Siftome Phase 3L

GSE208089

Comprehensive profile and contrastive analysis of circular RNA in cervical squamous carcinoma and adenocarcinoma

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
2022-07-13
Last update
2023-02-10
Organization
Peking university people's hospital
Department
Not available
Public date
2022-12-31
Experiment types
Non-coding RNA profiling by high throughput sequencing
Platforms
GPL24676 Illumina NovaSeq 6000 (Homo sapiens)
Series type
Series
SubSeries
Not available
BioProject
PRJNA858253
Supplementary files
XLSX: GSE208089_Readcount_TPM.xlsx
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
85% 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

3/15 pts

Unassigned or review-needed samples remain before analysis.

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

  • 6 samples need manual grouping review.
  • Secondary RNA assay context should be analyzed separately from ordinary bulk RNA-seq.

Next Steps

  • Resolve unassigned or review-needed samples in the grouping table.

Analysis Preparation Checklist

4/6 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

Needs review

6 review-needed samples and 0 unassigned samples remain.

Resolve ambiguous and unassigned samples before finalizing the contrast.

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.
  • One or more samples were flagged for manual review.
  • 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 90% Disease or condition metadata normalized. Organism normalized. Assay type normalized.
  • comparison suitability 0% Tumor and normal sample groups detected. No excluded sample type flags detected. Matched tumor/normal design boosted for colorectal tumor-vs-normal tissue triage. Patient tissue or biopsy specimens boosted for tissue comparison triage. 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 85% Sample source clarity: All samples have source metadata and clear GSE/GSM accessions. Group clarity: Rule-based grouping found both case and control samples. Disease clarity: Disease or condition metadata normalized. Tissue clarity: Tissue metadata was not normalized. Treatment clarity: Treatment status metadata normalized where treatment is part of the comparison. 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

  • TREATED_SAMPLES_NEED_REVIEW info Treated samples may need review depending on the comparison.
  • SECONDARY_ASSAY_CONTEXT warning Secondary RNA assay context such as small RNA, miRNA, circRNA, or non-coding RNA was detected.
  • TISSUE_TYPE_MISSING warning Tissue or cell type could not be normalized.

Intent Interpretation

  • Active intent Patient tissue tumor-vs-normal Ranks human colorectal tissue or biopsy cohorts where tumor samples can be compared with normal controls.
  • Organism expectation Homo sapiens Dataset organism is interpreted as Homo sapiens.
  • Assay expectation bulk RNA-seq Dataset assay is interpreted as bulk RNA-seq.
  • Specimen assumption patient tissue or biopsy Derived specimen/source is Tissue.
  • Control-group assumption matched normal, adjacent normal, paired normal, healthy tissue control, or otherwise normal tissue control Derived study design is Tumor vs matched normal; likely groups are tumor sample vs normal tissue.
  • Score caps Applied when matching conditions are present non-human datasets stay below the primary recommendation band, missing colorectal/colon/rectal/CRC context stays below the primary recommendation band, biofluid and model-system datasets cannot reach Recommended by default, microarray and secondary assays are capped unless explicitly enabled, or small cohorts are capped below high-confidence recommendations
  • Warning rules 3 active warnings missing or unclear control group, unclear disease context, unclear tissue source, mixed sample types, model-system markers, secondary assay context, missing processed data, or small cohort size
  • Downgrade or exclusion reason Downgraded disease context: colorectal/GI relevance is unclear. Derived from current-intent ranking reasons and warnings.

Applied Review Decisions

No active review decisions affect this ranking.

Ranking Facts

  • Recommendation Not suitable Dataset does not meet the current suitability threshold.
  • Supporting fact Tumor vs matched normal · Tissue · suitability 0%. Contributed to match or upgrade evidence.
  • Supporting fact Prioritized for patient tissue tumor-vs-normal triage. Contributed to match or upgrade evidence.
  • Supporting fact Prioritized assay: bulk RNA-seq is the active assay expectation. Contributed to match or upgrade evidence.
  • Supporting fact Downgraded disease context: colorectal/GI relevance is unclear. Contributed to match or upgrade evidence.
  • Supporting fact Processed data is available for downstream review. Contributed to match or upgrade evidence.
  • Supporting fact 3 warnings require review. Contributed to match or upgrade evidence.
  • Caution fact Treated samples may need review depending on the comparison. Contributed to downgrade or manual-review 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 Tissue or cell type could not be normalized. 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: Tissue clarity: Tissue metadata was not normalized. 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: colorectal/GI relevance is unclear. Contributed to downgrade or manual-review evidence.
  • Caution fact Missing or unclear metadata: Downgraded disease context: colorectal/GI relevance is unclear. Contributed to downgrade or manual-review evidence.
  • Caution fact Comparison suitability score is below the Phase 1 recommended threshold. Contributed to downgrade or manual-review evidence.

