Siftome Phase 3L

GSE97214

Transcriptome sequencing identify a recurrent CRYL1-IFT88 chimeric transcript in hepatocellular carcinoma

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
2017-03-29
Last update
2019-05-15
Organization
Fujian Provincial Hospital
Department
Department of Pathology
Public date
2017-04-28
Experiment types
Expression profiling by high throughput sequencing
Platforms
GPL16791 Illumina HiSeq 2500 (Homo sapiens)
Series type
Series
SubSeries
Not available
BioProject
PRJNA380984
Supplementary files
TAR: GSE97214_RAW.tar; TXT: GSE97214_genelist.txt.gz
Organism
Homo sapiens
Assay
bulk RNA-seq
Samples
18
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

Review before analysis
87% 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

12/15 pts

All non-excluded samples are assigned; excluded samples should still be confirmed.

Blocking warnings

0/10 pts

Critical warnings must be resolved before downstream analysis.

Metadata normalization

10/10 pts

Metadata quality is high enough to support downstream handoff.

Blockers

  • Critical dataset warnings must be resolved.

Next Steps

  • Confirm excluded samples before creating the final analysis metadata file.
  • Resolve critical warnings before downstream analysis.

Analysis Preparation Checklist

4/6 ready

Group labels reviewed

Needs review

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

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

Minimum sample count met

Ready

Both groups meet the minimum of 2 samples.

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

Processed counts available

Ready

Processed data availability is marked true in the GEO index.

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

Ambiguous samples handled

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

Needs review

6 samples have hard exclusion flags in the proposed grouping.

Confirm excluded samples and preserve the reason in the analysis handoff.

Source links preserved

Ready

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

Keep GEO dataset and sample links with exported metadata.

Bioinformatician Review

Bioinformatician review required

Ask a bioinformatician to review grouping, count availability, exclusions, and design before DE.

  • Analysis readiness has blockers that must be resolved before DE.
  • Critical dataset warnings are present.

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. Animal sample markers downgraded because this is a human dataset 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 6 samples
  • Likely control group normal tissue 6 samples

Warnings

  • ANIMAL_SAMPLES_IN_HUMAN_DATASET critical Animal sample markers were detected in a human dataset.
  • 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 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: not a colorectal/GI cancer cohort. Derived from current-intent ranking reasons and warnings.

Applied Review Decisions

No active review decisions affect this ranking.

Ranking Facts

  • Recommendation Not suitable Dataset does not meet the current suitability threshold.
  • Supporting fact Tumor vs 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: not a colorectal/GI cancer cohort. Contributed to match or upgrade evidence.
  • Supporting fact Processed data is available for downstream review. Contributed to match or upgrade evidence.
  • Supporting fact 2 warnings require review. Contributed to match or upgrade evidence.
  • Caution fact Animal sample markers were detected in a human dataset. Contributed to downgrade or manual-review 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 Animal sample markers downgraded because this is a human dataset 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: not a colorectal/GI cancer cohort. Contributed to downgrade or manual-review evidence.
  • Caution fact Comparison suitability score is below the Phase 1 recommended threshold. Contributed to downgrade or manual-review evidence.

Manual Corrections

0 active

Source Evidence

4 sources

GEO

Primary source

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

Dataset accession
GSE97214
Sample records
18 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
GSE97214
  • 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
GSE97214
  • 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
GSE97214
  • 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: GSE97214
dataset_title: Transcriptome sequencing identify a recurrent CRYL1-IFT88 chimeric transcript in hepatocellular carcinoma
organism: Homo sapiens
assay_type: bulk RNA-seq
processed_data_available: true
raw_data_available: true
submission_date: 2017-03-29
last_update_date: 2019-05-15
organization_name: Fujian Provincial Hospital
department: Department of Pathology
public_date: 2017-04-28
experiment_types: Expression profiling by high throughput sequencing
platforms: GPL16791 Illumina HiSeq 2500 (Homo sapiens)
sub_series: Not available
bioproject: PRJNA380984
supplementary_files: TAR: GSE97214_RAW.tar; TXT: GSE97214_genelist.txt.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: not a colorectal/GI cancer cohort.
  • Processed data is available for downstream review.
  • 2 warnings require review.

