Siftome Phase 3L

GSE192849

CircRNA expression profiling in human breast cancer

Not suitable Dataset does not meet the current suitability threshold.
Sample grouping CSV Contrast CSV DESeq2 metadata CSV R handoff notes Handoff report Download instructions Open GEO dataset
Source
GEO
Search intent
Patient tissue tumor-vs-normal
Intent behavior
search-intent-behavior-v1
Submission date
2021-12-31
Last update
2025-05-27
Organization
The Affiliated Cancer Hospital of Nanjing Medical University
Department
Not available
Public date
2024-12-31
Experiment types
Non-coding RNA profiling by high throughput sequencing
Platforms
GPL20795 HiSeq X Ten (Homo sapiens)
Series type
Series
SubSeries
Not available
BioProject
PRJNA793447
Supplementary files
TXT: GSE192849_Normalized_gene_counts_matrix.txt.gz; TXT: GSE192849_Raw_gene_counts_matrix.txt.gz
Organism
Homo sapiens
Assay
bulk RNA-seq
Samples
6
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

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. Matched tumor/normal design boosted for colorectal tumor-vs-normal tissue triage. Patient tissue or biopsy specimens boosted for tissue comparison triage. Small RNA, miRNA, circRNA, or extracellular-vesicle RNA context downgraded for primary mRNA tissue ranking. 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 fewer than ten samples limit cohort confidence. Overall score capped because secondary RNA assays are not primary mRNA tissue RNA-seq. 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 3 samples
  • Likely control group normal tissue 3 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 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 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 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: 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 Small RNA, miRNA, circRNA, or extracellular-vesicle RNA context downgraded for primary mRNA tissue ranking. 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 fewer than ten samples limit cohort confidence. Contributed to downgrade or manual-review evidence.
  • Caution fact Overall score capped because secondary RNA assays are not primary mRNA tissue RNA-seq. 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
GSE192849
Sample records
6 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
GSE192849
  • 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
GSE192849
  • 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
GSE192849
  • 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: GSE192849
dataset_title: CircRNA expression profiling in human breast cancer
organism: Homo sapiens
assay_type: bulk RNA-seq
processed_data_available: true
raw_data_available: true
submission_date: 2021-12-31
last_update_date: 2025-05-27
organization_name: The Affiliated Cancer Hospital of Nanjing Medical University
department: Not available
public_date: 2024-12-31
experiment_types: Non-coding RNA profiling by high throughput sequencing
platforms: GPL20795 HiSeq X Ten (Homo sapiens)
sub_series: Not available
bioproject: PRJNA793447
supplementary_files: TXT: GSE192849_Normalized_gene_counts_matrix.txt.gz; TXT: GSE192849_Raw_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: 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.
  • Small RNA, miRNA, circRNA, or extracellular-vesicle RNA context downgraded for primary mRNA tissue ranking.
  • 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 fewer than ten samples limit cohort confidence.
  • Overall score capped because secondary RNA assays are not primary mRNA tissue RNA-seq.
  • 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