Manual Corrections

0 active

Source Evidence

4 sources

GEO

Primary source

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

Dataset accession
GSE208089
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
GSE208089
  • 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
GSE208089
  • 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
GSE208089
  • 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: GSE208089
dataset_title: Comprehensive profile and contrastive analysis of circular RNA in cervical squamous carcinoma and adenocarcinoma
organism: Homo sapiens
assay_type: bulk RNA-seq
processed_data_available: true
raw_data_available: true
submission_date: 2022-07-13
last_update_date: 2023-02-10
organization_name: Peking university people's hospital
department: Not available
public_date: 2022-12-31
experiment_types: Non-coding RNA profiling by high throughput sequencing
platforms: GPL24676 Illumina NovaSeq 6000 (Homo sapiens)
sub_series: Not available
bioproject: PRJNA858253
supplementary_files: XLSX: GSE208089_Readcount_TPM.xlsx
series_type: Series

Why It Matched

  • Tumor vs matched normal · Tissue · suitability 0%.
  • Prioritized for patient tissue tumor-vs-normal triage.
  • Prioritized assay: bulk RNA-seq is the active assay expectation.
  • Downgraded disease context: colorectal/GI relevance is unclear.
  • Processed data is available for downstream review.
  • 3 warnings require review.

Why It May Not Be Suitable

  • Treated samples may need review depending on the comparison.
  • Secondary RNA assay context such as small RNA, miRNA, circRNA, or non-coding RNA was detected.
  • Tissue or cell type could not be normalized.
  • 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: Tissue clarity: Tissue metadata was not normalized.
  • 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: colorectal/GI relevance is unclear.
  • Missing or unclear metadata: Downgraded disease context: colorectal/GI relevance is unclear.
  • Comparison suitability score is below the Phase 1 recommended threshold.

Warnings

  • info TREATED_SAMPLES_NEED_REVIEW Treated samples may need review depending on the comparison.
  • warning SECONDARY_ASSAY_CONTEXT Secondary RNA assay context such as small RNA, miRNA, circRNA, or non-coding RNA was detected.
  • warning TISSUE_TYPE_MISSING Tissue or cell type could not be normalized.