Why It May Not Be Suitable

  • Animal sample markers were detected in a human dataset.
  • Disease or condition label could not be normalized.
  • Non-colorectal cancer context downgraded for colorectal tumor-vs-normal tissue ranking.
  • Animal sample markers downgraded because this is a human dataset 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: not a colorectal/GI cancer cohort.
  • Comparison suitability score is below the Phase 1 recommended threshold.

Warnings

  • critical ANIMAL_SAMPLES_IN_HUMAN_DATASET Animal sample markers were detected in a human dataset.
  • warning DISEASE_LABEL_UNCLEAR Disease or condition label could not be normalized.

Normalized Fields

38 fields
Field Value Source Origin Confidence Evidence Reason
assay_type bulk RNA-seq dataset GSE97214 Runtime Siftome inference GEO:dataset:GSE97214:94ffe118e09afbc90b58a5cd92b08e6c946c7b49a7de3ece26f2db23d667236e high confidence bulk rna-seq dataset_accession: GSE97214 dataset_title: Transcriptome sequencing identify a recurrent CRYL1-IFT88 chimeric transcript in hepatocellular carcinoma organism: Homo sapiens assay... keyword match keyword match: bulk rna-seq
organism Homo sapiens dataset GSE97214 Runtime Siftome inference GEO:dataset:GSE97214:94ffe118e09afbc90b58a5cd92b08e6c946c7b49a7de3ece26f2db23d667236e high confidence homo sapiens dataset_accession: GSE97214 dataset_title: Transcriptome sequencing identify a recurrent CRYL1-IFT88 chimeric transcript in hepatocellular carcinoma organism: Homo sapiens assay... keyword match keyword match: homo sapiens
sample_type normal tissue sample GSM2559738 Runtime Siftome inference GEO:sample:GSM2559738:b68c58b0088a163a3b235b3c0f69e6bef1736167dc3f21ccef532af375ea7e99 medium confidence non-tumor sample_accession: GSM2559738 sample_title: Poorly differentiated P10N source_name: liver, non-tumor characteristics: disease state: hepatocellular carcinoma (HCC); tissue: adjac... controlled vocabulary controlled vocabulary sample type match: non-tumor
sample_type tumor sample sample GSM2559739 Runtime Siftome inference GEO:sample:GSM2559739:b0ea27c4e2d79131252fde57f282164fdd376cd476ee0ad473a50042b9e28baa low confidence tumor sample_accession: GSM2559739 sample_title: Poorly differentiated P10T source_name: liver, tumor characteristics: disease state: hepatocellular carcinoma (HCC); tissue: liver tum... controlled vocabulary controlled vocabulary sample type match: tumor
sample_type normal tissue sample GSM2559740 Runtime Siftome inference GEO:sample:GSM2559740:c833ed77253c52425638a7751b55a912ed768d858464eaded1f339b898ad2f20 medium confidence non-tumor sample_accession: GSM2559740 sample_title: Poorly differentiated P14N source_name: liver, non-tumor characteristics: disease state: hepatocellular carcinoma (HCC); tissue: adjac... controlled vocabulary controlled vocabulary sample type match: non-tumor
sample_type tumor sample sample GSM2559741 Runtime Siftome inference GEO:sample:GSM2559741:da0a7c563e717de5628d8fe01f30eecf70af18417da946865f43724e5b86a6a9 low confidence tumor sample_accession: GSM2559741 sample_title: Poorly differentiated P14T source_name: liver, tumor characteristics: disease state: hepatocellular carcinoma (HCC); tissue: liver tum... controlled vocabulary controlled vocabulary sample type match: tumor
sample_type normal tissue sample GSM2559742 Runtime Siftome inference GEO:sample:GSM2559742:8037e0a80bd751699b9748f48945fe75dd73395880a29928da5c38a48f96d2fc medium confidence non-tumor sample_accession: GSM2559742 sample_title: Poorly differentiated P17N source_name: liver, non-tumor characteristics: disease state: hepatocellular carcinoma (HCC); tissue: adjac... controlled vocabulary controlled vocabulary sample type match: non-tumor
sample_type tumor sample sample GSM2559743 Runtime Siftome inference GEO:sample:GSM2559743:7dc7f9797a85db7c1e5e4138f705037adcd44a5a06deea8eb0ea50fe7ce23996 low confidence tumor sample_accession: GSM2559743 sample_title: Poorly differentiated P17T source_name: liver, tumor characteristics: disease state: hepatocellular carcinoma (HCC); tissue: liver tum... controlled vocabulary controlled vocabulary sample type match: tumor
