Siftome Phase 3L

GSE229571

Tumor-specific circRNAs elicit anti-tumor immune response via encoding cryptic peptides [RNA-Seq 2]

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
2023-04-12
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
Platforms
GPL24676 Illumina NovaSeq 6000 (Homo sapiens)
Series type
SubSeries
SubSeries
Not available
BioProject
PRJNA954954
Supplementary files
TXT: GSE229571_RNA.expression.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
100% 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

10/10 pts

No dataset warnings are present.

Metadata normalization

10/10 pts

Metadata quality is high enough to support downstream handoff.

Blockers

No readiness blockers detected.

Next Steps

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

Analysis Preparation Checklist

5/6 ready

Group labels reviewed

Needs review

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

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

Minimum sample count met

Ready

Both groups meet the minimum of 2 samples.

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

Processed counts available

Ready

Processed data availability is marked true in the GEO index.

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

Ambiguous samples handled

Ready

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

Still scan the grouping table for biology-specific ambiguity.

Exclusion decisions recorded

Ready

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

Record any manual exclusions in the downstream analysis notes.

Source links preserved

Ready

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

Keep GEO dataset and sample links with exported metadata.

Bioinformatician Review

Standard analyst review

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

No expert-review triggers were detected by Siftome.

Why This Is Ranked Here

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

Score Components

  • relevance 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

No ranking warnings are active.

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 0 active warnings missing or unclear control group, unclear disease context, unclear tissue source, mixed sample types, model-system markers, secondary assay context, missing processed data, or small cohort size
  • Downgrade or exclusion reason Downgraded disease context: not a colorectal/GI cancer cohort. Derived from current-intent ranking reasons and warnings.

Applied Review Decisions

No active review decisions affect this ranking.

Ranking Facts

  • Recommendation Not suitable Dataset does not meet the current suitability threshold.
  • Supporting fact Tumor vs 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.
  • 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
GSE229571
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
GSE229571
  • 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
GSE229571
  • 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
GSE229571
  • 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: GSE229571
dataset_title: Tumor-specific circRNAs elicit anti-tumor immune response via encoding cryptic peptides [RNA-Seq 2]
organism: Homo sapiens
assay_type: bulk RNA-seq
processed_data_available: true
raw_data_available: true
submission_date: 2023-04-12
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
platforms: GPL24676 Illumina NovaSeq 6000 (Homo sapiens)
sub_series: Not available
bioproject: PRJNA954954
supplementary_files: TXT: GSE229571_RNA.expression.txt.gz
series_type: SubSeries

Why It Matched

  • Tumor vs unmatched normal · Tissue · suitability 0%.
  • Prioritized assay: bulk RNA-seq is the active assay expectation.
  • Downgraded disease context: not a colorectal/GI cancer cohort.
  • Processed data is available for downstream review.