22 fields
Field Value Source Origin Confidence Evidence Reason
assay_type bulk RNA-seq dataset GSE192849 Runtime Siftome inference GEO:dataset:GSE192849:212527fe795c8cd988de842b5cf141a1b6e98f24c76b49b48ddda4ea5b8d79a1 high confidence bulk rna-seq dataset_accession: GSE192849 dataset_title: CircRNA expression profiling in human breast cancer organism: Homo sapiens assay_type: bulk RNA-seq processed_data_available: true ra... keyword match keyword match: bulk rna-seq
disease breast cancer dataset GSE192849 Runtime Siftome inference GEO:dataset:GSE192849:212527fe795c8cd988de842b5cf141a1b6e98f24c76b49b48ddda4ea5b8d79a1 high confidence breast cancer dataset_accession: GSE192849 dataset_title: CircRNA expression profiling in human breast cancer organism: Homo sapiens assay_type: bulk RNA-seq processed_data_available: true ra... controlled vocabulary controlled vocabulary disease match: breast cancer
disease breast cancer sample GSM5766814 Runtime Siftome inference GEO:sample:GSM5766814:d3f7acfb0b05e622850a10088f1b750c8c39b8adfbf87fddd6eee554c43ad6d3 high confidence breast cancer sample_accession: GSM5766814 sample_title: Patient1 breast cancer tissue source_name: breast characteristics: tissue: breast tumors; age: 55; Stage: III Patient1 breast cancer t... controlled vocabulary controlled vocabulary disease match: breast cancer
disease breast cancer sample GSM5766815 Runtime Siftome inference GEO:sample:GSM5766815:596b3e33f800efa15da30cfd87e2878da4425bbe93519520c2c12969b9bbf133 high confidence breast cancer sample_accession: GSM5766815 sample_title: Patient2 breast cancer tissue source_name: breast characteristics: tissue: breast tumors; age: 56; Stage: III Patient2 breast cancer t... controlled vocabulary controlled vocabulary disease match: breast cancer
disease breast cancer sample GSM5766816 Runtime Siftome inference GEO:sample:GSM5766816:8903a85b12970e2e2a5fec67eeb5f75f3520104a5a5e1a381af1cf14e8ed8ce3 high confidence breast cancer sample_accession: GSM5766816 sample_title: Patient3 breast cancer tissue source_name: breast characteristics: tissue: breast tumors; age: 58; Stage: III Patient3 breast cancer t... controlled vocabulary controlled vocabulary disease match: breast cancer
normal_tissue_type adjacent normal sample GSM5766817 Runtime Siftome inference GEO:sample:GSM5766817:e888567ea98745c3cba9902cb4415279673a49b6f476ca233108d8249f35bb49 high confidence adjacent normal sample_accession: GSM5766817 sample_title: Patient1 normal breast tissue source_name: breast characteristics: tissue: adjacent normal tissue; age: 55; Stage: III Patient1 normal... controlled vocabulary controlled vocabulary normal tissue type match: adjacent normal
normal_tissue_type adjacent normal sample GSM5766818 Runtime Siftome inference GEO:sample:GSM5766818:16c7518476fee5918f58109f6ab40252e7882a5ffe0286bb81611d41a9db906d high confidence adjacent normal sample_accession: GSM5766818 sample_title: Patient2 normal breast tissue source_name: breast characteristics: tissue: adjacent normal tissue; age: 56; Stage: III Patient2 normal... controlled vocabulary controlled vocabulary normal tissue type match: adjacent normal
normal_tissue_type adjacent normal sample GSM5766819 Runtime Siftome inference GEO:sample:GSM5766819:53386efca7a0d6c9c8942690f1e6720564b2c47e9f50c2d59343f1a62357023d high confidence adjacent normal sample_accession: GSM5766819 sample_title: Patient3 normal breast tissue source_name: breast characteristics: tissue: adjacent normal tissue; age: 58; Stage: III Patient3 normal... controlled vocabulary controlled vocabulary normal tissue type match: adjacent normal
organism Homo sapiens dataset GSE192849 Runtime Siftome inference GEO:dataset:GSE192849:212527fe795c8cd988de842b5cf141a1b6e98f24c76b49b48ddda4ea5b8d79a1 high confidence homo sapiens dataset_accession: GSE192849 dataset_title: CircRNA expression profiling in human breast cancer organism: Homo sapiens assay_type: bulk RNA-seq processed_data_available: true ra... keyword match keyword match: homo sapiens
sample_type tumor sample sample GSM5766814 Runtime Siftome inference GEO:sample:GSM5766814:d3f7acfb0b05e622850a10088f1b750c8c39b8adfbf87fddd6eee554c43ad6d3 low confidence tumor sample_accession: GSM5766814 sample_title: Patient1 breast cancer tissue source_name: breast characteristics: tissue: breast tumors; age: 55; Stage: III Patient1 breast cancer t... controlled vocabulary controlled vocabulary sample type match: tumor
sample_type tumor sample sample GSM5766815 Runtime Siftome inference GEO:sample:GSM5766815:596b3e33f800efa15da30cfd87e2878da4425bbe93519520c2c12969b9bbf133 low confidence tumor sample_accession: GSM5766815 sample_title: Patient2 breast cancer tissue source_name: breast characteristics: tissue: breast tumors; age: 56; Stage: III Patient2 breast cancer t... controlled vocabulary controlled vocabulary sample type match: tumor
