Siftome Phase 3L

GSE251942

Hight througput RNA sequencing in a cohort of HBV related HCC and healty liver samples

Not suitable Dataset does not meet the current suitability threshold.
Sample grouping CSV Contrast CSV DESeq2 metadata CSV R handoff notes Handoff report Download instructions Open GEO dataset
Source
GEO
Search intent
Patient tissue tumor-vs-normal
Intent behavior
search-intent-behavior-v1
Submission date
2023-12-22
Last update
2025-05-29
Organization
Université Claude Bernard Lyon 1, Inserm UMR 1350 - PaThLiv
Department
Not available
Public date
2025-05-29
Experiment types
Expression profiling by high throughput sequencing
Platforms
GPL18573 Illumina NextSeq 500 (Homo sapiens)
Series type
Series
SubSeries
Not available
BioProject
PRJNA1055956
Supplementary files
TSV: GSE251942_20231221_RSEM_RAW_counts.tsv.gz; TSV: GSE251942_20231221_STAR_RAW_counts.tsv.gz
Organism
Homo sapiens
Assay
bulk RNA-seq
Samples
25
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
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

No readiness blockers detected.

Next Steps

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

Analysis Preparation Checklist

5/6 ready

Group labels reviewed

Needs review

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

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

Minimum sample count met

Ready

Both groups meet the minimum of 2 samples.

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

Processed counts available

Ready

Processed data availability is marked true in the GEO index.

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

Ambiguous samples handled

Ready

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

Still scan the grouping table for biology-specific ambiguity.

Exclusion decisions recorded

Ready

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

Record any manual exclusions in the downstream analysis notes.

Source links preserved

Ready

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

Keep GEO dataset and sample links with exported metadata.

Bioinformatician Review

Standard analyst review

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

No expert-review triggers were detected by Siftome.

Why This Is Ranked Here

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

Score Components

  • relevance 60% Organism normalized. Assay type normalized. Tissue metadata normalized.
  • comparison suitability 0% Tumor and normal sample groups detected. No excluded sample type flags detected. Tumor/normal design boosted for colorectal tumor-vs-normal tissue triage. Patient tissue or biopsy specimens boosted for tissue comparison triage. Non-colorectal cancer context downgraded for colorectal tumor-vs-normal tissue ranking.
  • metadata quality 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 was not normalized. Tissue clarity: Tissue metadata normalized. Treatment clarity: No unclear treatment split detected in the sample metadata. Replicate clarity: No pooled sample or technical replicate flags detected. Data availability clarity: Dataset-level processed or raw data availability is explicit.
  • data availability 100% Processed data available. Raw data available.
  • overall 34% Weighted score: 30% relevance, 30% comparison suitability, 25% metadata quality, 15% data availability. Overall score capped because comparison suitability is weak for the selected search intent. Overall score capped because tumor/normal grouping is from a non-colorectal cancer context.

Derived Classifications

  • Organism Homo sapiens Organism remains rule-derived: Homo sapiens.
  • Assay bulk RNA-seq Assay remains rule-derived: bulk RNA-seq.
  • Study design Tumor vs unmatched normal Study design remains rule-derived: Tumor vs unmatched normal.
  • Specimen/source Tissue Specimen/source remains rule-derived: Tissue.
  • Likely case group tumor sample 10 samples
  • Likely control group normal tissue 15 samples

Warnings

  • DISEASE_LABEL_UNCLEAR warning Disease or condition label 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 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: 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 unmatched normal · Tissue · suitability 0%. Contributed to match or upgrade evidence.
  • Supporting fact Prioritized assay: bulk RNA-seq is the active assay expectation. Contributed to match or upgrade evidence.
  • Supporting fact Downgraded disease context: 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 1 warning 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 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: Disease clarity: Disease or condition 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 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
GSE251942
Sample records
25 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
GSE251942
  • 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
GSE251942
  • 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
GSE251942
  • 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: GSE251942
dataset_title: Hight througput RNA sequencing in a cohort of HBV related HCC and healty liver samples
organism: Homo sapiens
assay_type: bulk RNA-seq
processed_data_available: true
raw_data_available: true
submission_date: 2023-12-22
last_update_date: 2025-05-29
organization_name: Université Claude Bernard Lyon 1, Inserm UMR 1350 - PaThLiv
department: Not available
public_date: 2025-05-29
experiment_types: Expression profiling by high throughput sequencing
platforms: GPL18573 Illumina NextSeq 500 (Homo sapiens)
sub_series: Not available
bioproject: PRJNA1055956
supplementary_files: TSV: GSE251942_20231221_RSEM_RAW_counts.tsv.gz; TSV: GSE251942_20231221_STAR_RAW_counts.tsv.gz
series_type: Series

Why It Matched

  • Tumor vs unmatched normal · Tissue · suitability 0%.
  • 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.
  • 1 warning require review.

Why It May Not Be Suitable

  • Disease or condition label could not be normalized.
  • Non-colorectal cancer context downgraded for colorectal tumor-vs-normal tissue ranking.
  • Missing or unclear metadata: Disease clarity: Disease or condition 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 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

  • warning DISEASE_LABEL_UNCLEAR Disease or condition label could not be normalized.