Why It May Not Be Suitable

  • 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

No warnings

Normalized Fields

44 fields
Field Value Source Origin Confidence Evidence Reason
assay_type bulk RNA-seq dataset GSE229571 Runtime Siftome inference GEO:dataset:GSE229571:3e5c4eb7abf81c0a8f24a4d5b4dcdeee6f8bebd80d25dc3b6e7f22137a7dce23 high confidence bulk rna-seq dataset_accession: GSE229571 dataset_title: Tumor-specific circRNAs elicit anti-tumor immune response via encoding cryptic peptides [RNA-Seq 2] organism: Homo sapiens assay_type... keyword match keyword match: bulk rna-seq
disease breast cancer sample GSM7165682 Runtime Siftome inference GEO:sample:GSM7165682:f17e1e2af6bd464bb63a6213224cfe7eb05fb7a4cbf4e043da3faa91d7762706 high confidence breast cancer sample_accession: GSM7165682 sample_title: RNA-Seq P10-N source_name: normal characteristics: tissue: normal; diagnosis: breast cancer; Sex: female; age: 56; tumor stage: II RNA... controlled vocabulary controlled vocabulary disease match: breast cancer
disease breast cancer sample GSM7165683 Runtime Siftome inference GEO:sample:GSM7165683:3e55e39dbca1ec55fd9086a48eb809e822ac154f3797c8f798e241cfdd14c7d9 high confidence breast cancer sample_accession: GSM7165683 sample_title: RNA-Seq P10-T source_name: tumor characteristics: tissue: tumor; diagnosis: breast cancer; Sex: female; age: 56; tumor stage: II RNA-S... controlled vocabulary controlled vocabulary disease match: breast cancer
disease breast cancer sample GSM7165684 Runtime Siftome inference GEO:sample:GSM7165684:7f79553a007d6a1cd76729a859d98fdfc3b7470191aff02c03a8f9a5e4a6fda2 high confidence breast cancer sample_accession: GSM7165684 sample_title: RNA-Seq P11-N source_name: normal characteristics: tissue: normal; diagnosis: breast cancer; Sex: female; age: 45; tumor stage: II RNA... controlled vocabulary controlled vocabulary disease match: breast cancer
disease breast cancer sample GSM7165685 Runtime Siftome inference GEO:sample:GSM7165685:15dc39612ac62a03ca1b79297d985f476c1daf3386deb86e3c0c7e09b1ac011b high confidence breast cancer sample_accession: GSM7165685 sample_title: RNA-Seq P11-T source_name: tumor characteristics: tissue: tumor; diagnosis: breast cancer; Sex: female; age: 45; tumor stage: II RNA-S... controlled vocabulary controlled vocabulary disease match: breast cancer
disease breast cancer sample GSM7165686 Runtime Siftome inference GEO:sample:GSM7165686:b79e99f3dcccf7a7cfa3dce9f0d1a1c28b17bc1156b9295a6c7b7c60590ff47a high confidence breast cancer sample_accession: GSM7165686 sample_title: RNA-Seq P12-N source_name: normal characteristics: tissue: normal; diagnosis: breast cancer; Sex: female; age: 57; tumor stage: II RNA... controlled vocabulary controlled vocabulary disease match: breast cancer
disease breast cancer sample GSM7165687 Runtime Siftome inference GEO:sample:GSM7165687:72c9f020fe307b5f08aa30feae7f7f6579ef1f472bc740dcc8d9c76f52d1f777 high confidence breast cancer sample_accession: GSM7165687 sample_title: RNA-Seq P12-T source_name: tumor characteristics: tissue: tumor; diagnosis: breast cancer; Sex: female; age: 57; tumor stage: II RNA-S... controlled vocabulary controlled vocabulary disease match: breast cancer
disease breast cancer sample GSM7165688 Runtime Siftome inference GEO:sample:GSM7165688:d6a5c3ba1931d5b5ea271e9f48b67da27fe77019634cf2194c880f6f7a9e5b3a high confidence breast cancer sample_accession: GSM7165688 sample_title: RNA-Seq P7-N source_name: normal characteristics: tissue: normal; diagnosis: breast cancer; Sex: female; age: 52; tumor stage: II RNA-... controlled vocabulary controlled vocabulary disease match: breast cancer