sample_type normal tissue sample GSM2559744 Runtime Siftome inference GEO:sample:GSM2559744:ba788a4e3c3b838ec39a1927acb04a1f1a42bbbbf668b6d5e0f0837b69a1b8ec medium confidence non-tumor sample_accession: GSM2559744 sample_title: Moderately differentiated P26N source_name: liver, non-tumor characteristics: disease state: hepatocellular carcinoma (HCC); tissue: a... controlled vocabulary controlled vocabulary sample type match: non-tumor
sample_type tumor sample sample GSM2559745 Runtime Siftome inference GEO:sample:GSM2559745:13019a0b2d641c0f88d912255a464a5e1694a70b2706783639bf0190310f129e low confidence tumor sample_accession: GSM2559745 sample_title: Moderately differentiated P26T source_name: liver, tumor characteristics: disease state: hepatocellular carcinoma (HCC); tissue: liver... controlled vocabulary controlled vocabulary sample type match: tumor
sample_type normal tissue sample GSM2559746 Runtime Siftome inference GEO:sample:GSM2559746:83f91f5d3d0bf7c5c84390b355a7003c949149ef52248602fe49c5205a81e75a medium confidence non-tumor sample_accession: GSM2559746 sample_title: Moderately differentiated P29N source_name: liver, non-tumor characteristics: disease state: hepatocellular carcinoma (HCC); tissue: a... controlled vocabulary controlled vocabulary sample type match: non-tumor
sample_type tumor sample sample GSM2559747 Runtime Siftome inference GEO:sample:GSM2559747:94a664a0e0a86186edf63b6007e1917e3065d9d4c224d3bab7bbb03c9176a99d low confidence tumor sample_accession: GSM2559747 sample_title: Moderately differentiated P29T source_name: liver, tumor characteristics: disease state: hepatocellular carcinoma (HCC); tissue: liver... controlled vocabulary controlled vocabulary sample type match: tumor
sample_type normal tissue sample GSM2559748 Runtime Siftome inference GEO:sample:GSM2559748:ca6cffa683b4b3d145ea2877fdd4ba4cc70f2378dffc67e6bcc62260ecfc9fe2 medium confidence non-tumor sample_accession: GSM2559748 sample_title: Moderately differentiated P36N source_name: liver, non-tumor characteristics: disease state: hepatocellular carcinoma (HCC); tissue: a... controlled vocabulary controlled vocabulary sample type match: non-tumor
sample_type tumor sample sample GSM2559749 Runtime Siftome inference GEO:sample:GSM2559749:a970a441a74b1a0b33b45a7271da75aca4116c41b1635e156f3a963394663632 low confidence tumor sample_accession: GSM2559749 sample_title: Moderately differentiated P36T source_name: liver, tumor characteristics: disease state: hepatocellular carcinoma (HCC); tissue: liver... controlled vocabulary controlled vocabulary sample type match: tumor
sample_type normal tissue sample GSM2559750 Runtime Siftome inference GEO:sample:GSM2559750:a986a87f75627917884449f55a7e50f62a5faaa639dbc4ee4323eeadde3762dd medium confidence non-tumor sample_accession: GSM2559750 sample_title: Highly differentiated P21N source_name: liver, non-tumor characteristics: disease state: hepatocellular carcinoma (HCC); tissue: adjac... controlled vocabulary controlled vocabulary sample type match: non-tumor
sample_type tumor sample sample GSM2559751 Runtime Siftome inference GEO:sample:GSM2559751:305b009afa21308c54cad5283924d5632fb7b51b82713bafa3c3a62f9498ad2c low confidence tumor sample_accession: GSM2559751 sample_title: Highly differentiated P21T source_name: liver, tumor characteristics: disease state: hepatocellular carcinoma (HCC); tissue: liver tum... controlled vocabulary controlled vocabulary sample type match: tumor
sample_type normal tissue sample GSM2559752 Runtime Siftome inference GEO:sample:GSM2559752:4e5c89a9893ed553737905729dc521a60cff7be0aa6ac54559f9ac6512a84279 medium confidence non-tumor sample_accession: GSM2559752 sample_title: Highly differentiated P24N source_name: liver, non-tumor characteristics: disease state: hepatocellular carcinoma (HCC); tissue: adjac... controlled vocabulary controlled vocabulary sample type match: non-tumor
sample_type tumor sample sample GSM2559753 Runtime Siftome inference GEO:sample:GSM2559753:a87ed3161e550a99da670e5c8fb31e588dc41e0a88372fe83629d3d53b51aaef low confidence tumor sample_accession: GSM2559753 sample_title: Highly differentiated P24T source_name: liver, tumor characteristics: disease state: hepatocellular carcinoma (HCC); tissue: liver tum... controlled vocabulary controlled vocabulary sample type match: tumor