Normalized Fields

53 fields
Field Value Source Origin Confidence Evidence Reason
assay_type bulk RNA-seq dataset GSE251942 Runtime Siftome inference GEO:dataset:GSE251942:1fc5a561e2b86b0a6a8a77f19465178536eefea63319eab6fba547135675b490 high confidence bulk rna-seq dataset_accession: GSE251942 dataset_title: Hight througput RNA sequencing in a cohort of HBV related HCC and healty liver samples organism: Homo sapiens assay_type: bulk RNA-se... keyword match keyword match: bulk rna-seq
organism Homo sapiens dataset GSE251942 Runtime Siftome inference GEO:dataset:GSE251942:1fc5a561e2b86b0a6a8a77f19465178536eefea63319eab6fba547135675b490 high confidence homo sapiens dataset_accession: GSE251942 dataset_title: Hight througput RNA sequencing in a cohort of HBV related HCC and healty liver samples organism: Homo sapiens assay_type: bulk RNA-se... keyword match keyword match: homo sapiens
sample_type normal tissue sample GSM7990394 Runtime Siftome inference GEO:sample:GSM7990394:7d34f6ac4d4fb9d87208b4a5cfe50e70407b21dc26de043094a31c541f71af33 high confidence non tumor sample_accession: GSM7990394 sample_title: Sample 113NT Non tumor tissue source_name: Liver characteristics: disease state: HBV-related HCC; tissue: Liver; tissue type: Non tumo... controlled vocabulary controlled vocabulary sample type match: non tumor
sample_type tumor sample sample GSM7990395 Runtime Siftome inference GEO:sample:GSM7990395:e9da68d5883749b35e8cb3a60fa649ea2e66e851d04a252b9064011d964492d1 low confidence tumor sample_accession: GSM7990395 sample_title: Sample 113T Tumor tissue source_name: Liver characteristics: disease state: HBV-related HCC; tissue: Liver; tissue type: Tumor tissue ... controlled vocabulary controlled vocabulary sample type match: tumor
sample_type normal tissue sample GSM7990396 Runtime Siftome inference GEO:sample:GSM7990396:2ed355923d2c1643ec41afdbb7a96be3170edcaf5dc1ef55d0dc492b5f2945fe high confidence non tumor sample_accession: GSM7990396 sample_title: Sample 43NT Non tumor tissue source_name: Liver characteristics: disease state: HBV-related HCC; tissue: Liver; tissue type: Non tumor... controlled vocabulary controlled vocabulary sample type match: non tumor
sample_type tumor sample sample GSM7990397 Runtime Siftome inference GEO:sample:GSM7990397:6d69043701cc34ae28bea98302e31ee74dc513befbd7a872224e9dcc1f1fdfb9 low confidence tumor sample_accession: GSM7990397 sample_title: Sample 43T Tumor tissue source_name: Liver characteristics: disease state: HBV-related HCC; tissue: Liver; tissue type: Tumor tissue S... controlled vocabulary controlled vocabulary sample type match: tumor
sample_type normal tissue sample GSM7990398 Runtime Siftome inference GEO:sample:GSM7990398:33cbe1b04bce197e0d9e832e7fd27ebf76f77f8f2803f814f5739c49468ecc85 low confidence normal sample_accession: GSM7990398 sample_title: Sample FS1_NT Normal liver tissue source_name: Liver characteristics: disease state: control; tissue: Liver; tissue type: Normal liver... controlled vocabulary controlled vocabulary sample type match: normal
sample_type normal tissue sample GSM7990399 Runtime Siftome inference GEO:sample:GSM7990399:84e819739c03632594577c153b680b37d14d203dd6326a5d95f2ba2ff989cc0f low confidence normal sample_accession: GSM7990399 sample_title: Sample FS2_NT Normal liver tissue source_name: Liver characteristics: disease state: control; tissue: Liver; tissue type: Normal liver... controlled vocabulary controlled vocabulary sample type match: normal
sample_type normal tissue sample GSM7990400 Runtime Siftome inference GEO:sample:GSM7990400:e98563cda3ca8c2285a8de0226a2ee2b344d0d978131d9873063095600baeba3 low confidence normal sample_accession: GSM7990400 sample_title: Sample FS6_NT Normal liver tissue source_name: Liver characteristics: disease state: control; tissue: Liver; tissue type: Normal liver... controlled vocabulary controlled vocabulary sample type match: normal
sample_type normal tissue sample GSM7990401 Runtime Siftome inference GEO:sample:GSM7990401:5c08625d2a9192bfcf9aa52c1cec167cc3b59c1030cb374ecc2ffd90bcea4c13 low confidence normal sample_accession: GSM7990401 sample_title: Sample FS12_NT Normal liver tissue source_name: Liver characteristics: disease state: control; tissue: Liver; tissue type: Normal live... controlled vocabulary controlled vocabulary sample type match: normal