disease breast cancer sample GSM7165689 Runtime Siftome inference GEO:sample:GSM7165689:c7057456fd2f9e13b2dbec7227acd4be29582ca7ad72e850bec5c438e7be4358 high confidence breast cancer sample_accession: GSM7165689 sample_title: RNA-Seq P7-T source_name: tumor characteristics: tissue: tumor; diagnosis: breast cancer; Sex: female; age: 52; tumor stage: II RNA-Se... controlled vocabulary controlled vocabulary disease match: breast cancer
disease breast cancer sample GSM7165690 Runtime Siftome inference GEO:sample:GSM7165690:269f57d574db2aa342f8605f2ff548bffd6ace0915d3b838a7df58793d12fa34 high confidence breast cancer sample_accession: GSM7165690 sample_title: RNA-Seq P8-N source_name: normal characteristics: tissue: normal; diagnosis: breast cancer; Sex: female; age: 48; tumor stage: II RNA-... controlled vocabulary controlled vocabulary disease match: breast cancer
disease breast cancer sample GSM7165691 Runtime Siftome inference GEO:sample:GSM7165691:49310ae46cfdaff17ffdfc94119f55af7dfce02eebfe3df160a6ea38d6e51c31 high confidence breast cancer sample_accession: GSM7165691 sample_title: RNA-Seq P8-T source_name: tumor characteristics: tissue: tumor; diagnosis: breast cancer; Sex: female; age: 48; tumor stage: II RNA-Se... controlled vocabulary controlled vocabulary disease match: breast cancer
disease breast cancer sample GSM7165692 Runtime Siftome inference GEO:sample:GSM7165692:b788a49c51b7fcd237f1b14ac1a80bf75d55fda1c1aa1978f500f47ac433f718 high confidence breast cancer sample_accession: GSM7165692 sample_title: RNA-Seq P9-N source_name: normal characteristics: tissue: normal; diagnosis: breast cancer; Sex: female; age: 63; tumor stage: II RNA-... controlled vocabulary controlled vocabulary disease match: breast cancer
disease breast cancer sample GSM7165693 Runtime Siftome inference GEO:sample:GSM7165693:02002ccaf2c15c5d3d97a23b1b75b93c0e6838da7d5492b2ee379dd4418f6298 high confidence breast cancer sample_accession: GSM7165693 sample_title: RNA-Seq P9-T source_name: tumor characteristics: tissue: tumor; diagnosis: breast cancer; Sex: female; age: 63; tumor stage: II RNA-Se... controlled vocabulary controlled vocabulary disease match: breast cancer
organism Homo sapiens dataset GSE229571 Runtime Siftome inference GEO:dataset:GSE229571:3e5c4eb7abf81c0a8f24a4d5b4dcdeee6f8bebd80d25dc3b6e7f22137a7dce23 high confidence homo sapiens dataset_accession: GSE229571 dataset_title: Tumor-specific circRNAs elicit anti-tumor immune response via encoding cryptic peptides [RNA-Seq 2] organism: Homo sapiens assay_type... keyword match keyword match: homo sapiens
sample_type normal tissue sample GSM7165682 Runtime Siftome inference GEO:sample:GSM7165682:f17e1e2af6bd464bb63a6213224cfe7eb05fb7a4cbf4e043da3faa91d7762706 low confidence normal sample_accession: GSM7165682 sample_title: RNA-Seq P10-N source_name: normal characteristics: tissue: normal; diagnosis: breast cancer; Sex: female; age: 56; tumor stage: II RNA... controlled vocabulary controlled vocabulary sample type match: normal
sample_type tumor sample sample GSM7165682 Runtime Siftome inference GEO:sample:GSM7165682:f17e1e2af6bd464bb63a6213224cfe7eb05fb7a4cbf4e043da3faa91d7762706 low confidence tumor sample_accession: GSM7165682 sample_title: RNA-Seq P10-N source_name: normal characteristics: tissue: normal; diagnosis: breast cancer; Sex: female; age: 56; tumor stage: II RNA... controlled vocabulary controlled vocabulary sample type match: tumor
sample_type tumor sample sample GSM7165683 Runtime Siftome inference GEO:sample:GSM7165683:3e55e39dbca1ec55fd9086a48eb809e822ac154f3797c8f798e241cfdd14c7d9 low confidence tumor sample_accession: GSM7165683 sample_title: RNA-Seq P10-T source_name: tumor characteristics: tissue: tumor; diagnosis: breast cancer; Sex: female; age: 56; tumor stage: II RNA-S... controlled vocabulary controlled vocabulary sample type match: tumor