sample_type tumor sample sample GSM5766816 Runtime Siftome inference GEO:sample:GSM5766816:8903a85b12970e2e2a5fec67eeb5f75f3520104a5a5e1a381af1cf14e8ed8ce3 low confidence tumor sample_accession: GSM5766816 sample_title: Patient3 breast cancer tissue source_name: breast characteristics: tissue: breast tumors; age: 58; Stage: III Patient3 breast cancer t... controlled vocabulary controlled vocabulary sample type match: tumor
sample_type normal tissue sample GSM5766817 Runtime Siftome inference GEO:sample:GSM5766817:e888567ea98745c3cba9902cb4415279673a49b6f476ca233108d8249f35bb49 high confidence adjacent normal sample_accession: GSM5766817 sample_title: Patient1 normal breast tissue source_name: breast characteristics: tissue: adjacent normal tissue; age: 55; Stage: III Patient1 normal... controlled vocabulary controlled vocabulary sample type match: adjacent normal
sample_type normal tissue sample GSM5766818 Runtime Siftome inference GEO:sample:GSM5766818:16c7518476fee5918f58109f6ab40252e7882a5ffe0286bb81611d41a9db906d high confidence adjacent normal sample_accession: GSM5766818 sample_title: Patient2 normal breast tissue source_name: breast characteristics: tissue: adjacent normal tissue; age: 56; Stage: III Patient2 normal... controlled vocabulary controlled vocabulary sample type match: adjacent normal
sample_type normal tissue sample GSM5766819 Runtime Siftome inference GEO:sample:GSM5766819:53386efca7a0d6c9c8942690f1e6720564b2c47e9f50c2d59343f1a62357023d high confidence adjacent normal sample_accession: GSM5766819 sample_title: Patient3 normal breast tissue source_name: breast characteristics: tissue: adjacent normal tissue; age: 58; Stage: III Patient3 normal... controlled vocabulary controlled vocabulary sample type match: adjacent normal
tissue breast dataset GSE192849 Runtime Siftome inference GEO:dataset:GSE192849:212527fe795c8cd988de842b5cf141a1b6e98f24c76b49b48ddda4ea5b8d79a1 low confidence breast dataset_accession: GSE192849 dataset_title: CircRNA expression profiling in human breast cancer organism: Homo sapiens assay_type: bulk RNA-seq processed_data_available: true ra... controlled vocabulary controlled vocabulary tissue match: breast
tissue breast sample GSM5766814 Runtime Siftome inference GEO:sample:GSM5766814:d3f7acfb0b05e622850a10088f1b750c8c39b8adfbf87fddd6eee554c43ad6d3 low confidence breast sample_accession: GSM5766814 sample_title: Patient1 breast cancer tissue source_name: breast characteristics: tissue: breast tumors; age: 55; Stage: III Patient1 breast cancer t... controlled vocabulary controlled vocabulary tissue match: breast
tissue breast sample GSM5766815 Runtime Siftome inference GEO:sample:GSM5766815:596b3e33f800efa15da30cfd87e2878da4425bbe93519520c2c12969b9bbf133 low confidence breast sample_accession: GSM5766815 sample_title: Patient2 breast cancer tissue source_name: breast characteristics: tissue: breast tumors; age: 56; Stage: III Patient2 breast cancer t... controlled vocabulary controlled vocabulary tissue match: breast
tissue breast sample GSM5766816 Runtime Siftome inference GEO:sample:GSM5766816:8903a85b12970e2e2a5fec67eeb5f75f3520104a5a5e1a381af1cf14e8ed8ce3 low confidence breast sample_accession: GSM5766816 sample_title: Patient3 breast cancer tissue source_name: breast characteristics: tissue: breast tumors; age: 58; Stage: III Patient3 breast cancer t... controlled vocabulary controlled vocabulary tissue match: breast
tissue breast sample GSM5766817 Runtime Siftome inference GEO:sample:GSM5766817:e888567ea98745c3cba9902cb4415279673a49b6f476ca233108d8249f35bb49 low confidence breast sample_accession: GSM5766817 sample_title: Patient1 normal breast tissue source_name: breast characteristics: tissue: adjacent normal tissue; age: 55; Stage: III Patient1 normal... controlled vocabulary controlled vocabulary tissue match: breast
tissue breast sample GSM5766818 Runtime Siftome inference GEO:sample:GSM5766818:16c7518476fee5918f58109f6ab40252e7882a5ffe0286bb81611d41a9db906d low confidence breast sample_accession: GSM5766818 sample_title: Patient2 normal breast tissue source_name: breast characteristics: tissue: adjacent normal tissue; age: 56; Stage: III Patient2 normal... controlled vocabulary controlled vocabulary tissue match: breast
tissue breast sample GSM5766819 Runtime Siftome inference GEO:sample:GSM5766819:53386efca7a0d6c9c8942690f1e6720564b2c47e9f50c2d59343f1a62357023d low confidence breast sample_accession: GSM5766819 sample_title: Patient3 normal breast tissue source_name: breast characteristics: tissue: adjacent normal tissue; age: 58; Stage: III Patient3 normal... controlled vocabulary controlled vocabulary tissue match: breast