sample_type normal tissue sample GSM7990402 Runtime Siftome inference GEO:sample:GSM7990402:f31211d0ec230a7d7c8f56897794019cd23e81d874515f5d0bc0240c7670d573 low confidence normal sample_accession: GSM7990402 sample_title: Sample FS43_NT Normal liver tissue source_name: Liver characteristics: disease state: control; tissue: Liver; tissue type: Normal live... controlled vocabulary controlled vocabulary sample type match: normal
sample_type normal tissue sample GSM7990403 Runtime Siftome inference GEO:sample:GSM7990403:4ab1e7f3771fe2798948b3c44fc9f7bf6c98b0874fef25bbef17657e641603e2 high confidence non tumor sample_accession: GSM7990403 sample_title: Sample 105NT Non tumor tissue source_name: Liver characteristics: disease state: HBV-related HCC; tissue: Liver; tissue type: Non tumo... controlled vocabulary controlled vocabulary sample type match: non tumor
sample_type tumor sample sample GSM7990404 Runtime Siftome inference GEO:sample:GSM7990404:4eba5e62e54fc5488f84fc0b8d184100b039c75b824172f2bb76a14fa49a373d low confidence tumor sample_accession: GSM7990404 sample_title: Sample 34T Tumor tissue source_name: Liver characteristics: disease state: HBV-related HCC; tissue: Liver; tissue type: Tumor tissue S... controlled vocabulary controlled vocabulary sample type match: tumor
sample_type normal tissue sample GSM7990405 Runtime Siftome inference GEO:sample:GSM7990405:d683ed898fdfe622783484d221b8aca525638898f65ffa1b5c9c5de9897825fe high confidence non tumor sample_accession: GSM7990405 sample_title: Sample 51NT Non tumor tissue source_name: Liver characteristics: disease state: HBV-related HCC; tissue: Liver; tissue type: Non tumor... controlled vocabulary controlled vocabulary sample type match: non tumor
sample_type tumor sample sample GSM7990406 Runtime Siftome inference GEO:sample:GSM7990406:a95902b8aa51772bf149ac342e67caace52859d39c41a1ea5c855c8f473e3565 low confidence tumor sample_accession: GSM7990406 sample_title: Sample 51T Tumor tissue source_name: Liver characteristics: disease state: HBV-related HCC; tissue: Liver; tissue type: Tumor tissue S... controlled vocabulary controlled vocabulary sample type match: tumor
sample_type normal tissue sample GSM7990407 Runtime Siftome inference GEO:sample:GSM7990407:7806d4321cbc2e3bb4971e19ad3112069106a19fabe8a794702b5f2e37c1ac43 high confidence non tumor sample_accession: GSM7990407 sample_title: Sample 150NT Non tumor tissue source_name: Liver characteristics: disease state: HBV-related HCC; tissue: Liver; tissue type: Non tumo... controlled vocabulary controlled vocabulary sample type match: non tumor
sample_type tumor sample sample GSM7990408 Runtime Siftome inference GEO:sample:GSM7990408:65a898fa6bf36701aa795a27e313db2579e3f922feefcc6fc2165eedc7fbbea2 low confidence tumor sample_accession: GSM7990408 sample_title: Sample 150T Tumor tissue source_name: Liver characteristics: disease state: HBV-related HCC; tissue: Liver; tissue type: Tumor tissue ... controlled vocabulary controlled vocabulary sample type match: tumor
sample_type normal tissue sample GSM7990409 Runtime Siftome inference GEO:sample:GSM7990409:02ec2179a80d25751ca486c02a4fc4ec7db52102e9ad06d8cb2418e31da0f71e high confidence non tumor sample_accession: GSM7990409 sample_title: Sample 141NT Non tumor tissue source_name: Liver characteristics: disease state: HBV-related HCC; tissue: Liver; tissue type: Non tumo... controlled vocabulary controlled vocabulary sample type match: non tumor
sample_type tumor sample sample GSM7990410 Runtime Siftome inference GEO:sample:GSM7990410:9c5165bc16fbad2ad2fe4b9092bcdecd80df188494bc27b556af0c742b49e928 low confidence tumor sample_accession: GSM7990410 sample_title: Sample 141T Tumor tissue source_name: Liver characteristics: disease state: HBV-related HCC; tissue: Liver; tissue type: Tumor tissue ... controlled vocabulary controlled vocabulary sample type match: tumor
sample_type tumor sample sample GSM7990411 Runtime Siftome inference GEO:sample:GSM7990411:bfa7bca819795a9d319a4ff18b8bdcaee0054828855055925f387d8d0cf71115 low confidence tumor sample_accession: GSM7990411 sample_title: Sample 105T Tumor tissue source_name: Liver characteristics: disease state: HBV-related HCC; tissue: Liver; tissue type: Tumor tissue ... controlled vocabulary controlled vocabulary sample type match: tumor
sample_type normal tissue sample GSM7990412 Runtime Siftome inference GEO:sample:GSM7990412:4305246348691c0d79509c21bf58dbdc682831318edd2864d2d5adf739b90a1a high confidence non tumor sample_accession: GSM7990412 sample_title: Sample 144NT Non tumor tissue source_name: Liver characteristics: disease state: HBV-related HCC; tissue: Liver; tissue type: Non tumo... controlled vocabulary controlled vocabulary sample type match: non tumor
