Siftome Phase 3L

GSE201365

Transcriptome analysis revealed potential neuro-immune interaction in papillary thyroid carcinoma tissues

Exploratory only Dataset can inform exploration but is not strong enough for primary analysis.
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
2022-04-23
Last update
2023-02-03
Organization
Department of Pain Medicine and Shenzhen Municipal Key Laboratory for Pain Medicine
Department
Shenzhen Nanshan People's Hospital and the 6th Affiliated Hospital of Shenzhen University Health Science Center
Public date
2022-05-08
Experiment types
Expression profiling by high throughput sequencing
Platforms
GPL23227 BGISEQ-500 (Homo sapiens)
Series type
Series
SubSeries
Not available
BioProject
PRJNA831114
Supplementary files
XLSX: GSE201365_Processed_data.xlsx; TAR: GSE201365_RAW.tar
Organism
Homo sapiens
Assay
bulk RNA-seq
Samples
12
Study design
Tumor vs matched normal
Specimen/source
Tissue
Scoring version
intent-aware-scoring-v15
Ranking batch
b69568dd1e4fe1b9ee2d880bf5495d748a7e4c5c11e4107f02528c3be0e76012
Ranking created
2026-06-05T20:20:27.088676Z
Warning version
intent-aware-warnings-v2

Current Intent Interpretation

Patient tissue tumor-vs-normal

Expectations

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

Rules

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

Study Classification

Tumor vs matched normal Tissue

Analysis Readiness

Ready after review
94% DE readiness

Contrast completeness

25/25 pts

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

Minimum group size

20/20 pts

Each contrast group has at least 2 samples.

Processed data availability

20/20 pts

Processed data is marked available in the GEO index.

Sample decision clarity

15/15 pts

All samples are assigned to a case or control group.

Blocking warnings

7/10 pts

Warnings are present, but none are critical blockers.

Metadata normalization

7/10 pts

Metadata quality is usable, but still deserves review.

Blockers

No readiness blockers detected.

Next Steps

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

Analysis Preparation Checklist

5/6 ready

Group labels reviewed

Needs review

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

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

Minimum sample count met

Ready

Both groups meet the minimum of 2 samples.

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

Processed counts available

Ready

Processed data availability is marked true in the GEO index.

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

Ambiguous samples handled

Ready

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

Still scan the grouping table for biology-specific ambiguity.

Exclusion decisions recorded

Ready

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

Record any manual exclusions in the downstream analysis notes.

Source links preserved

Ready

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

Keep GEO dataset and sample links with exported metadata.

Bioinformatician Review

Standard analyst review

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

No expert-review triggers were detected by Siftome.

Why This Is Ranked Here

Patient tissue tumor-vs-normal
Exploratory only Dataset can inform exploration but is not strong enough for primary analysis.

Score Components

  • relevance 50% Organism normalized. Assay type normalized.
  • comparison suitability 10% 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. Missing colorectal disease context downgraded for tumor-vs-normal tissue ranking.
  • metadata quality 70% Sample source clarity: All samples have source metadata and clear GSE/GSM accessions. Group clarity: Rule-based grouping found both case and control samples. Disease clarity: Disease or condition metadata was not normalized. Tissue clarity: Tissue metadata was not normalized. Treatment clarity: No unclear treatment split detected in the sample metadata. Replicate clarity: No pooled sample or technical replicate flags detected. Data availability clarity: Dataset-level processed or raw data availability is explicit.
  • data availability 100% Processed data available. Raw data available.
  • overall 45% 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 colorectal/CRC disease context is not explicit.

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 6 samples
  • Likely control group normal tissue 6 samples

Warnings

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

Intent Interpretation

  • Active intent Patient tissue tumor-vs-normal Ranks human colorectal tissue or biopsy cohorts where tumor samples can be compared with normal controls.
  • Organism expectation Homo sapiens Dataset organism is interpreted as Homo sapiens.
  • Assay expectation bulk RNA-seq Dataset assay is interpreted as bulk RNA-seq.
  • Specimen assumption patient tissue or biopsy Derived specimen/source is Tissue.
  • Control-group assumption matched normal, adjacent normal, paired normal, healthy tissue control, or otherwise normal tissue control Derived study design is Tumor vs matched normal; likely groups are tumor sample vs normal tissue.
  • Score caps Applied when matching conditions are present non-human datasets stay below the primary recommendation band, missing colorectal/colon/rectal/CRC context stays below the primary recommendation band, biofluid and model-system datasets cannot reach Recommended by default, microarray and secondary assays are capped unless explicitly enabled, or small cohorts are capped below high-confidence recommendations
  • Warning rules 2 active warnings missing or unclear control group, unclear disease context, unclear tissue source, mixed sample types, model-system markers, secondary assay context, missing processed data, or small cohort size
  • Downgrade or exclusion reason Downgraded disease context: colorectal/GI relevance is unclear. Derived from current-intent ranking reasons and warnings.