sample_type normal tissue sample GSM7165684 Runtime Siftome inference GEO:sample:GSM7165684:7f79553a007d6a1cd76729a859d98fdfc3b7470191aff02c03a8f9a5e4a6fda2 low confidence normal sample_accession: GSM7165684 sample_title: RNA-Seq P11-N source_name: normal characteristics: tissue: normal; diagnosis: breast cancer; Sex: female; age: 45; tumor stage: II RNA... controlled vocabulary controlled vocabulary sample type match: normal
sample_type tumor sample sample GSM7165684 Runtime Siftome inference GEO:sample:GSM7165684:7f79553a007d6a1cd76729a859d98fdfc3b7470191aff02c03a8f9a5e4a6fda2 low confidence tumor sample_accession: GSM7165684 sample_title: RNA-Seq P11-N source_name: normal characteristics: tissue: normal; diagnosis: breast cancer; Sex: female; age: 45; tumor stage: II RNA... controlled vocabulary controlled vocabulary sample type match: tumor
sample_type tumor sample sample GSM7165685 Runtime Siftome inference GEO:sample:GSM7165685:15dc39612ac62a03ca1b79297d985f476c1daf3386deb86e3c0c7e09b1ac011b low confidence tumor sample_accession: GSM7165685 sample_title: RNA-Seq P11-T source_name: tumor characteristics: tissue: tumor; diagnosis: breast cancer; Sex: female; age: 45; tumor stage: II RNA-S... controlled vocabulary controlled vocabulary sample type match: tumor
sample_type normal tissue sample GSM7165686 Runtime Siftome inference GEO:sample:GSM7165686:b79e99f3dcccf7a7cfa3dce9f0d1a1c28b17bc1156b9295a6c7b7c60590ff47a low confidence normal sample_accession: GSM7165686 sample_title: RNA-Seq P12-N source_name: normal characteristics: tissue: normal; diagnosis: breast cancer; Sex: female; age: 57; tumor stage: II RNA... controlled vocabulary controlled vocabulary sample type match: normal
sample_type tumor sample sample GSM7165686 Runtime Siftome inference GEO:sample:GSM7165686:b79e99f3dcccf7a7cfa3dce9f0d1a1c28b17bc1156b9295a6c7b7c60590ff47a low confidence tumor sample_accession: GSM7165686 sample_title: RNA-Seq P12-N source_name: normal characteristics: tissue: normal; diagnosis: breast cancer; Sex: female; age: 57; tumor stage: II RNA... controlled vocabulary controlled vocabulary sample type match: tumor
sample_type tumor sample sample GSM7165687 Runtime Siftome inference GEO:sample:GSM7165687:72c9f020fe307b5f08aa30feae7f7f6579ef1f472bc740dcc8d9c76f52d1f777 low confidence tumor sample_accession: GSM7165687 sample_title: RNA-Seq P12-T source_name: tumor characteristics: tissue: tumor; diagnosis: breast cancer; Sex: female; age: 57; tumor stage: II RNA-S... controlled vocabulary controlled vocabulary sample type match: tumor
sample_type normal tissue sample GSM7165688 Runtime Siftome inference GEO:sample:GSM7165688:d6a5c3ba1931d5b5ea271e9f48b67da27fe77019634cf2194c880f6f7a9e5b3a low confidence normal sample_accession: GSM7165688 sample_title: RNA-Seq P7-N source_name: normal characteristics: tissue: normal; diagnosis: breast cancer; Sex: female; age: 52; tumor stage: II RNA-... controlled vocabulary controlled vocabulary sample type match: normal
sample_type tumor sample sample GSM7165688 Runtime Siftome inference GEO:sample:GSM7165688:d6a5c3ba1931d5b5ea271e9f48b67da27fe77019634cf2194c880f6f7a9e5b3a low confidence tumor sample_accession: GSM7165688 sample_title: RNA-Seq P7-N source_name: normal characteristics: tissue: normal; diagnosis: breast cancer; Sex: female; age: 52; tumor stage: II RNA-... controlled vocabulary controlled vocabulary sample type match: tumor
sample_type tumor sample sample GSM7165689 Runtime Siftome inference GEO:sample:GSM7165689:c7057456fd2f9e13b2dbec7227acd4be29582ca7ad72e850bec5c438e7be4358 low confidence tumor sample_accession: GSM7165689 sample_title: RNA-Seq P7-T source_name: tumor characteristics: tissue: tumor; diagnosis: breast cancer; Sex: female; age: 52; tumor stage: II RNA-Se... controlled vocabulary controlled vocabulary sample type match: tumor