sample_type tumor sample sample GSM7990413 Runtime Siftome inference GEO:sample:GSM7990413:8b60c785b15d4014b28338a22dfb0cde0e3364f88128915d671d0d459a819536 low confidence tumor sample_accession: GSM7990413 sample_title: Sample 144T Tumor tissue source_name: Liver characteristics: disease state: HBV-related HCC; tissue: Liver; tissue type: Tumor tissue ... controlled vocabulary controlled vocabulary sample type match: tumor
sample_type normal tissue sample GSM7990414 Runtime Siftome inference GEO:sample:GSM7990414:80d3d3944800e5b531d67dc321798dbd0b077576ce5ab99c2c82af45eaca5a69 high confidence non tumor sample_accession: GSM7990414 sample_title: Sample 13NT Non tumor tissue source_name: Liver characteristics: disease state: HBV-related HCC; tissue: Liver; tissue type: Non tumor... controlled vocabulary controlled vocabulary sample type match: non tumor
sample_type tumor sample sample GSM7990415 Runtime Siftome inference GEO:sample:GSM7990415:c9dd123527d9e1c8069820078222c17f739d6eeed7edab85b184aeb662572a21 low confidence tumor sample_accession: GSM7990415 sample_title: Sample 13T Tumor tissue source_name: Liver characteristics: disease state: HBV-related HCC; tissue: Liver; tissue type: Tumor tissue S... controlled vocabulary controlled vocabulary sample type match: tumor
sample_type normal tissue sample GSM7990416 Runtime Siftome inference GEO:sample:GSM7990416:315f056b11896e964a375762acaaf2d4262822c23e9a8772c5565b1cc6ef24ef high confidence non tumor sample_accession: GSM7990416 sample_title: Sample 28NT Non tumor tissue source_name: Liver characteristics: disease state: HBV-related HCC; tissue: Liver; tissue type: Non tumor... controlled vocabulary controlled vocabulary sample type match: non tumor
sample_type tumor sample sample GSM7990417 Runtime Siftome inference GEO:sample:GSM7990417:64de9810b5cf5cf4fb000a2b00db8f52ca2585eb653420d862633bf78f4f846e low confidence tumor sample_accession: GSM7990417 sample_title: Sample 28T Tumor tissue source_name: Liver characteristics: disease state: HBV-related HCC; tissue: Liver; tissue type: Tumor tissue S... controlled vocabulary controlled vocabulary sample type match: tumor
sample_type normal tissue sample GSM7990418 Runtime Siftome inference GEO:sample:GSM7990418:97600120c246b85d2c47f71758c09d73288fe7f4759f3177df76fec2805669f1 high confidence non tumor sample_accession: GSM7990418 sample_title: Sample 34NT Non tumor tissue source_name: Liver characteristics: disease state: HBV-related HCC; tissue: Liver; tissue type: Non tumor... controlled vocabulary controlled vocabulary sample type match: non tumor
tissue liver dataset GSE251942 Runtime Siftome inference GEO:dataset:GSE251942:1fc5a561e2b86b0a6a8a77f19465178536eefea63319eab6fba547135675b490 low confidence liver dataset_accession: GSE251942 dataset_title: Hight througput RNA sequencing in a cohort of HBV related HCC and healty liver samples organism: Homo sapiens assay_type: bulk RNA-se... controlled vocabulary controlled vocabulary tissue match: liver
tissue liver sample GSM7990394 Runtime Siftome inference GEO:sample:GSM7990394:7d34f6ac4d4fb9d87208b4a5cfe50e70407b21dc26de043094a31c541f71af33 low confidence liver sample_accession: GSM7990394 sample_title: Sample 113NT Non tumor tissue source_name: Liver characteristics: disease state: HBV-related HCC; tissue: Liver; tissue type: Non tumo... controlled vocabulary controlled vocabulary tissue match: liver
tissue liver sample GSM7990395 Runtime Siftome inference GEO:sample:GSM7990395:e9da68d5883749b35e8cb3a60fa649ea2e66e851d04a252b9064011d964492d1 low confidence liver sample_accession: GSM7990395 sample_title: Sample 113T Tumor tissue source_name: Liver characteristics: disease state: HBV-related HCC; tissue: Liver; tissue type: Tumor tissue ... controlled vocabulary controlled vocabulary tissue match: liver
tissue liver sample GSM7990396 Runtime Siftome inference GEO:sample:GSM7990396:2ed355923d2c1643ec41afdbb7a96be3170edcaf5dc1ef55d0dc492b5f2945fe low confidence liver sample_accession: GSM7990396 sample_title: Sample 43NT Non tumor tissue source_name: Liver characteristics: disease state: HBV-related HCC; tissue: Liver; tissue type: Non tumor... controlled vocabulary controlled vocabulary tissue match: liver