sample_type normal tissue sample GSM2559754 Runtime Siftome inference GEO:sample:GSM2559754:fe701a59de23b167c26cb8593391477c9e54b8bc2091d20829c1fd7551abb193 medium confidence non-tumor sample_accession: GSM2559754 sample_title: Highly differentiated P40N source_name: liver, non-tumor characteristics: disease state: hepatocellular carcinoma (HCC); tissue: adjac... controlled vocabulary controlled vocabulary sample type match: non-tumor
sample_type tumor sample sample GSM2559755 Runtime Siftome inference GEO:sample:GSM2559755:8137227b7e05670c2cc506cc469bb7d4405d7e925dccd725a0a5ae9c9e9d2817 low confidence tumor sample_accession: GSM2559755 sample_title: Highly differentiated P40T source_name: liver, tumor characteristics: disease state: hepatocellular carcinoma (HCC); tissue: liver tum... controlled vocabulary controlled vocabulary sample type match: tumor
tissue liver sample GSM2559738 Runtime Siftome inference GEO:sample:GSM2559738:b68c58b0088a163a3b235b3c0f69e6bef1736167dc3f21ccef532af375ea7e99 low confidence liver sample_accession: GSM2559738 sample_title: Poorly differentiated P10N source_name: liver, non-tumor characteristics: disease state: hepatocellular carcinoma (HCC); tissue: adjac... controlled vocabulary controlled vocabulary tissue match: liver
tissue liver sample GSM2559739 Runtime Siftome inference GEO:sample:GSM2559739:b0ea27c4e2d79131252fde57f282164fdd376cd476ee0ad473a50042b9e28baa low confidence liver sample_accession: GSM2559739 sample_title: Poorly differentiated P10T source_name: liver, tumor characteristics: disease state: hepatocellular carcinoma (HCC); tissue: liver tum... controlled vocabulary controlled vocabulary tissue match: liver
tissue liver sample GSM2559740 Runtime Siftome inference GEO:sample:GSM2559740:c833ed77253c52425638a7751b55a912ed768d858464eaded1f339b898ad2f20 low confidence liver sample_accession: GSM2559740 sample_title: Poorly differentiated P14N source_name: liver, non-tumor characteristics: disease state: hepatocellular carcinoma (HCC); tissue: adjac... controlled vocabulary controlled vocabulary tissue match: liver
tissue liver sample GSM2559741 Runtime Siftome inference GEO:sample:GSM2559741:da0a7c563e717de5628d8fe01f30eecf70af18417da946865f43724e5b86a6a9 low confidence liver sample_accession: GSM2559741 sample_title: Poorly differentiated P14T source_name: liver, tumor characteristics: disease state: hepatocellular carcinoma (HCC); tissue: liver tum... controlled vocabulary controlled vocabulary tissue match: liver
tissue liver sample GSM2559742 Runtime Siftome inference GEO:sample:GSM2559742:8037e0a80bd751699b9748f48945fe75dd73395880a29928da5c38a48f96d2fc low confidence liver sample_accession: GSM2559742 sample_title: Poorly differentiated P17N source_name: liver, non-tumor characteristics: disease state: hepatocellular carcinoma (HCC); tissue: adjac... controlled vocabulary controlled vocabulary tissue match: liver
tissue liver sample GSM2559743 Runtime Siftome inference GEO:sample:GSM2559743:7dc7f9797a85db7c1e5e4138f705037adcd44a5a06deea8eb0ea50fe7ce23996 low confidence liver sample_accession: GSM2559743 sample_title: Poorly differentiated P17T source_name: liver, tumor characteristics: disease state: hepatocellular carcinoma (HCC); tissue: liver tum... controlled vocabulary controlled vocabulary tissue match: liver
tissue liver sample GSM2559744 Runtime Siftome inference GEO:sample:GSM2559744:ba788a4e3c3b838ec39a1927acb04a1f1a42bbbbf668b6d5e0f0837b69a1b8ec low confidence liver sample_accession: GSM2559744 sample_title: Moderately differentiated P26N source_name: liver, non-tumor characteristics: disease state: hepatocellular carcinoma (HCC); tissue: a... controlled vocabulary controlled vocabulary tissue match: liver
tissue liver sample GSM2559745 Runtime Siftome inference GEO:sample:GSM2559745:13019a0b2d641c0f88d912255a464a5e1694a70b2706783639bf0190310f129e low confidence liver sample_accession: GSM2559745 sample_title: Moderately differentiated P26T source_name: liver, tumor characteristics: disease state: hepatocellular carcinoma (HCC); tissue: liver... controlled vocabulary controlled vocabulary tissue match: liver