Normalized Fields

21 fields
Field Value Source Origin Confidence Evidence Reason
assay_type bulk RNA-seq dataset GSE208089 Runtime Siftome inference GEO:dataset:GSE208089:d77375899349d1b7be67ca7cdb3a15cc8605bad2df3829e23582ad1e8e2b4b3c high confidence bulk rna-seq dataset_accession: GSE208089 dataset_title: Comprehensive profile and contrastive analysis of circular RNA in cervical squamous carcinoma and adenocarcinoma organism: Homo sapie... keyword match keyword match: bulk rna-seq
disease colorectal cancer dataset GSE208089 Runtime Siftome inference GEO:dataset:GSE208089:d77375899349d1b7be67ca7cdb3a15cc8605bad2df3829e23582ad1e8e2b4b3c medium confidence read dataset_accession: GSE208089 dataset_title: Comprehensive profile and contrastive analysis of circular RNA in cervical squamous carcinoma and adenocarcinoma organism: Homo sapie... controlled vocabulary controlled vocabulary disease match: read
normal_tissue_type adjacent normal sample GSM6336945 Runtime Siftome inference GEO:sample:GSM6336945:2fc32cf60601530452ba8d4a6f5ba758707942a793cb8b9035c46046deb6f5ac high confidence adjacent normal sample_accession: GSM6336945 sample_title: Adjacent normal tissue of cervical squamous carcinoma [S_2] source_name: Adjacent normal tissue of cervical squamous carcinoma charact... controlled vocabulary controlled vocabulary normal tissue type match: adjacent normal
normal_tissue_type adjacent normal sample GSM6336947 Runtime Siftome inference GEO:sample:GSM6336947:2a61e1fd9228a95ef9cc465718428a84933e2efd7f436896b74f83e870ba7a51 high confidence adjacent normal sample_accession: GSM6336947 sample_title: Adjacent normal tissue of cervical adenocarcinoma [A_2] source_name: Adjacent normal tissue of cervical adenocarcinoma characteristics... controlled vocabulary controlled vocabulary normal tissue type match: adjacent normal
normal_tissue_type adjacent normal sample GSM6336949 Runtime Siftome inference GEO:sample:GSM6336949:115156e22a29200312fa7fd11859567ea7580ac5e65533d9fc501ab7cf5ad4fd high confidence adjacent normal sample_accession: GSM6336949 sample_title: Adjacent normal tissue of cervical adenosquamous carcinoma [AS_2] source_name: Adjacent normal tissue of cervical adenosquamous carcin... controlled vocabulary controlled vocabulary normal tissue type match: adjacent normal
organism Homo sapiens dataset GSE208089 Runtime Siftome inference GEO:dataset:GSE208089:d77375899349d1b7be67ca7cdb3a15cc8605bad2df3829e23582ad1e8e2b4b3c high confidence homo sapiens dataset_accession: GSE208089 dataset_title: Comprehensive profile and contrastive analysis of circular RNA in cervical squamous carcinoma and adenocarcinoma organism: Homo sapie... keyword match keyword match: homo sapiens
sample_type tumor sample sample GSM6336944 Runtime Siftome inference GEO:sample:GSM6336944:20da128f13fee196196b2068817d59457f484ad003ddb01102689ae9e7444dba low confidence tumor sample_accession: GSM6336944 sample_title: Cervical squamous carcinoma tissue [S_1] source_name: Cervical squamous carcinoma tissue characteristics: tumor stage: IB1; hpv types_... controlled vocabulary controlled vocabulary sample type match: tumor
sample_type normal tissue sample GSM6336945 Runtime Siftome inference GEO:sample:GSM6336945:2fc32cf60601530452ba8d4a6f5ba758707942a793cb8b9035c46046deb6f5ac high confidence adjacent normal sample_accession: GSM6336945 sample_title: Adjacent normal tissue of cervical squamous carcinoma [S_2] source_name: Adjacent normal tissue of cervical squamous carcinoma charact... controlled vocabulary controlled vocabulary sample type match: adjacent normal
sample_type tumor sample sample GSM6336945 Runtime Siftome inference GEO:sample:GSM6336945:2fc32cf60601530452ba8d4a6f5ba758707942a793cb8b9035c46046deb6f5ac low confidence tumor sample_accession: GSM6336945 sample_title: Adjacent normal tissue of cervical squamous carcinoma [S_2] source_name: Adjacent normal tissue of cervical squamous carcinoma charact... controlled vocabulary controlled vocabulary sample type match: tumor
sample_type tumor sample sample GSM6336946 Runtime Siftome inference GEO:sample:GSM6336946:ed52c68a595417d4b12072468cc04db87026ae0b1dcb8b30bc51a1e14af35228 low confidence tumor sample_accession: GSM6336946 sample_title: Cervical adenocarcinoma tissue [A_1] source_name: Cervical adenocarcinoma tissue characteristics: tumor stage: IB1; hpv types_infected... controlled vocabulary controlled vocabulary sample type match: tumor