tissue liver sample GSM7990397 Runtime Siftome inference GEO:sample:GSM7990397:6d69043701cc34ae28bea98302e31ee74dc513befbd7a872224e9dcc1f1fdfb9 low confidence liver sample_accession: GSM7990397 sample_title: Sample 43T Tumor tissue source_name: Liver characteristics: disease state: HBV-related HCC; tissue: Liver; tissue type: Tumor tissue S... controlled vocabulary controlled vocabulary tissue match: liver
tissue liver sample GSM7990398 Runtime Siftome inference GEO:sample:GSM7990398:33cbe1b04bce197e0d9e832e7fd27ebf76f77f8f2803f814f5739c49468ecc85 low confidence liver sample_accession: GSM7990398 sample_title: Sample FS1_NT Normal liver tissue source_name: Liver characteristics: disease state: control; tissue: Liver; tissue type: Normal liver... controlled vocabulary controlled vocabulary tissue match: liver
tissue liver sample GSM7990399 Runtime Siftome inference GEO:sample:GSM7990399:84e819739c03632594577c153b680b37d14d203dd6326a5d95f2ba2ff989cc0f low confidence liver sample_accession: GSM7990399 sample_title: Sample FS2_NT Normal liver tissue source_name: Liver characteristics: disease state: control; tissue: Liver; tissue type: Normal liver... controlled vocabulary controlled vocabulary tissue match: liver
tissue liver sample GSM7990400 Runtime Siftome inference GEO:sample:GSM7990400:e98563cda3ca8c2285a8de0226a2ee2b344d0d978131d9873063095600baeba3 low confidence liver sample_accession: GSM7990400 sample_title: Sample FS6_NT Normal liver tissue source_name: Liver characteristics: disease state: control; tissue: Liver; tissue type: Normal liver... controlled vocabulary controlled vocabulary tissue match: liver
tissue liver sample GSM7990401 Runtime Siftome inference GEO:sample:GSM7990401:5c08625d2a9192bfcf9aa52c1cec167cc3b59c1030cb374ecc2ffd90bcea4c13 low confidence liver sample_accession: GSM7990401 sample_title: Sample FS12_NT Normal liver tissue source_name: Liver characteristics: disease state: control; tissue: Liver; tissue type: Normal live... controlled vocabulary controlled vocabulary tissue match: liver
tissue liver sample GSM7990402 Runtime Siftome inference GEO:sample:GSM7990402:f31211d0ec230a7d7c8f56897794019cd23e81d874515f5d0bc0240c7670d573 low confidence liver sample_accession: GSM7990402 sample_title: Sample FS43_NT Normal liver tissue source_name: Liver characteristics: disease state: control; tissue: Liver; tissue type: Normal live... controlled vocabulary controlled vocabulary tissue match: liver
tissue liver sample GSM7990403 Runtime Siftome inference GEO:sample:GSM7990403:4ab1e7f3771fe2798948b3c44fc9f7bf6c98b0874fef25bbef17657e641603e2 low confidence liver sample_accession: GSM7990403 sample_title: Sample 105NT Non tumor tissue source_name: Liver characteristics: disease state: HBV-related HCC; tissue: Liver; tissue type: Non tumo... controlled vocabulary controlled vocabulary tissue match: liver
tissue liver sample GSM7990404 Runtime Siftome inference GEO:sample:GSM7990404:4eba5e62e54fc5488f84fc0b8d184100b039c75b824172f2bb76a14fa49a373d low confidence liver sample_accession: GSM7990404 sample_title: Sample 34T Tumor tissue source_name: Liver characteristics: disease state: HBV-related HCC; tissue: Liver; tissue type: Tumor tissue S... controlled vocabulary controlled vocabulary tissue match: liver
tissue liver sample GSM7990405 Runtime Siftome inference GEO:sample:GSM7990405:d683ed898fdfe622783484d221b8aca525638898f65ffa1b5c9c5de9897825fe low confidence liver sample_accession: GSM7990405 sample_title: Sample 51NT Non tumor tissue source_name: Liver characteristics: disease state: HBV-related HCC; tissue: Liver; tissue type: Non tumor... controlled vocabulary controlled vocabulary tissue match: liver
tissue liver sample GSM7990406 Runtime Siftome inference GEO:sample:GSM7990406:a95902b8aa51772bf149ac342e67caace52859d39c41a1ea5c855c8f473e3565 low confidence liver sample_accession: GSM7990406 sample_title: Sample 51T Tumor tissue source_name: Liver characteristics: disease state: HBV-related HCC; tissue: Liver; tissue type: Tumor tissue S... controlled vocabulary controlled vocabulary tissue match: liver
tissue liver sample GSM7990407 Runtime Siftome inference GEO:sample:GSM7990407:7806d4321cbc2e3bb4971e19ad3112069106a19fabe8a794702b5f2e37c1ac43 low confidence liver sample_accession: GSM7990407 sample_title: Sample 150NT Non tumor tissue source_name: Liver characteristics: disease state: HBV-related HCC; tissue: Liver; tissue type: Non tumo... controlled vocabulary controlled vocabulary tissue match: liver