Applied Review Decisions

No active review decisions affect this ranking.

Ranking Facts

  • Recommendation Exploratory only Dataset can inform exploration but is not strong enough for primary analysis.
  • Supporting fact Tumor vs matched normal · Tissue · suitability 10%. Contributed to match or upgrade evidence.
  • Supporting fact Prioritized for patient tissue tumor-vs-normal triage. Contributed to match or upgrade evidence.
  • Supporting fact Prioritized assay: bulk RNA-seq is the active assay expectation. Contributed to match or upgrade evidence.
  • Supporting fact Downgraded disease context: colorectal/GI relevance is unclear. Contributed to match or upgrade evidence.
  • Supporting fact Processed data is available for downstream review. Contributed to match or upgrade evidence.
  • Supporting fact 2 warnings require review. Contributed to match or upgrade evidence.
  • Caution fact Disease or condition label could not be normalized. Contributed to downgrade or manual-review evidence.
  • Caution fact Tissue or cell type could not be normalized. Contributed to downgrade or manual-review evidence.
  • Caution fact Missing colorectal disease context downgraded for tumor-vs-normal tissue ranking. Contributed to downgrade or manual-review evidence.
  • Caution fact Missing or unclear metadata: Missing colorectal disease context downgraded for tumor-vs-normal tissue ranking. Contributed to downgrade or manual-review evidence.
  • Caution fact Missing or unclear metadata: Disease clarity: Disease or condition metadata was not normalized. Contributed to downgrade or manual-review evidence.
  • Caution fact Missing or unclear metadata: Tissue clarity: Tissue metadata was not normalized. Contributed to downgrade or manual-review evidence.
  • Caution fact Missing or unclear metadata: Treatment clarity: No unclear treatment split detected in the sample metadata. Contributed to downgrade or manual-review evidence.
  • Caution fact Overall score capped because comparison suitability is weak for the selected search intent. Contributed to downgrade or manual-review evidence.
  • Caution fact Overall score capped because colorectal/CRC disease context is not explicit. 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
GSE201365
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
GSE201365
  • 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
GSE201365
  • 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
GSE201365
  • 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: GSE201365
dataset_title: Transcriptome analysis revealed potential neuro-immune interaction in papillary thyroid carcinoma tissues
organism: Homo sapiens
assay_type: bulk RNA-seq
processed_data_available: true
raw_data_available: true
submission_date: 2022-04-23
last_update_date: 2023-02-03
organization_name: Department of Pain Medicine and Shenzhen Municipal Key Laboratory for Pain Medicine
department: Shenzhen Nanshan People's Hospital and the 6th Affiliated Hospital of Shenzhen University Health Science Center
public_date: 2022-05-08
experiment_types: Expression profiling by high throughput sequencing
platforms: GPL23227 BGISEQ-500 (Homo sapiens)
sub_series: Not available
bioproject: PRJNA831114
supplementary_files: XLSX: GSE201365_Processed_data.xlsx; TAR: GSE201365_RAW.tar
series_type: Series

Why It Matched

  • Tumor vs matched normal · Tissue · suitability 10%.
  • Prioritized for patient tissue tumor-vs-normal triage.
  • Prioritized assay: bulk RNA-seq is the active assay expectation.
  • Downgraded disease context: colorectal/GI relevance is unclear.
  • Processed data is available for downstream review.
  • 2 warnings require review.

Why It May Not Be Suitable

  • Disease or condition label could not be normalized.
  • Tissue or cell type could not be normalized.
  • Missing colorectal disease context downgraded for tumor-vs-normal tissue ranking.
  • Missing or unclear metadata: Missing colorectal disease context downgraded for tumor-vs-normal tissue ranking.
  • Missing or unclear metadata: Disease clarity: Disease or condition metadata was not normalized.
  • Missing or unclear metadata: Tissue clarity: Tissue metadata was not normalized.
  • Missing or unclear metadata: Treatment clarity: No unclear treatment split detected in the sample metadata.
  • Overall score capped because comparison suitability is weak for the selected search intent.
  • Overall score capped because colorectal/CRC disease context is not explicit.
  • Downgraded disease context: colorectal/GI relevance is unclear.
  • Missing or unclear metadata: Downgraded disease context: colorectal/GI relevance is unclear.
  • Comparison suitability score is below the Phase 1 recommended threshold.