sample_type normal tissue sample GSM6336947 Runtime Siftome inference GEO:sample:GSM6336947:2a61e1fd9228a95ef9cc465718428a84933e2efd7f436896b74f83e870ba7a51 high confidence adjacent normal sample_accession: GSM6336947 sample_title: Adjacent normal tissue of cervical adenocarcinoma [A_2] source_name: Adjacent normal tissue of cervical adenocarcinoma characteristics... controlled vocabulary controlled vocabulary sample type match: adjacent normal
sample_type tumor sample sample GSM6336947 Runtime Siftome inference GEO:sample:GSM6336947:2a61e1fd9228a95ef9cc465718428a84933e2efd7f436896b74f83e870ba7a51 low confidence tumor sample_accession: GSM6336947 sample_title: Adjacent normal tissue of cervical adenocarcinoma [A_2] source_name: Adjacent normal tissue of cervical adenocarcinoma characteristics... controlled vocabulary controlled vocabulary sample type match: tumor
sample_type tumor sample sample GSM6336948 Runtime Siftome inference GEO:sample:GSM6336948:7f586030dfea135ce64646237008fa8c44e3d0040dd97ec4b280ce168d00c210 low confidence tumor sample_accession: GSM6336948 sample_title: Cervical adenosquamous carcinoma tissue [AS_1] source_name: Cervical adenosquamous carcinoma tissue characteristics: tumor stage: IB1;... controlled vocabulary controlled vocabulary sample type match: tumor
sample_type normal tissue sample GSM6336949 Runtime Siftome inference GEO:sample:GSM6336949:115156e22a29200312fa7fd11859567ea7580ac5e65533d9fc501ab7cf5ad4fd high confidence adjacent normal sample_accession: GSM6336949 sample_title: Adjacent normal tissue of cervical adenosquamous carcinoma [AS_2] source_name: Adjacent normal tissue of cervical adenosquamous carcin... controlled vocabulary controlled vocabulary sample type match: adjacent normal
sample_type tumor sample sample GSM6336949 Runtime Siftome inference GEO:sample:GSM6336949:115156e22a29200312fa7fd11859567ea7580ac5e65533d9fc501ab7cf5ad4fd low confidence tumor sample_accession: GSM6336949 sample_title: Adjacent normal tissue of cervical adenosquamous carcinoma [AS_2] source_name: Adjacent normal tissue of cervical adenosquamous carcin... controlled vocabulary controlled vocabulary sample type match: tumor
treatment_status treated sample GSM6336944 Runtime Siftome inference GEO:sample:GSM6336944:20da128f13fee196196b2068817d59457f484ad003ddb01102689ae9e7444dba medium confidence infected sample_accession: GSM6336944 sample_title: Cervical squamous carcinoma tissue [S_1] source_name: Cervical squamous carcinoma tissue characteristics: tumor stage: IB1; hpv types_... controlled vocabulary controlled vocabulary treatment status match: infected
treatment_status treated sample GSM6336945 Runtime Siftome inference GEO:sample:GSM6336945:2fc32cf60601530452ba8d4a6f5ba758707942a793cb8b9035c46046deb6f5ac medium confidence infected sample_accession: GSM6336945 sample_title: Adjacent normal tissue of cervical squamous carcinoma [S_2] source_name: Adjacent normal tissue of cervical squamous carcinoma charact... controlled vocabulary controlled vocabulary treatment status match: infected
treatment_status treated sample GSM6336946 Runtime Siftome inference GEO:sample:GSM6336946:ed52c68a595417d4b12072468cc04db87026ae0b1dcb8b30bc51a1e14af35228 medium confidence infected sample_accession: GSM6336946 sample_title: Cervical adenocarcinoma tissue [A_1] source_name: Cervical adenocarcinoma tissue characteristics: tumor stage: IB1; hpv types_infected... controlled vocabulary controlled vocabulary treatment status match: infected
treatment_status treated sample GSM6336947 Runtime Siftome inference GEO:sample:GSM6336947:2a61e1fd9228a95ef9cc465718428a84933e2efd7f436896b74f83e870ba7a51 medium confidence infected sample_accession: GSM6336947 sample_title: Adjacent normal tissue of cervical adenocarcinoma [A_2] source_name: Adjacent normal tissue of cervical adenocarcinoma characteristics... controlled vocabulary controlled vocabulary treatment status match: infected
treatment_status treated sample GSM6336948 Runtime Siftome inference GEO:sample:GSM6336948:7f586030dfea135ce64646237008fa8c44e3d0040dd97ec4b280ce168d00c210 medium confidence infected sample_accession: GSM6336948 sample_title: Cervical adenosquamous carcinoma tissue [AS_1] source_name: Cervical adenosquamous carcinoma tissue characteristics: tumor stage: IB1;... controlled vocabulary controlled vocabulary treatment status match: infected
treatment_status treated sample GSM6336949 Runtime Siftome inference GEO:sample:GSM6336949:115156e22a29200312fa7fd11859567ea7580ac5e65533d9fc501ab7cf5ad4fd medium confidence infected sample_accession: GSM6336949 sample_title: Adjacent normal tissue of cervical adenosquamous carcinoma [AS_2] source_name: Adjacent normal tissue of cervical adenosquamous carcin... controlled vocabulary controlled vocabulary treatment status match: infected