tissue liver sample GSM7990408 Runtime Siftome inference GEO:sample:GSM7990408:65a898fa6bf36701aa795a27e313db2579e3f922feefcc6fc2165eedc7fbbea2 low confidence liver sample_accession: GSM7990408 sample_title: Sample 150T Tumor tissue source_name: Liver characteristics: disease state: HBV-related HCC; tissue: Liver; tissue type: Tumor tissue ... controlled vocabulary controlled vocabulary tissue match: liver
tissue liver sample GSM7990409 Runtime Siftome inference GEO:sample:GSM7990409:02ec2179a80d25751ca486c02a4fc4ec7db52102e9ad06d8cb2418e31da0f71e low confidence liver sample_accession: GSM7990409 sample_title: Sample 141NT Non tumor tissue source_name: Liver characteristics: disease state: HBV-related HCC; tissue: Liver; tissue type: Non tumo... controlled vocabulary controlled vocabulary tissue match: liver
tissue liver sample GSM7990410 Runtime Siftome inference GEO:sample:GSM7990410:9c5165bc16fbad2ad2fe4b9092bcdecd80df188494bc27b556af0c742b49e928 low confidence liver sample_accession: GSM7990410 sample_title: Sample 141T Tumor tissue source_name: Liver characteristics: disease state: HBV-related HCC; tissue: Liver; tissue type: Tumor tissue ... controlled vocabulary controlled vocabulary tissue match: liver
tissue liver sample GSM7990411 Runtime Siftome inference GEO:sample:GSM7990411:bfa7bca819795a9d319a4ff18b8bdcaee0054828855055925f387d8d0cf71115 low confidence liver sample_accession: GSM7990411 sample_title: Sample 105T Tumor tissue source_name: Liver characteristics: disease state: HBV-related HCC; tissue: Liver; tissue type: Tumor tissue ... controlled vocabulary controlled vocabulary tissue match: liver
tissue liver sample GSM7990412 Runtime Siftome inference GEO:sample:GSM7990412:4305246348691c0d79509c21bf58dbdc682831318edd2864d2d5adf739b90a1a low confidence liver sample_accession: GSM7990412 sample_title: Sample 144NT Non tumor tissue source_name: Liver characteristics: disease state: HBV-related HCC; tissue: Liver; tissue type: Non tumo... controlled vocabulary controlled vocabulary tissue match: liver
tissue liver sample GSM7990413 Runtime Siftome inference GEO:sample:GSM7990413:8b60c785b15d4014b28338a22dfb0cde0e3364f88128915d671d0d459a819536 low confidence liver sample_accession: GSM7990413 sample_title: Sample 144T Tumor tissue source_name: Liver characteristics: disease state: HBV-related HCC; tissue: Liver; tissue type: Tumor tissue ... controlled vocabulary controlled vocabulary tissue match: liver
tissue liver sample GSM7990414 Runtime Siftome inference GEO:sample:GSM7990414:80d3d3944800e5b531d67dc321798dbd0b077576ce5ab99c2c82af45eaca5a69 low confidence liver sample_accession: GSM7990414 sample_title: Sample 13NT Non tumor tissue source_name: Liver characteristics: disease state: HBV-related HCC; tissue: Liver; tissue type: Non tumor... controlled vocabulary controlled vocabulary tissue match: liver
tissue liver sample GSM7990415 Runtime Siftome inference GEO:sample:GSM7990415:c9dd123527d9e1c8069820078222c17f739d6eeed7edab85b184aeb662572a21 low confidence liver sample_accession: GSM7990415 sample_title: Sample 13T Tumor tissue source_name: Liver characteristics: disease state: HBV-related HCC; tissue: Liver; tissue type: Tumor tissue S... controlled vocabulary controlled vocabulary tissue match: liver
tissue liver sample GSM7990416 Runtime Siftome inference GEO:sample:GSM7990416:315f056b11896e964a375762acaaf2d4262822c23e9a8772c5565b1cc6ef24ef low confidence liver sample_accession: GSM7990416 sample_title: Sample 28NT Non tumor tissue source_name: Liver characteristics: disease state: HBV-related HCC; tissue: Liver; tissue type: Non tumor... controlled vocabulary controlled vocabulary tissue match: liver
tissue liver sample GSM7990417 Runtime Siftome inference GEO:sample:GSM7990417:64de9810b5cf5cf4fb000a2b00db8f52ca2585eb653420d862633bf78f4f846e low confidence liver sample_accession: GSM7990417 sample_title: Sample 28T Tumor tissue source_name: Liver characteristics: disease state: HBV-related HCC; tissue: Liver; tissue type: Tumor tissue S... controlled vocabulary controlled vocabulary tissue match: liver
tissue liver sample GSM7990418 Runtime Siftome inference GEO:sample:GSM7990418:97600120c246b85d2c47f71758c09d73288fe7f4759f3177df76fec2805669f1 low confidence liver sample_accession: GSM7990418 sample_title: Sample 34NT Non tumor tissue source_name: Liver characteristics: disease state: HBV-related HCC; tissue: Liver; tissue type: Non tumor... controlled vocabulary controlled vocabulary tissue match: liver