tissue liver sample GSM2559746 Runtime Siftome inference GEO:sample:GSM2559746:83f91f5d3d0bf7c5c84390b355a7003c949149ef52248602fe49c5205a81e75a low confidence liver sample_accession: GSM2559746 sample_title: Moderately differentiated P29N source_name: liver, non-tumor characteristics: disease state: hepatocellular carcinoma (HCC); tissue: a... controlled vocabulary controlled vocabulary tissue match: liver
tissue liver sample GSM2559747 Runtime Siftome inference GEO:sample:GSM2559747:94a664a0e0a86186edf63b6007e1917e3065d9d4c224d3bab7bbb03c9176a99d low confidence liver sample_accession: GSM2559747 sample_title: Moderately differentiated P29T source_name: liver, tumor characteristics: disease state: hepatocellular carcinoma (HCC); tissue: liver... controlled vocabulary controlled vocabulary tissue match: liver
tissue liver sample GSM2559748 Runtime Siftome inference GEO:sample:GSM2559748:ca6cffa683b4b3d145ea2877fdd4ba4cc70f2378dffc67e6bcc62260ecfc9fe2 low confidence liver sample_accession: GSM2559748 sample_title: Moderately differentiated P36N source_name: liver, non-tumor characteristics: disease state: hepatocellular carcinoma (HCC); tissue: a... controlled vocabulary controlled vocabulary tissue match: liver
tissue liver sample GSM2559749 Runtime Siftome inference GEO:sample:GSM2559749:a970a441a74b1a0b33b45a7271da75aca4116c41b1635e156f3a963394663632 low confidence liver sample_accession: GSM2559749 sample_title: Moderately differentiated P36T source_name: liver, tumor characteristics: disease state: hepatocellular carcinoma (HCC); tissue: liver... controlled vocabulary controlled vocabulary tissue match: liver
tissue liver sample GSM2559750 Runtime Siftome inference GEO:sample:GSM2559750:a986a87f75627917884449f55a7e50f62a5faaa639dbc4ee4323eeadde3762dd low confidence liver sample_accession: GSM2559750 sample_title: Highly differentiated P21N source_name: liver, non-tumor characteristics: disease state: hepatocellular carcinoma (HCC); tissue: adjac... controlled vocabulary controlled vocabulary tissue match: liver
tissue liver sample GSM2559751 Runtime Siftome inference GEO:sample:GSM2559751:305b009afa21308c54cad5283924d5632fb7b51b82713bafa3c3a62f9498ad2c low confidence liver sample_accession: GSM2559751 sample_title: Highly differentiated P21T source_name: liver, tumor characteristics: disease state: hepatocellular carcinoma (HCC); tissue: liver tum... controlled vocabulary controlled vocabulary tissue match: liver
tissue liver sample GSM2559752 Runtime Siftome inference GEO:sample:GSM2559752:4e5c89a9893ed553737905729dc521a60cff7be0aa6ac54559f9ac6512a84279 low confidence liver sample_accession: GSM2559752 sample_title: Highly differentiated P24N source_name: liver, non-tumor characteristics: disease state: hepatocellular carcinoma (HCC); tissue: adjac... controlled vocabulary controlled vocabulary tissue match: liver
tissue liver sample GSM2559753 Runtime Siftome inference GEO:sample:GSM2559753:a87ed3161e550a99da670e5c8fb31e588dc41e0a88372fe83629d3d53b51aaef low confidence liver sample_accession: GSM2559753 sample_title: Highly differentiated P24T source_name: liver, tumor characteristics: disease state: hepatocellular carcinoma (HCC); tissue: liver tum... controlled vocabulary controlled vocabulary tissue match: liver
tissue liver sample GSM2559754 Runtime Siftome inference GEO:sample:GSM2559754:fe701a59de23b167c26cb8593391477c9e54b8bc2091d20829c1fd7551abb193 low confidence liver sample_accession: GSM2559754 sample_title: Highly differentiated P40N source_name: liver, non-tumor characteristics: disease state: hepatocellular carcinoma (HCC); tissue: adjac... controlled vocabulary controlled vocabulary tissue match: liver
tissue liver sample GSM2559755 Runtime Siftome inference GEO:sample:GSM2559755:8137227b7e05670c2cc506cc469bb7d4405d7e925dccd725a0a5ae9c9e9d2817 low confidence liver sample_accession: GSM2559755 sample_title: Highly differentiated P40T source_name: liver, tumor characteristics: disease state: hepatocellular carcinoma (HCC); tissue: liver tum... controlled vocabulary controlled vocabulary tissue match: liver

