; tumor grade: II; outcome: r... controlled vocabulary controlled vocabulary sample type match: tumor
tissue breast sample GSM6437631 Runtime Siftome inference GEO:sample:GSM6437631:6175df02bc462a160a9b67301e1f876668d6235bb262803ca83bb1428cdd5a91 low confidence breast sample_accession: GSM6437631 sample_title: T1 (RNA-seq) source_name: cancer tissue characteristics: Sex: female; age: 46; ethnicity: Han nationality; tumor grade: II; outcome: r... controlled vocabulary controlled vocabulary tissue match: breast
tissue breast sample GSM6437632 Runtime Siftome inference GEO:sample:GSM6437632:67993f3d6cd9f7052115b0210e1bf781b6e8749876b58f7bf05c6cd6d0ea1fa1 low confidence breast sample_accession: GSM6437632 sample_title: T2 (RNA-seq) source_name: cancer tissue characteristics: Sex: female; age: 52; ethnicity: Han nationality; tumor grade: III; outcome: ... controlled vocabulary controlled vocabulary tissue match: breast
tissue breast sample GSM6437633 Runtime Siftome inference GEO:sample:GSM6437633:b6eb86f5d0549c424809605eab4b282aefe4ccd7d9d1431cdf87585877e4fad9 low confidence breast sample_accession: GSM6437633 sample_title: T3 (RNA-seq) source_name: cancer tissue characteristics: Sex: female; age: 47; ethnicity: Han nationality; tumor grade: III; outcome: ... controlled vocabulary controlled vocabulary tissue match: breast
tissue breast sample GSM6437634 Runtime Siftome inference GEO:sample:GSM6437634:0b5881b50d8a6f5a88c5bc7b2329afc18624a0858d09bc0dd4107fe56dd2acff low confidence breast sample_accession: GSM6437634 sample_title: T4 (RNA-seq) source_name: cancer tissue characteristics: Sex: female; age: 56; ethnicity: Han nationality; tumor grade: II; outcome: r... controlled vocabulary controlled vocabulary tissue match: breast
tissue breast sample GSM6437635 Runtime Siftome inference GEO:sample:GSM6437635:e4876198cc1444035f14eecf2b561f8d14e5c8cfe7aa8d9ad252426fbb199b8d low confidence breast sample_accession: GSM6437635 sample_title: T5 (RNA-seq) source_name: cancer tissue characteristics: Sex: female; age: 49; ethnicity: Han nationality; tumor grade: II; outcome: r... controlled vocabulary controlled vocabulary tissue match: breast
tissue breast sample GSM6437636 Runtime Siftome inference GEO:sample:GSM6437636:024d0450058635dfe315ee186f60cbdbd67a5557a0a853bbd3ae505f4ef1aaff low confidence breast sample_accession: GSM6437636 sample_title: T6 (RNA-seq) source_name: cancer tissue characteristics: Sex: female; age: 51; ethnicity: Han nationality; tumor grade: II; outcome: r... controlled vocabulary controlled vocabulary tissue match: breast

Sample Group Preview

Possible case samples

Samples currently treated as the comparison case group.

6
  • GSM6437631 T1 (RNA-seq) tumor sample Case marker detected. cancer tissue Sex: female; age: 46; ethnicity: Han nationality; tumor grade: II; outcome: recovery; tissue: breast cancer tissue
  • GSM6437632 T2 (RNA-seq) tumor sample Case marker detected. cancer tissue Sex: female; age: 52; ethnicity: Han nationality; tumor grade: III; outcome: recovery; tissue: breast cancer tissue
  • GSM6437633 T3 (RNA-seq) tumor sample Case marker detected. cancer tissue Sex: female; age: 47; ethnicity: Han nationality; tumor grade: III; outcome: recovery; tissue: breast cancer tissue
  • GSM6437634 T4 (RNA-seq) tumor sample Case marker detected. cancer tissue Sex: female; age: 56; ethnicity: Han nationality; tumor grade: II; outcome: recovery; tissue: breast cancer tissue
  • GSM6437635 T5 (RNA-seq) tumor sample Case marker detected. cancer tissue Sex: female; age: 49; ethnicity: Han nationality; tumor grade: II; outcome: recovery; tissue: breast cancer tissue
  • GSM6437636 T6 (RNA-seq) tumor sample Case marker detected. cancer tissue Sex: female; age: 51; ethnicity: Han nationality; tumor grade: II; outcome: recovery; tissue: breast cancer tissue

Possible control samples

Samples currently treated as controls or baseline.