Sample Group Preview

Possible case samples

Samples currently treated as the comparison case group.

10
  • GSM7990395 Sample 113T Tumor tissue tumor sample Case marker detected. Liver disease state: HBV-related HCC; tissue: Liver; tissue type: Tumor tissue
  • GSM7990397 Sample 43T Tumor tissue tumor sample Case marker detected. Liver disease state: HBV-related HCC; tissue: Liver; tissue type: Tumor tissue
  • GSM7990404 Sample 34T Tumor tissue tumor sample Case marker detected. Liver disease state: HBV-related HCC; tissue: Liver; tissue type: Tumor tissue
  • GSM7990406 Sample 51T Tumor tissue tumor sample Case marker detected. Liver disease state: HBV-related HCC; tissue: Liver; tissue type: Tumor tissue
  • GSM7990408 Sample 150T Tumor tissue tumor sample Case marker detected. Liver disease state: HBV-related HCC; tissue: Liver; tissue type: Tumor tissue
  • GSM7990410 Sample 141T Tumor tissue tumor sample Case marker detected. Liver disease state: HBV-related HCC; tissue: Liver; tissue type: Tumor tissue
  • GSM7990411 Sample 105T Tumor tissue tumor sample Case marker detected. Liver disease state: HBV-related HCC; tissue: Liver; tissue type: Tumor tissue
  • GSM7990413 Sample 144T Tumor tissue tumor sample Case marker detected. Liver disease state: HBV-related HCC; tissue: Liver; tissue type: Tumor tissue
  • GSM7990415 Sample 13T Tumor tissue tumor sample Case marker detected. Liver disease state: HBV-related HCC; tissue: Liver; tissue type: Tumor tissue
  • GSM7990417 Sample 28T Tumor tissue tumor sample Case marker detected. Liver disease state: HBV-related HCC; tissue: Liver; tissue type: Tumor tissue

Possible control samples

Samples currently treated as controls or baseline.

15
  • GSM7990394 Sample 113NT Non tumor tissue normal tissue Control marker detected. Liver disease state: HBV-related HCC; tissue: Liver; tissue type: Non tumor tissue
  • GSM7990396 Sample 43NT Non tumor tissue normal tissue Control marker detected. Liver disease state: HBV-related HCC; tissue: Liver; tissue type: Non tumor tissue
  • GSM7990398 Sample FS1_NT Normal liver tissue normal tissue Control marker detected. Liver disease state: control; tissue: Liver; tissue type: Normal liver tissue
  • GSM7990399 Sample FS2_NT Normal liver tissue normal tissue Control marker detected. Liver disease state: control; tissue: Liver; tissue type: Normal liver tissue
  • GSM7990400 Sample FS6_NT Normal liver tissue normal tissue Control marker detected. Liver disease state: control; tissue: Liver; tissue type: Normal liver tissue
  • GSM7990401 Sample FS12_NT Normal liver tissue normal tissue Control marker detected. Liver disease state: control; tissue: Liver; tissue type: Normal liver tissue
  • GSM7990402 Sample FS43_NT Normal liver tissue normal tissue Control marker detected. Liver disease state: control; tissue: Liver; tissue type: Normal liver tissue
  • GSM7990403 Sample 105NT Non tumor tissue normal tissue Control marker detected. Liver disease state: HBV-related HCC; tissue: Liver; tissue type: Non tumor tissue
  • GSM7990405 Sample 51NT Non tumor tissue normal tissue Control marker detected. Liver disease state: HBV-related HCC; tissue: Liver; tissue type: Non tumor tissue
  • GSM7990407 Sample 150NT Non tumor tissue normal tissue Control marker detected. Liver disease state: HBV-related HCC; tissue: Liver; tissue type: Non tumor tissue
  • GSM7990409 Sample 141NT Non tumor tissue normal tissue Control marker detected. Liver disease state: HBV-related HCC; tissue: Liver; tissue type: Non tumor tissue
  • GSM7990412 Sample 144NT Non tumor tissue normal tissue Control marker detected. Liver disease state: HBV-related HCC; tissue: Liver; tissue type: Non tumor tissue
  • GSM7990414 Sample 13NT Non tumor tissue normal tissue Control marker detected. Liver disease state: HBV-related HCC; tissue: Liver; tissue type: Non tumor tissue
  • GSM7990416 Sample 28NT Non tumor tissue normal tissue Control marker detected. Liver disease state: HBV-related HCC; tissue: Liver; tissue type: Non tumor tissue
  • GSM7990418 Sample 34NT Non tumor tissue normal tissue Control marker detected. Liver disease state: HBV-related HCC; tissue: Liver; tissue type: Non tumor 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

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 was not normalized. Tissue clarity: Tissue metadata normalized. Treatment clarity: No unclear treatment split detected in the sample metadata. Replicate clarity: No pooled sample or technical replicate flags detected. Data availability clarity: Dataset-level processed or raw data availability is explicit.