sample_type normal tissue sample GSM7165690 Runtime Siftome inference GEO:sample:GSM7165690:269f57d574db2aa342f8605f2ff548bffd6ace0915d3b838a7df58793d12fa34 low confidence normal sample_accession: GSM7165690 sample_title: RNA-Seq P8-N source_name: normal characteristics: tissue: normal; diagnosis: breast cancer; Sex: female; age: 48; tumor stage: II RNA-... controlled vocabulary controlled vocabulary sample type match: normal
sample_type tumor sample sample GSM7165690 Runtime Siftome inference GEO:sample:GSM7165690:269f57d574db2aa342f8605f2ff548bffd6ace0915d3b838a7df58793d12fa34 low confidence tumor sample_accession: GSM7165690 sample_title: RNA-Seq P8-N source_name: normal characteristics: tissue: normal; diagnosis: breast cancer; Sex: female; age: 48; tumor stage: II RNA-... controlled vocabulary controlled vocabulary sample type match: tumor
sample_type tumor sample sample GSM7165691 Runtime Siftome inference GEO:sample:GSM7165691:49310ae46cfdaff17ffdfc94119f55af7dfce02eebfe3df160a6ea38d6e51c31 low confidence tumor sample_accession: GSM7165691 sample_title: RNA-Seq P8-T source_name: tumor characteristics: tissue: tumor; diagnosis: breast cancer; Sex: female; age: 48; tumor stage: II RNA-Se... controlled vocabulary controlled vocabulary sample type match: tumor
sample_type normal tissue sample GSM7165692 Runtime Siftome inference GEO:sample:GSM7165692:b788a49c51b7fcd237f1b14ac1a80bf75d55fda1c1aa1978f500f47ac433f718 low confidence normal sample_accession: GSM7165692 sample_title: RNA-Seq P9-N source_name: normal characteristics: tissue: normal; diagnosis: breast cancer; Sex: female; age: 63; tumor stage: II RNA-... controlled vocabulary controlled vocabulary sample type match: normal
sample_type tumor sample sample GSM7165692 Runtime Siftome inference GEO:sample:GSM7165692:b788a49c51b7fcd237f1b14ac1a80bf75d55fda1c1aa1978f500f47ac433f718 low confidence tumor sample_accession: GSM7165692 sample_title: RNA-Seq P9-N source_name: normal characteristics: tissue: normal; diagnosis: breast cancer; Sex: female; age: 63; tumor stage: II RNA-... controlled vocabulary controlled vocabulary sample type match: tumor
sample_type tumor sample sample GSM7165693 Runtime Siftome inference GEO:sample:GSM7165693:02002ccaf2c15c5d3d97a23b1b75b93c0e6838da7d5492b2ee379dd4418f6298 low confidence tumor sample_accession: GSM7165693 sample_title: RNA-Seq P9-T source_name: tumor characteristics: tissue: tumor; diagnosis: breast cancer; Sex: female; age: 63; tumor stage: II RNA-Se... controlled vocabulary controlled vocabulary sample type match: tumor
tissue breast sample GSM7165682 Runtime Siftome inference GEO:sample:GSM7165682:f17e1e2af6bd464bb63a6213224cfe7eb05fb7a4cbf4e043da3faa91d7762706 low confidence breast sample_accession: GSM7165682 sample_title: RNA-Seq P10-N source_name: normal characteristics: tissue: normal; diagnosis: breast cancer; Sex: female; age: 56; tumor stage: II RNA... controlled vocabulary controlled vocabulary tissue match: breast
tissue breast sample GSM7165683 Runtime Siftome inference GEO:sample:GSM7165683:3e55e39dbca1ec55fd9086a48eb809e822ac154f3797c8f798e241cfdd14c7d9 low confidence breast sample_accession: GSM7165683 sample_title: RNA-Seq P10-T source_name: tumor characteristics: tissue: tumor; diagnosis: breast cancer; Sex: female; age: 56; tumor stage: II RNA-S... controlled vocabulary controlled vocabulary tissue match: breast
tissue breast sample GSM7165684 Runtime Siftome inference GEO:sample:GSM7165684:7f79553a007d6a1cd76729a859d98fdfc3b7470191aff02c03a8f9a5e4a6fda2 low confidence breast sample_accession: GSM7165684 sample_title: RNA-Seq P11-N source_name: normal characteristics: tissue: normal; diagnosis: breast cancer; Sex: female; age: 45; tumor stage: II RNA... controlled vocabulary controlled vocabulary tissue match: breast
