Siftome Phase 3L

GSE224356

RNA-seq of papillary thyroid carcinoma (PTC) patient's tissues and paired normal 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
2023-02-02
Last update
2026-01-27
Organization
Tianjin Cancer Institute and Hospital
Department
Not available
Public date
2025-05-27
Experiment types
Expression profiling by high throughput sequencing
Platforms
GPL20795 HiSeq X Ten (Homo sapiens)
Series type
SubSeries
SubSeries
Not available
BioProject
PRJNA930711
Supplementary files
XLSX: GSE224356_T1_N1_Down_genes.xlsx; XLSX: GSE224356_T1_N1_Up_genes.xlsx; XLSX: GSE224356_T2_N2_Down_genes.xlsx; XLSX: GSE224356_T2_N2_Up_genes.xlsx; XLSX: GSE224356_T3_N3_Down_genes.xlsx; XLSX: GSE224356_T3_N3_Up_genes.xlsx
Organism
Homo sapiens
Assay
bulk RNA-seq
Samples
6
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
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 5% 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. 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 fewer than ten samples limit cohort confidence. 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 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 3 samples
  • Likely control group normal tissue 3 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 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 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 unmatched normal · Tissue · suitability 5%. 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 fewer than ten samples limit cohort confidence. 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
GSE224356
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
GSE224356
  • 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
GSE224356
  • 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
GSE224356
  • 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: GSE224356
dataset_title: RNA-seq of papillary thyroid carcinoma (PTC)  patient's tissues and paired normal tissues
organism: Homo sapiens
assay_type: bulk RNA-seq
processed_data_available: true
raw_data_available: true
submission_date: 2023-02-02
last_update_date: 2026-01-27
organization_name: Tianjin Cancer Institute and Hospital
department: Not available
public_date: 2025-05-27
experiment_types: Expression profiling by high throughput sequencing
platforms: GPL20795 HiSeq X Ten (Homo sapiens)
sub_series: Not available
bioproject: PRJNA930711
supplementary_files: XLSX: GSE224356_T1_N1_Down_genes.xlsx; XLSX: GSE224356_T1_N1_Up_genes.xlsx; XLSX: GSE224356_T2_N2_Down_genes.xlsx; XLSX: GSE224356_T2_N2_Up_genes.xlsx; XLSX: GSE224356_T3_N3_Down_genes.xlsx; XLSX: GSE224356_T3_N3_Up_genes.xlsx
series_type: SubSeries

Why It Matched

  • Tumor vs unmatched normal · Tissue · suitability 5%.
  • 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 fewer than ten samples limit cohort confidence.
  • 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

11 fields
Field Value Source Origin Confidence Evidence Reason
assay_type bulk RNA-seq dataset GSE224356 Runtime Siftome inference GEO:dataset:GSE224356:4388af82aeadaf2021dabb67950c23dc123104fac8897734b6c2187593e303d7 high confidence bulk rna-seq dataset_accession: GSE224356 dataset_title: RNA-seq of papillary thyroid carcinoma (PTC) patient's tissues and paired normal tissues organism: Homo sapiens assay_type: bulk RNA-... keyword match keyword match: bulk rna-seq
organism Homo sapiens dataset GSE224356 Runtime Siftome inference GEO:dataset:GSE224356:4388af82aeadaf2021dabb67950c23dc123104fac8897734b6c2187593e303d7 high confidence homo sapiens dataset_accession: GSE224356 dataset_title: RNA-seq of papillary thyroid carcinoma (PTC) patient's tissues and paired normal tissues organism: Homo sapiens assay_type: bulk RNA-... keyword match keyword match: homo sapiens
sample_type normal tissue sample GSM7020412 Runtime Siftome inference GEO:sample:GSM7020412:93261a449d746be7145b14a9fb36004ace9d42ea8eda18aa874c2e461d65ee95 low confidence normal sample_accession: GSM7020412 sample_title: Normal tissue_1 source_name: Normal tissue_1 characteristics: patient diagnosis: papillary thyroid carcinoma; subject number: 1; tissu... controlled vocabulary controlled vocabulary sample type match: normal
sample_type tumor sample sample GSM7020412 Runtime Siftome inference GEO:sample:GSM7020412:93261a449d746be7145b14a9fb36004ace9d42ea8eda18aa874c2e461d65ee95 medium confidence carcinoma sample_accession: GSM7020412 sample_title: Normal tissue_1 source_name: Normal tissue_1 characteristics: patient diagnosis: papillary thyroid carcinoma; subject number: 1; tissu... controlled vocabulary controlled vocabulary sample type match: carcinoma
sample_type tumor sample sample GSM7020413 Runtime Siftome inference GEO:sample:GSM7020413:83629068d77c0f1ee4448e63bf8e00c917f0658c10870b095ebca5fdfe37c6b6 low confidence tumor sample_accession: GSM7020413 sample_title: Tumor tissue_1 source_name: Tumor tissue_1 characteristics: patient diagnosis: papillary thyroid carcinoma; subject number: 1; tissue:... controlled vocabulary controlled vocabulary sample type match: tumor
sample_type normal tissue sample GSM7020414 Runtime Siftome inference GEO:sample:GSM7020414:cc68d04e73e1f6b586ac973f1bc9321f85f8ecd5e400aa0fab67d0c368efc726 low confidence normal sample_accession: GSM7020414 sample_title: Normal tissue_2 source_name: Normal tissue_2 characteristics: patient diagnosis: papillary thyroid carcinoma; subject number: 2; tissu... controlled vocabulary controlled vocabulary sample type match: normal
sample_type tumor sample sample GSM7020414 Runtime Siftome inference GEO:sample:GSM7020414:cc68d04e73e1f6b586ac973f1bc9321f85f8ecd5e400aa0fab67d0c368efc726 medium confidence carcinoma sample_accession: GSM7020414 sample_title: Normal tissue_2 source_name: Normal tissue_2 characteristics: patient diagnosis: papillary thyroid carcinoma; subject number: 2; tissu... controlled vocabulary controlled vocabulary sample type match: carcinoma
sample_type tumor sample sample GSM7020415 Runtime Siftome inference GEO:sample:GSM7020415:53e03cb0ccd95571aac5de5b139c00490dbb7d836ed68ac04f1ff27f723bd65d low confidence tumor sample_accession: GSM7020415 sample_title: Tumor tissue_2 source_name: Tumor tissue_2 characteristics: patient diagnosis: papillary thyroid carcinoma; subject number: 2; tissue:... controlled vocabulary controlled vocabulary sample type match: tumor
sample_type normal tissue sample GSM7020416 Runtime Siftome inference GEO:sample:GSM7020416:f211aecfcee9964163d4fe3311fb804a9f0c0e58b729243d82f930ec6666771e low confidence normal sample_accession: GSM7020416 sample_title: Normal tissue_3 source_name: Normal tissue_3 characteristics: patient diagnosis: papillary thyroid carcinoma; subject number: 3; tissu... controlled vocabulary controlled vocabulary sample type match: normal
sample_type tumor sample sample GSM7020416 Runtime Siftome inference GEO:sample:GSM7020416:f211aecfcee9964163d4fe3311fb804a9f0c0e58b729243d82f930ec6666771e medium confidence carcinoma sample_accession: GSM7020416 sample_title: Normal tissue_3 source_name: Normal tissue_3 characteristics: patient diagnosis: papillary thyroid carcinoma; subject number: 3; tissu... controlled vocabulary controlled vocabulary sample type match: carcinoma
sample_type tumor sample sample GSM7020417 Runtime Siftome inference GEO:sample:GSM7020417:fe9f5e6d9c4c2504c4a76d6cf36e897733e3999a66012439fda0a033c00ac9e1 low confidence tumor sample_accession: GSM7020417 sample_title: Tumor tissue_3 source_name: Tumor tissue_3 characteristics: patient diagnosis: papillary thyroid carcinoma; subject number: 3; tissue:... controlled vocabulary controlled vocabulary sample type match: tumor