Warnings

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

Normalized Fields

20 fields
Field Value Source Origin Confidence Evidence Reason
assay_type bulk RNA-seq dataset GSE201365 Runtime Siftome inference GEO:dataset:GSE201365:af3740d7648b38f40af07161a82fa9a7c50a991419069a68aac6cad681966a64 high confidence bulk rna-seq dataset_accession: GSE201365 dataset_title: Transcriptome analysis revealed potential neuro-immune interaction in papillary thyroid carcinoma tissues organism: Homo sapiens assa... keyword match keyword match: bulk rna-seq
normal_tissue_type adjacent normal sample GSM6062096 Runtime Siftome inference GEO:sample:GSM6062096:41ab42d91d76f5bb6ded9204044c104dfcf6c21fb13b4ae54643d818995f99bf high confidence paired normal sample_accession: GSM6062096 sample_title: normal_1 source_name: paired normal tissue characteristics: tissue: paired normal tissue normal_1 controlled vocabulary controlled vocabulary normal tissue type match: paired normal
normal_tissue_type adjacent normal sample GSM6062097 Runtime Siftome inference GEO:sample:GSM6062097:4e434aad299292d4f1359f8670fd6bd22617f6773ef38f0c51f8492c0f054c98 high confidence paired normal sample_accession: GSM6062097 sample_title: normal_2 source_name: paired normal tissue characteristics: tissue: paired normal tissue normal_2 controlled vocabulary controlled vocabulary normal tissue type match: paired normal
normal_tissue_type adjacent normal sample GSM6062098 Runtime Siftome inference GEO:sample:GSM6062098:b3261570f8ea7f8f471cc62991e055a55f4b09057e46bc57457c3efd0ceb1f96 high confidence paired normal sample_accession: GSM6062098 sample_title: normal_3 source_name: paired normal tissue characteristics: tissue: paired normal tissue normal_3 controlled vocabulary controlled vocabulary normal tissue type match: paired normal
normal_tissue_type adjacent normal sample GSM6062099 Runtime Siftome inference GEO:sample:GSM6062099:ce07a95573242097642462783e09e9113a57d818c45b35fffd4594a3d5451235 high confidence paired normal sample_accession: GSM6062099 sample_title: normal_4 source_name: paired normal tissue characteristics: tissue: paired normal tissue normal_4 controlled vocabulary controlled vocabulary normal tissue type match: paired normal
normal_tissue_type adjacent normal sample GSM6062100 Runtime Siftome inference GEO:sample:GSM6062100:56f08e2d699c26c394c9dd3bfe2fccf932cbca011a487e7c3d270a87af1ae25f high confidence paired normal sample_accession: GSM6062100 sample_title: normal_5 source_name: paired normal tissue characteristics: tissue: paired normal tissue normal_5 controlled vocabulary controlled vocabulary normal tissue type match: paired normal
normal_tissue_type adjacent normal sample GSM6062101 Runtime Siftome inference GEO:sample:GSM6062101:f0f186a8a85f64b807f4077e7aa61065cb385a29f7fe3a79f853b63006130bc6 high confidence paired normal sample_accession: GSM6062101 sample_title: normal_6 source_name: paired normal tissue characteristics: tissue: paired normal tissue normal_6 controlled vocabulary controlled vocabulary normal tissue type match: paired normal
organism Homo sapiens dataset GSE201365 Runtime Siftome inference GEO:dataset:GSE201365:af3740d7648b38f40af07161a82fa9a7c50a991419069a68aac6cad681966a64 high confidence homo sapiens dataset_accession: GSE201365 dataset_title: Transcriptome analysis revealed potential neuro-immune interaction in papillary thyroid carcinoma tissues organism: Homo sapiens assa... keyword match keyword match: homo sapiens
sample_type normal tissue sample GSM6062096 Runtime Siftome inference GEO:sample:GSM6062096:41ab42d91d76f5bb6ded9204044c104dfcf6c21fb13b4ae54643d818995f99bf low confidence normal sample_accession: GSM6062096 sample_title: normal_1 source_name: paired normal tissue characteristics: tissue: paired normal tissue normal_1 controlled vocabulary controlled vocabulary sample type match: normal
sample_type normal tissue sample GSM6062097 Runtime Siftome inference GEO:sample:GSM6062097:4e434aad299292d4f1359f8670fd6bd22617f6773ef38f0c51f8492c0f054c98 low confidence normal sample_accession: GSM6062097 sample_title: normal_2 source_name: paired normal tissue characteristics: tissue: paired normal tissue normal_2 controlled vocabulary controlled vocabulary sample type match: normal