tissue breast sample GSM7165685 Runtime Siftome inference GEO:sample:GSM7165685:15dc39612ac62a03ca1b79297d985f476c1daf3386deb86e3c0c7e09b1ac011b low confidence breast sample_accession: GSM7165685 sample_title: RNA-Seq P11-T source_name: tumor characteristics: tissue: tumor; diagnosis: breast cancer; Sex: female; age: 45; tumor stage: II RNA-S... controlled vocabulary controlled vocabulary tissue match: breast
tissue breast sample GSM7165686 Runtime Siftome inference GEO:sample:GSM7165686:b79e99f3dcccf7a7cfa3dce9f0d1a1c28b17bc1156b9295a6c7b7c60590ff47a low confidence breast sample_accession: GSM7165686 sample_title: RNA-Seq P12-N source_name: normal characteristics: tissue: normal; diagnosis: breast cancer; Sex: female; age: 57; tumor stage: II RNA... controlled vocabulary controlled vocabulary tissue match: breast
tissue breast sample GSM7165687 Runtime Siftome inference GEO:sample:GSM7165687:72c9f020fe307b5f08aa30feae7f7f6579ef1f472bc740dcc8d9c76f52d1f777 low confidence breast sample_accession: GSM7165687 sample_title: RNA-Seq P12-T source_name: tumor characteristics: tissue: tumor; diagnosis: breast cancer; Sex: female; age: 57; tumor stage: II RNA-S... controlled vocabulary controlled vocabulary tissue match: breast
tissue breast sample GSM7165688 Runtime Siftome inference GEO:sample:GSM7165688:d6a5c3ba1931d5b5ea271e9f48b67da27fe77019634cf2194c880f6f7a9e5b3a low confidence breast sample_accession: GSM7165688 sample_title: RNA-Seq P7-N source_name: normal characteristics: tissue: normal; diagnosis: breast cancer; Sex: female; age: 52; tumor stage: II RNA-... controlled vocabulary controlled vocabulary tissue match: breast
tissue breast sample GSM7165689 Runtime Siftome inference GEO:sample:GSM7165689:c7057456fd2f9e13b2dbec7227acd4be29582ca7ad72e850bec5c438e7be4358 low confidence breast sample_accession: GSM7165689 sample_title: RNA-Seq P7-T source_name: tumor characteristics: tissue: tumor; diagnosis: breast cancer; Sex: female; age: 52; tumor stage: II RNA-Se... controlled vocabulary controlled vocabulary tissue match: breast
tissue breast sample GSM7165690 Runtime Siftome inference GEO:sample:GSM7165690:269f57d574db2aa342f8605f2ff548bffd6ace0915d3b838a7df58793d12fa34 low confidence breast sample_accession: GSM7165690 sample_title: RNA-Seq P8-N source_name: normal characteristics: tissue: normal; diagnosis: breast cancer; Sex: female; age: 48; tumor stage: II RNA-... controlled vocabulary controlled vocabulary tissue match: breast
tissue breast sample GSM7165691 Runtime Siftome inference GEO:sample:GSM7165691:49310ae46cfdaff17ffdfc94119f55af7dfce02eebfe3df160a6ea38d6e51c31 low confidence breast sample_accession: GSM7165691 sample_title: RNA-Seq P8-T source_name: tumor characteristics: tissue: tumor; diagnosis: breast cancer; Sex: female; age: 48; tumor stage: II RNA-Se... controlled vocabulary controlled vocabulary tissue match: breast
tissue breast sample GSM7165692 Runtime Siftome inference GEO:sample:GSM7165692:b788a49c51b7fcd237f1b14ac1a80bf75d55fda1c1aa1978f500f47ac433f718 low confidence breast sample_accession: GSM7165692 sample_title: RNA-Seq P9-N source_name: normal characteristics: tissue: normal; diagnosis: breast cancer; Sex: female; age: 63; tumor stage: II RNA-... controlled vocabulary controlled vocabulary tissue match: breast
tissue breast sample GSM7165693 Runtime Siftome inference GEO:sample:GSM7165693:02002ccaf2c15c5d3d97a23b1b75b93c0e6838da7d5492b2ee379dd4418f6298 low confidence breast sample_accession: GSM7165693 sample_title: RNA-Seq P9-T source_name: tumor characteristics: tissue: tumor; diagnosis: breast cancer; Sex: female; age: 63; tumor stage: II RNA-Se... controlled vocabulary controlled vocabulary tissue match: breast