Sample Group Preview

Possible case samples

Samples currently treated as the comparison case group.

6
  • GSM2559739 Poorly differentiated P10T tumor sample Case marker detected. liver, tumor disease state: hepatocellular carcinoma (HCC); tissue: liver tumor; differentiation: Poorly; tumor stage: A2(BCLC); patient id: P10
  • GSM2559741 Poorly differentiated P14T tumor sample Case marker detected. liver, tumor disease state: hepatocellular carcinoma (HCC); tissue: liver tumor; differentiation: Poorly; tumor stage: B(BCLC); patient id: P14
  • GSM2559743 Poorly differentiated P17T tumor sample Case marker detected. liver, tumor disease state: hepatocellular carcinoma (HCC); tissue: liver tumor; differentiation: Poorly; tumor stage: A3(BCLC); patient id: P17
  • GSM2559751 Highly differentiated P21T tumor sample Case marker detected. liver, tumor disease state: hepatocellular carcinoma (HCC); tissue: liver tumor; differentiation: Highly; tumor stage: 0(BCLC); patient id: P21
  • GSM2559753 Highly differentiated P24T tumor sample Case marker detected. liver, tumor disease state: hepatocellular carcinoma (HCC); tissue: liver tumor; differentiation: Highly; tumor stage: B(BCLC); patient id: P24
  • GSM2559755 Highly differentiated P40T tumor sample Case marker detected. liver, tumor disease state: hepatocellular carcinoma (HCC); tissue: liver tumor; differentiation: Highly; tumor stage: A1(BCLC); patient id: P40

Possible control samples

Samples currently treated as controls or baseline.

6
  • GSM2559738 Poorly differentiated P10N normal tissue Control marker detected. liver, non-tumor disease state: hepatocellular carcinoma (HCC); tissue: adjacent non-tumorous liver; differentiation: Poorly; tumor stage: A2(BCLC); patient id: P10
  • GSM2559740 Poorly differentiated P14N normal tissue Control marker detected. liver, non-tumor disease state: hepatocellular carcinoma (HCC); tissue: adjacent non-tumorous liver; differentiation: Poorly; tumor stage: B(BCLC); patient id: P14
  • GSM2559742 Poorly differentiated P17N normal tissue Control marker detected. liver, non-tumor disease state: hepatocellular carcinoma (HCC); tissue: adjacent non-tumorous liver; differentiation: Poorly; tumor stage: A3(BCLC); patient id: P17
  • GSM2559750 Highly differentiated P21N normal tissue Control marker detected. liver, non-tumor disease state: hepatocellular carcinoma (HCC); tissue: adjacent non-tumorous liver; differentiation: Highly; tumor stage: 0(BCLC); patient id: P21
  • GSM2559752 Highly differentiated P24N normal tissue Control marker detected. liver, non-tumor disease state: hepatocellular carcinoma (HCC); tissue: adjacent non-tumorous liver; differentiation: Highly; tumor stage: B(BCLC); patient id: P24
  • GSM2559754 Highly differentiated P40N normal tissue Control marker detected. liver, non-tumor disease state: hepatocellular carcinoma (HCC); tissue: adjacent non-tumorous liver; differentiation: Highly; tumor stage: A1(BCLC); patient id: P40

Unassigned samples

Samples with no explicit case or control marker.