sample_type normal tissue sample GSM6062098 Runtime Siftome inference GEO:sample:GSM6062098:b3261570f8ea7f8f471cc62991e055a55f4b09057e46bc57457c3efd0ceb1f96 low confidence normal sample_accession: GSM6062098 sample_title: normal_3 source_name: paired normal tissue characteristics: tissue: paired normal tissue normal_3 controlled vocabulary controlled vocabulary sample type match: normal
sample_type normal tissue sample GSM6062099 Runtime Siftome inference GEO:sample:GSM6062099:ce07a95573242097642462783e09e9113a57d818c45b35fffd4594a3d5451235 low confidence normal sample_accession: GSM6062099 sample_title: normal_4 source_name: paired normal tissue characteristics: tissue: paired normal tissue normal_4 controlled vocabulary controlled vocabulary sample type match: normal
sample_type normal tissue sample GSM6062100 Runtime Siftome inference GEO:sample:GSM6062100:56f08e2d699c26c394c9dd3bfe2fccf932cbca011a487e7c3d270a87af1ae25f low confidence normal sample_accession: GSM6062100 sample_title: normal_5 source_name: paired normal tissue characteristics: tissue: paired normal tissue normal_5 controlled vocabulary controlled vocabulary sample type match: normal
sample_type normal tissue sample GSM6062101 Runtime Siftome inference GEO:sample:GSM6062101:f0f186a8a85f64b807f4077e7aa61065cb385a29f7fe3a79f853b63006130bc6 low confidence normal sample_accession: GSM6062101 sample_title: normal_6 source_name: paired normal tissue characteristics: tissue: paired normal tissue normal_6 controlled vocabulary controlled vocabulary sample type match: normal
sample_type tumor sample sample GSM6062102 Runtime Siftome inference GEO:sample:GSM6062102:aab56736cfcf61ac7f7532f21a2be1c03501ea7192e72a8baed0e875a6533651 medium confidence carcinoma sample_accession: GSM6062102 sample_title: PTC_1 source_name: Papillary thyroid carcinoma characteristics: tissue: Papillary thyroid carcinoma PTC_1 controlled vocabulary controlled vocabulary sample type match: carcinoma
sample_type tumor sample sample GSM6062103 Runtime Siftome inference GEO:sample:GSM6062103:283aafb8b79e71623f125588b875376833d819c465b179f33b19b669662271ab medium confidence carcinoma sample_accession: GSM6062103 sample_title: PTC_2 source_name: Papillary thyroid carcinoma characteristics: tissue: Papillary thyroid carcinoma PTC_2 controlled vocabulary controlled vocabulary sample type match: carcinoma
sample_type tumor sample sample GSM6062104 Runtime Siftome inference GEO:sample:GSM6062104:e4fb031bcb99e42899cd246a6f8dc4b4575702065b29ee4636cb73ea246a3ccb medium confidence carcinoma sample_accession: GSM6062104 sample_title: PTC_3 source_name: Papillary thyroid carcinoma characteristics: tissue: Papillary thyroid carcinoma PTC_3 controlled vocabulary controlled vocabulary sample type match: carcinoma
sample_type tumor sample sample GSM6062105 Runtime Siftome inference GEO:sample:GSM6062105:9c123905e13cbc683490dcf7ad49e2ad587773674ea3dd629eb6825d343fe9aa medium confidence carcinoma sample_accession: GSM6062105 sample_title: PTC_4 source_name: Papillary thyroid carcinoma characteristics: tissue: Papillary thyroid carcinoma PTC_4 controlled vocabulary controlled vocabulary sample type match: carcinoma
sample_type tumor sample sample GSM6062106 Runtime Siftome inference GEO:sample:GSM6062106:1242267ecae95868418d628b52af32bfeb6a7f3ab9d4dff6c87cc6bc5feaca23 medium confidence carcinoma sample_accession: GSM6062106 sample_title: PTC_5 source_name: Papillary thyroid carcinoma characteristics: tissue: Papillary thyroid carcinoma PTC_5 controlled vocabulary controlled vocabulary sample type match: carcinoma
sample_type tumor sample sample GSM6062107 Runtime Siftome inference GEO:sample:GSM6062107:6d41fc525bb13ee825da2b76da2ec09c3dbfd76cdaa8e20a1e620b1e6c925c4c medium confidence carcinoma sample_accession: GSM6062107 sample_title: PTC_6 source_name: Papillary thyroid carcinoma characteristics: tissue: Papillary thyroid carcinoma PTC_6 controlled vocabulary controlled vocabulary sample type match: carcinoma