Sample Group Preview

Possible case samples

Samples currently treated as the comparison case group.

3
  • GSM5766814 Patient1 breast cancer tissue tumor sample Case marker detected. breast tissue: breast tumors; age: 55; Stage: III
  • GSM5766815 Patient2 breast cancer tissue tumor sample Case marker detected. breast tissue: breast tumors; age: 56; Stage: III
  • GSM5766816 Patient3 breast cancer tissue tumor sample Case marker detected. breast tissue: breast tumors; age: 58; Stage: III

Possible control samples

Samples currently treated as controls or baseline.

3
  • GSM5766817 Patient1 normal breast tissue normal tissue Control marker detected. breast tissue: adjacent normal tissue; age: 55; Stage: III
  • GSM5766818 Patient2 normal breast tissue normal tissue Control marker detected. breast tissue: adjacent normal tissue; age: 56; Stage: III
  • GSM5766819 Patient3 normal breast tissue normal tissue Control marker detected. breast tissue: adjacent normal tissue; age: 58; Stage: III

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

tumor sample

3 samples
  • GSM5766814 Patient1 breast cancer tissue breast tissue: breast tumors; age: 55; Stage: III
  • GSM5766815 Patient2 breast cancer tissue breast tissue: breast tumors; age: 56; Stage: III
  • GSM5766816 Patient3 breast cancer tissue breast tissue: breast tumors; age: 58; Stage: III

normal tissue

3 samples
  • GSM5766817 Patient1 normal breast tissue breast tissue: adjacent normal tissue; age: 55; Stage: III
  • GSM5766818 Patient2 normal breast tissue breast tissue: adjacent normal tissue; age: 56; Stage: III
  • GSM5766819 Patient3 normal breast tissue breast tissue: adjacent normal tissue; age: 58; Stage: III

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.
  • Matched tumor/normal design boosted for colorectal tumor-vs-normal tissue triage.
  • Patient tissue or biopsy specimens boosted for tissue comparison triage.
  • Small RNA, miRNA, circRNA, or extracellular-vesicle RNA context downgraded for primary mRNA tissue ranking.
  • 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 fewer than ten samples limit cohort confidence.
  • Overall score capped because secondary RNA assays are not primary mRNA tissue RNA-seq.
  • Overall score capped because tumor/normal grouping is from a non-colorectal cancer context.

Sample Links

6 samples

Review Audit Trail

0 decisions

No review decisions have been stored for this dataset.