Sample Group Preview

Possible case samples

Samples currently treated as the comparison case group.

3
  • GSM7020413 Tumor tissue_1 tumor sample Case marker detected. Tumor tissue_1 patient diagnosis: papillary thyroid carcinoma; subject number: 1; tissue: Tumor tissue
  • GSM7020415 Tumor tissue_2 tumor sample Case marker detected. Tumor tissue_2 patient diagnosis: papillary thyroid carcinoma; subject number: 2; tissue: Tumor tissue
  • GSM7020417 Tumor tissue_3 tumor sample Case marker detected. Tumor tissue_3 patient diagnosis: papillary thyroid carcinoma; subject number: 3; tissue: Tumor tissue

Possible control samples

Samples currently treated as controls or baseline.

3
  • GSM7020412 Normal tissue_1 normal tissue Control marker detected. Normal tissue_1 patient diagnosis: papillary thyroid carcinoma; subject number: 1; tissue: Normal tissue
  • GSM7020414 Normal tissue_2 normal tissue Control marker detected. Normal tissue_2 patient diagnosis: papillary thyroid carcinoma; subject number: 2; tissue: Normal tissue
  • GSM7020416 Normal tissue_3 normal tissue Control marker detected. Normal tissue_3 patient diagnosis: papillary thyroid carcinoma; subject number: 3; tissue: Normal tissue

Unassigned samples

Samples with no explicit case or control marker.

0

No samples

Excluded samples

Samples excluded from grouping by hard exclusion rules.

0

No samples

Ambiguous samples

Samples that need manual review before trusting grouping.

0

No samples

Metadata Quality Components

Persisted metadata quality

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

3 samples
  • GSM7020412 Normal tissue_1 Normal tissue_1 patient diagnosis: papillary thyroid carcinoma; subject number: 1; tissue: Normal tissue
  • GSM7020414 Normal tissue_2 Normal tissue_2 patient diagnosis: papillary thyroid carcinoma; subject number: 2; tissue: Normal tissue
  • GSM7020416 Normal tissue_3 Normal tissue_3 patient diagnosis: papillary thyroid carcinoma; subject number: 3; tissue: Normal tissue

tumor sample

3 samples
  • GSM7020413 Tumor tissue_1 Tumor tissue_1 patient diagnosis: papillary thyroid carcinoma; subject number: 1; tissue: Tumor tissue
  • GSM7020415 Tumor tissue_2 Tumor tissue_2 patient diagnosis: papillary thyroid carcinoma; subject number: 2; tissue: Tumor tissue
  • GSM7020417 Tumor tissue_3 Tumor tissue_3 patient diagnosis: papillary thyroid carcinoma; subject number: 3; tissue: Tumor tissue

Score Breakdown

50%

relevance

  • Organism normalized.
  • Assay type normalized.
5%

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.
  • 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 fewer than ten samples limit cohort confidence.
  • Overall score capped because colorectal/CRC disease context is not explicit.

Sample Links

6 samples

Review Audit Trail

0 decisions

No review decisions have been stored for this dataset.