Sample Group Preview

Possible case samples

Samples currently treated as the comparison case group.

6
  • GSM6062102 PTC_1 tumor sample Case marker detected. Papillary thyroid carcinoma tissue: Papillary thyroid carcinoma
  • GSM6062103 PTC_2 tumor sample Case marker detected. Papillary thyroid carcinoma tissue: Papillary thyroid carcinoma
  • GSM6062104 PTC_3 tumor sample Case marker detected. Papillary thyroid carcinoma tissue: Papillary thyroid carcinoma
  • GSM6062105 PTC_4 tumor sample Case marker detected. Papillary thyroid carcinoma tissue: Papillary thyroid carcinoma
  • GSM6062106 PTC_5 tumor sample Case marker detected. Papillary thyroid carcinoma tissue: Papillary thyroid carcinoma
  • GSM6062107 PTC_6 tumor sample Case marker detected. Papillary thyroid carcinoma tissue: Papillary thyroid carcinoma

Possible control samples

Samples currently treated as controls or baseline.

6
  • GSM6062096 normal_1 normal tissue Control marker detected. paired normal tissue tissue: paired normal tissue
  • GSM6062097 normal_2 normal tissue Control marker detected. paired normal tissue tissue: paired normal tissue
  • GSM6062098 normal_3 normal tissue Control marker detected. paired normal tissue tissue: paired normal tissue
  • GSM6062099 normal_4 normal tissue Control marker detected. paired normal tissue tissue: paired normal tissue
  • GSM6062100 normal_5 normal tissue Control marker detected. paired normal tissue tissue: paired normal tissue
  • GSM6062101 normal_6 normal tissue Control marker detected. paired normal tissue tissue: paired normal tissue

Unassigned samples

Samples with no explicit case or control marker.

0

No samples

Excluded samples

Samples excluded from grouping by hard exclusion rules.

0

No samples

Ambiguous samples

Samples that need manual review before trusting grouping.

0

No samples

Metadata Quality Components

Persisted metadata quality

70 pts
Clarity
70%
Weight
100 pts

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

Detected Sample Groups

normal tissue

6 samples
  • GSM6062096 normal_1 paired normal tissue tissue: paired normal tissue
  • GSM6062097 normal_2 paired normal tissue tissue: paired normal tissue
  • GSM6062098 normal_3 paired normal tissue tissue: paired normal tissue
  • GSM6062099 normal_4 paired normal tissue tissue: paired normal tissue
  • GSM6062100 normal_5 paired normal tissue tissue: paired normal tissue
  • GSM6062101 normal_6 paired normal tissue tissue: paired normal tissue

tumor sample

6 samples
  • GSM6062102 PTC_1 Papillary thyroid carcinoma tissue: Papillary thyroid carcinoma
  • GSM6062103 PTC_2 Papillary thyroid carcinoma tissue: Papillary thyroid carcinoma
  • GSM6062104 PTC_3 Papillary thyroid carcinoma tissue: Papillary thyroid carcinoma
  • GSM6062105 PTC_4 Papillary thyroid carcinoma tissue: Papillary thyroid carcinoma
  • GSM6062106 PTC_5 Papillary thyroid carcinoma tissue: Papillary thyroid carcinoma
  • GSM6062107 PTC_6 Papillary thyroid carcinoma tissue: Papillary thyroid carcinoma

Score Breakdown

50%

relevance

  • Organism normalized.
  • Assay type normalized.
10%

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.
  • Missing colorectal disease context downgraded for tumor-vs-normal tissue ranking.
70%

metadata quality

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

data availability

  • Processed data available.
  • Raw data available.
45%

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 colorectal/CRC disease context is not explicit.

Sample Links

12 samples

Review Audit Trail

0 decisions

No review decisions have been stored for this dataset.