6
  • GSM6437625 N1 (RNA-seq) normal tissue Control marker detected. normal tissue Sex: female; age: 46; ethnicity: Han nationality; tumor grade: II; outcome: recovery; tissue: normal tissue
  • GSM6437626 N2 (RNA-seq) normal tissue Control marker detected. normal tissue Sex: female; age: 52; ethnicity: Han nationality; tumor grade: III; outcome: recovery; tissue: normal tissue
  • GSM6437627 N3 (RNA-seq) normal tissue Control marker detected. normal tissue Sex: female; age: 47; ethnicity: Han nationality; tumor grade: III; outcome: recovery; tissue: normal tissue
  • GSM6437628 N4 (RNA-seq) normal tissue Control marker detected. normal tissue Sex: female; age: 56; ethnicity: Han nationality; tumor grade: II; outcome: recovery; tissue: normal tissue
  • GSM6437629 N5 (RNA-seq) normal tissue Control marker detected. normal tissue Sex: female; age: 49; ethnicity: Han nationality; tumor grade: II; outcome: recovery; tissue: normal tissue
  • GSM6437630 N6 (RNA-seq) normal tissue Control marker detected. normal tissue Sex: female; age: 51; ethnicity: Han nationality; tumor grade: II; outcome: recovery; tissue: normal tissue

Unassigned samples

Samples with no explicit case or control marker.

0

No samples

Excluded samples

Samples excluded from grouping by hard exclusion rules.

0

No samples

Ambiguous samples

Samples that need manual review before trusting grouping.

0

No samples

Metadata Quality Components

Persisted metadata quality

100 pts
Clarity
100%
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 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

6 samples
  • GSM6437625 N1 (RNA-seq) normal tissue Sex: female; age: 46; ethnicity: Han nationality; tumor grade: II; outcome: recovery; tissue: normal tissue
  • GSM6437626 N2 (RNA-seq) normal tissue Sex: female; age: 52; ethnicity: Han nationality; tumor grade: III; outcome: recovery; tissue: normal tissue
  • GSM6437627 N3 (RNA-seq) normal tissue Sex: female; age: 47; ethnicity: Han nationality; tumor grade: III; outcome: recovery; tissue: normal tissue
  • GSM6437628 N4 (RNA-seq) normal tissue Sex: female; age: 56; ethnicity: Han nationality; tumor grade: II; outcome: recovery; tissue: normal tissue
  • GSM6437629 N5 (RNA-seq) normal tissue Sex: female; age: 49; ethnicity: Han nationality; tumor grade: II; outcome: recovery; tissue: normal tissue
  • GSM6437630 N6 (RNA-seq) normal tissue Sex: female; age: 51; ethnicity: Han nationality; tumor grade: II; outcome: recovery; tissue: normal tissue

tumor sample

6 samples
  • GSM6437631 T1 (RNA-seq) cancer tissue Sex: female; age: 46; ethnicity: Han nationality; tumor grade: II; outcome: recovery; tissue: breast cancer tissue
  • GSM6437632 T2 (RNA-seq) cancer tissue Sex: female; age: 52; ethnicity: Han nationality; tumor grade: III; outcome: recovery; tissue: breast cancer tissue
  • GSM6437633 T3 (RNA-seq) cancer tissue Sex: female; age: 47; ethnicity: Han nationality; tumor grade: III; outcome: recovery; tissue: breast cancer tissue
  • GSM6437634 T4 (RNA-seq) cancer tissue Sex: female; age: 56; ethnicity: Han nationality; tumor grade: II; outcome: recovery; tissue: breast cancer tissue
  • GSM6437635 T5 (RNA-seq) cancer tissue Sex: female; age: 49; ethnicity: Han nationality; tumor grade: II; outcome: recovery; tissue: breast cancer tissue
  • GSM6437636 T6 (RNA-seq) cancer tissue Sex: female; age: 51; ethnicity: Han nationality; tumor grade: II; outcome: recovery; tissue: breast cancer tissue

Score Breakdown

100%

relevance

  • Disease or condition metadata normalized.
  • 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.
100%

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 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

12 samples

Review Audit Trail

0 decisions

No review decisions have been stored for this dataset.