Detected Sample Groups

normal tissue

15 samples
  • GSM7990394 Sample 113NT Non tumor tissue Liver disease state: HBV-related HCC; tissue: Liver; tissue type: Non tumor tissue
  • GSM7990396 Sample 43NT Non tumor tissue Liver disease state: HBV-related HCC; tissue: Liver; tissue type: Non tumor tissue
  • GSM7990398 Sample FS1_NT Normal liver tissue Liver disease state: control; tissue: Liver; tissue type: Normal liver tissue
  • GSM7990399 Sample FS2_NT Normal liver tissue Liver disease state: control; tissue: Liver; tissue type: Normal liver tissue
  • GSM7990400 Sample FS6_NT Normal liver tissue Liver disease state: control; tissue: Liver; tissue type: Normal liver tissue
  • GSM7990401 Sample FS12_NT Normal liver tissue Liver disease state: control; tissue: Liver; tissue type: Normal liver tissue
  • GSM7990402 Sample FS43_NT Normal liver tissue Liver disease state: control; tissue: Liver; tissue type: Normal liver tissue
  • GSM7990403 Sample 105NT Non tumor tissue Liver disease state: HBV-related HCC; tissue: Liver; tissue type: Non tumor tissue
  • GSM7990405 Sample 51NT Non tumor tissue Liver disease state: HBV-related HCC; tissue: Liver; tissue type: Non tumor tissue
  • GSM7990407 Sample 150NT Non tumor tissue Liver disease state: HBV-related HCC; tissue: Liver; tissue type: Non tumor tissue
  • GSM7990409 Sample 141NT Non tumor tissue Liver disease state: HBV-related HCC; tissue: Liver; tissue type: Non tumor tissue
  • GSM7990412 Sample 144NT Non tumor tissue Liver disease state: HBV-related HCC; tissue: Liver; tissue type: Non tumor tissue
  • GSM7990414 Sample 13NT Non tumor tissue Liver disease state: HBV-related HCC; tissue: Liver; tissue type: Non tumor tissue
  • GSM7990416 Sample 28NT Non tumor tissue Liver disease state: HBV-related HCC; tissue: Liver; tissue type: Non tumor tissue
  • GSM7990418 Sample 34NT Non tumor tissue Liver disease state: HBV-related HCC; tissue: Liver; tissue type: Non tumor tissue

tumor sample

10 samples
  • GSM7990395 Sample 113T Tumor tissue Liver disease state: HBV-related HCC; tissue: Liver; tissue type: Tumor tissue
  • GSM7990397 Sample 43T Tumor tissue Liver disease state: HBV-related HCC; tissue: Liver; tissue type: Tumor tissue
  • GSM7990404 Sample 34T Tumor tissue Liver disease state: HBV-related HCC; tissue: Liver; tissue type: Tumor tissue
  • GSM7990406 Sample 51T Tumor tissue Liver disease state: HBV-related HCC; tissue: Liver; tissue type: Tumor tissue
  • GSM7990408 Sample 150T Tumor tissue Liver disease state: HBV-related HCC; tissue: Liver; tissue type: Tumor tissue
  • GSM7990410 Sample 141T Tumor tissue Liver disease state: HBV-related HCC; tissue: Liver; tissue type: Tumor tissue
  • GSM7990411 Sample 105T Tumor tissue Liver disease state: HBV-related HCC; tissue: Liver; tissue type: Tumor tissue
  • GSM7990413 Sample 144T Tumor tissue Liver disease state: HBV-related HCC; tissue: Liver; tissue type: Tumor tissue
  • GSM7990415 Sample 13T Tumor tissue Liver disease state: HBV-related HCC; tissue: Liver; tissue type: Tumor tissue
  • GSM7990417 Sample 28T Tumor tissue Liver disease state: HBV-related HCC; tissue: Liver; tissue type: Tumor tissue

Score Breakdown

60%

relevance

  • Organism normalized.
  • Assay type normalized.
  • Tissue metadata normalized.
0%

comparison suitability

  • Tumor and normal sample groups detected.
  • No excluded sample type flags detected.
  • Tumor/normal design boosted for colorectal tumor-vs-normal tissue triage.
  • Patient tissue or biopsy specimens boosted for tissue comparison triage.
  • Non-colorectal cancer context downgraded for colorectal tumor-vs-normal tissue ranking.
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 was not normalized.
  • Tissue clarity: Tissue metadata normalized.
  • Treatment clarity: No unclear treatment split detected in the sample metadata.
  • Replicate clarity: No pooled sample or technical replicate flags detected.
  • Data availability clarity: Dataset-level processed or raw data availability is explicit.
100%

data availability

  • Processed data available.
  • Raw data available.
34%

overall

  • Weighted score: 30% relevance, 30% comparison suitability, 25% metadata quality, 15% data availability.
  • Overall score capped because comparison suitability is weak for the selected search intent.
  • Overall score capped because tumor/normal grouping is from a non-colorectal cancer context.

Sample Links

25 samples

Review Audit Trail

0 decisions

No review decisions have been stored for this dataset.