Sample Group Preview

Possible case samples

Samples currently treated as the comparison case group.

6
  • GSM7165683 RNA-Seq P10-T tumor sample Case marker detected. tumor tissue: tumor; diagnosis: breast cancer; Sex: female; age: 56; tumor stage: II
  • GSM7165685 RNA-Seq P11-T tumor sample Case marker detected. tumor tissue: tumor; diagnosis: breast cancer; Sex: female; age: 45; tumor stage: II
  • GSM7165687 RNA-Seq P12-T tumor sample Case marker detected. tumor tissue: tumor; diagnosis: breast cancer; Sex: female; age: 57; tumor stage: II
  • GSM7165689 RNA-Seq P7-T tumor sample Case marker detected. tumor tissue: tumor; diagnosis: breast cancer; Sex: female; age: 52; tumor stage: II
  • GSM7165691 RNA-Seq P8-T tumor sample Case marker detected. tumor tissue: tumor; diagnosis: breast cancer; Sex: female; age: 48; tumor stage: II
  • GSM7165693 RNA-Seq P9-T tumor sample Case marker detected. tumor tissue: tumor; diagnosis: breast cancer; Sex: female; age: 63; tumor stage: II

Possible control samples

Samples currently treated as controls or baseline.

6
  • GSM7165682 RNA-Seq P10-N normal tissue Control marker detected. normal tissue: normal; diagnosis: breast cancer; Sex: female; age: 56; tumor stage: II
  • GSM7165684 RNA-Seq P11-N normal tissue Control marker detected. normal tissue: normal; diagnosis: breast cancer; Sex: female; age: 45; tumor stage: II
  • GSM7165686 RNA-Seq P12-N normal tissue Control marker detected. normal tissue: normal; diagnosis: breast cancer; Sex: female; age: 57; tumor stage: II
  • GSM7165688 RNA-Seq P7-N normal tissue Control marker detected. normal tissue: normal; diagnosis: breast cancer; Sex: female; age: 52; tumor stage: II
  • GSM7165690 RNA-Seq P8-N normal tissue Control marker detected. normal tissue: normal; diagnosis: breast cancer; Sex: female; age: 48; tumor stage: II
  • GSM7165692 RNA-Seq P9-N normal tissue Control marker detected. normal tissue: normal; diagnosis: breast cancer; Sex: female; age: 63; tumor stage: II

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
  • GSM7165682 RNA-Seq P10-N normal tissue: normal; diagnosis: breast cancer; Sex: female; age: 56; tumor stage: II
  • GSM7165684 RNA-Seq P11-N normal tissue: normal; diagnosis: breast cancer; Sex: female; age: 45; tumor stage: II
  • GSM7165686 RNA-Seq P12-N normal tissue: normal; diagnosis: breast cancer; Sex: female; age: 57; tumor stage: II
  • GSM7165688 RNA-Seq P7-N normal tissue: normal; diagnosis: breast cancer; Sex: female; age: 52; tumor stage: II
  • GSM7165690 RNA-Seq P8-N normal tissue: normal; diagnosis: breast cancer; Sex: female; age: 48; tumor stage: II
  • GSM7165692 RNA-Seq P9-N normal tissue: normal; diagnosis: breast cancer; Sex: female; age: 63; tumor stage: II

tumor sample

6 samples
  • GSM7165683 RNA-Seq P10-T tumor tissue: tumor; diagnosis: breast cancer; Sex: female; age: 56; tumor stage: II
  • GSM7165685 RNA-Seq P11-T tumor tissue: tumor; diagnosis: breast cancer; Sex: female; age: 45; tumor stage: II
  • GSM7165687 RNA-Seq P12-T tumor tissue: tumor; diagnosis: breast cancer; Sex: female; age: 57; tumor stage: II
  • GSM7165689 RNA-Seq P7-T tumor tissue: tumor; diagnosis: breast cancer; Sex: female; age: 52; tumor stage: II
  • GSM7165691 RNA-Seq P8-T tumor tissue: tumor; diagnosis: breast cancer; Sex: female; age: 48; tumor stage: II
  • GSM7165693 RNA-Seq P9-T tumor tissue: tumor; diagnosis: breast cancer; Sex: female; age: 63; tumor stage: II

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.