Sample Group Preview

Possible case samples

Samples currently treated as the comparison case group.

3
  • GSM6336944 Cervical squamous carcinoma tissue [S_1] tumor sample treated sample: Treated sample may need exclusion outside treatment comparisons. Cervical squamous carcinoma tissue tumor stage: IB1; hpv types_infected: HPV-16; disease: cervical cancer; Sex: female; age: 60y; tissue: Cervical squamous carcinoma tissue
  • GSM6336946 Cervical adenocarcinoma tissue [A_1] tumor sample treated sample: Treated sample may need exclusion outside treatment comparisons. Cervical adenocarcinoma tissue tumor stage: IB1; hpv types_infected: HPV-16; disease: cervical cancer; Sex: female; age: 38y; tissue: Cervical adenocarcinoma tissue
  • GSM6336948 Cervical adenosquamous carcinoma tissue [AS_1] tumor sample treated sample: Treated sample may need exclusion outside treatment comparisons. Cervical adenosquamous carcinoma tissue tumor stage: IB1; hpv types_infected: HPV-16; disease: cervical cancer; Sex: female; age: 57y; tissue: Cervical adenosquamous carcinoma tissue

Possible control samples

Samples currently treated as controls or baseline.

3
  • GSM6336945 Adjacent normal tissue of cervical squamous carcinoma [S_2] normal tissue treated sample: Treated sample may need exclusion outside treatment comparisons. Adjacent normal tissue of cervical squamous carcinoma tumor stage: IB1; hpv types_infected: HPV-16; disease: cervical cancer; Sex: female; age: 60y; tissue: Adjacent normal tissue of cervical squamous carcinoma
  • GSM6336947 Adjacent normal tissue of cervical adenocarcinoma [A_2] normal tissue treated sample: Treated sample may need exclusion outside treatment comparisons. Adjacent normal tissue of cervical adenocarcinoma tumor stage: IB1; hpv types_infected: HPV-16; disease: cervical cancer; Sex: female; age: 38y; tissue: Adjacent normal tissue of cervical adenocarcinoma
  • GSM6336949 Adjacent normal tissue of cervical adenosquamous carcinoma [AS_2] normal tissue treated sample: Treated sample may need exclusion outside treatment comparisons. Adjacent normal tissue of cervical adenosquamous carcinoma tumor stage: IB1; hpv types_infected: HPV-16; disease: cervical cancer; Sex: female; age: 57y; tissue: Adjacent normal tissue of cervical adenosquamous carcinoma

Unassigned samples

Samples with no explicit case or control marker.

0

No samples

Excluded samples

Samples excluded from grouping by hard exclusion rules.

0

No samples

Ambiguous samples

Samples that need manual review before trusting grouping.

0

No samples

Metadata Quality Components

Persisted metadata quality

85 pts
Clarity
85%
Weight
100 pts

Sample source clarity: All samples have source metadata and clear GSE/GSM accessions. Group clarity: Rule-based grouping found both case and control samples. Disease clarity: Disease or condition metadata normalized. Tissue clarity: Tissue metadata was not normalized. Treatment clarity: Treatment status metadata normalized where treatment is part of the comparison. 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
  • GSM6336944 Cervical squamous carcinoma tissue [S_1] Cervical squamous carcinoma tissue tumor stage: IB1; hpv types_infected: HPV-16; disease: cervical cancer; Sex: female; age: 60y; tissue: Cervical squamous carcinoma tissue
  • GSM6336946 Cervical adenocarcinoma tissue [A_1] Cervical adenocarcinoma tissue tumor stage: IB1; hpv types_infected: HPV-16; disease: cervical cancer; Sex: female; age: 38y; tissue: Cervical adenocarcinoma tissue
  • GSM6336948 Cervical adenosquamous carcinoma tissue [AS_1] Cervical adenosquamous carcinoma tissue tumor stage: IB1; hpv types_infected: HPV-16; disease: cervical cancer; Sex: female; age: 57y; tissue: Cervical adenosquamous carcinoma tissue

normal tissue

3 samples
  • GSM6336945 Adjacent normal tissue of cervical squamous carcinoma [S_2] Adjacent normal tissue of cervical squamous carcinoma tumor stage: IB1; hpv types_infected: HPV-16; disease: cervical cancer; Sex: female; age: 60y; tissue: Adjacent normal tissue of cervical squamous carcinoma
  • GSM6336947 Adjacent normal tissue of cervical adenocarcinoma [A_2] Adjacent normal tissue of cervical adenocarcinoma tumor stage: IB1; hpv types_infected: HPV-16; disease: cervical cancer; Sex: female; age: 38y; tissue: Adjacent normal tissue of cervical adenocarcinoma
  • GSM6336949 Adjacent normal tissue of cervical adenosquamous carcinoma [AS_2] Adjacent normal tissue of cervical adenosquamous carcinoma tumor stage: IB1; hpv types_infected: HPV-16; disease: cervical cancer; Sex: female; age: 57y; tissue: Adjacent normal tissue of cervical adenosquamous carcinoma

Score Breakdown

90%

relevance

  • Disease or condition metadata normalized.
  • Organism normalized.
  • Assay type normalized.
0%

comparison suitability

  • Tumor and normal sample groups detected.
  • No excluded sample type flags detected.
  • Matched tumor/normal design boosted for colorectal tumor-vs-normal tissue triage.
  • Patient tissue or biopsy specimens boosted for tissue comparison triage.
  • 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.
85%

metadata quality

  • Sample source clarity: All samples have source metadata and clear GSE/GSM accessions.
  • Group clarity: Rule-based grouping found both case and control samples.
  • Disease clarity: Disease or condition metadata normalized.
  • Tissue clarity: Tissue metadata was not normalized.
  • Treatment clarity: Treatment status metadata normalized where treatment is part of the comparison.
  • 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.