0

No samples

Excluded samples

Samples excluded from grouping by hard exclusion rules.

6
  • GSM2559744 Moderately differentiated P26N excluded: animal sample in human dataset animal sample in human dataset: Animal sample marker detected in a human dataset. liver, non-tumor disease state: hepatocellular carcinoma (HCC); tissue: adjacent non-tumorous liver; differentiation: Moderately; tumor stage: B(BCLC); patient id: P26
  • GSM2559745 Moderately differentiated P26T excluded: animal sample in human dataset animal sample in human dataset: Animal sample marker detected in a human dataset. liver, tumor disease state: hepatocellular carcinoma (HCC); tissue: liver tumor; differentiation: Moderately; tumor stage: B(BCLC); patient id: P26
  • GSM2559746 Moderately differentiated P29N excluded: animal sample in human dataset animal sample in human dataset: Animal sample marker detected in a human dataset. liver, non-tumor disease state: hepatocellular carcinoma (HCC); tissue: adjacent non-tumorous liver; differentiation: Moderately; tumor stage: A2(BCLC); patient id: P29
  • GSM2559747 Moderately differentiated P29T excluded: animal sample in human dataset animal sample in human dataset: Animal sample marker detected in a human dataset. liver, tumor disease state: hepatocellular carcinoma (HCC); tissue: liver tumor; differentiation: Moderately; tumor stage: A2(BCLC); patient id: P29
  • GSM2559748 Moderately differentiated P36N excluded: animal sample in human dataset animal sample in human dataset: Animal sample marker detected in a human dataset. liver, non-tumor disease state: hepatocellular carcinoma (HCC); tissue: adjacent non-tumorous liver; differentiation: Moderately; tumor stage: B(BCLC); patient id: P36
  • GSM2559749 Moderately differentiated P36T excluded: animal sample in human dataset animal sample in human dataset: Animal sample marker detected in a human dataset. liver, tumor disease state: hepatocellular carcinoma (HCC); tissue: liver tumor; differentiation: Moderately; tumor stage: B(BCLC); patient id: P36

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

6 samples
  • GSM2559738 Poorly differentiated P10N liver, non-tumor disease state: hepatocellular carcinoma (HCC); tissue: adjacent non-tumorous liver; differentiation: Poorly; tumor stage: A2(BCLC); patient id: P10
  • GSM2559740 Poorly differentiated P14N liver, non-tumor disease state: hepatocellular carcinoma (HCC); tissue: adjacent non-tumorous liver; differentiation: Poorly; tumor stage: B(BCLC); patient id: P14
  • GSM2559742 Poorly differentiated P17N liver, non-tumor disease state: hepatocellular carcinoma (HCC); tissue: adjacent non-tumorous liver; differentiation: Poorly; tumor stage: A3(BCLC); patient id: P17
  • GSM2559750 Highly differentiated P21N liver, non-tumor disease state: hepatocellular carcinoma (HCC); tissue: adjacent non-tumorous liver; differentiation: Highly; tumor stage: 0(BCLC); patient id: P21
  • GSM2559752 Highly differentiated P24N liver, non-tumor disease state: hepatocellular carcinoma (HCC); tissue: adjacent non-tumorous liver; differentiation: Highly; tumor stage: B(BCLC); patient id: P24
  • GSM2559754 Highly differentiated P40N liver, non-tumor disease state: hepatocellular carcinoma (HCC); tissue: adjacent non-tumorous liver; differentiation: Highly; tumor stage: A1(BCLC); patient id: P40

tumor sample

6 samples
  • GSM2559739 Poorly differentiated P10T liver, tumor disease state: hepatocellular carcinoma (HCC); tissue: liver tumor; differentiation: Poorly; tumor stage: A2(BCLC); patient id: P10
  • GSM2559741 Poorly differentiated P14T liver, tumor disease state: hepatocellular carcinoma (HCC); tissue: liver tumor; differentiation: Poorly; tumor stage: B(BCLC); patient id: P14
  • GSM2559743 Poorly differentiated P17T liver, tumor disease state: hepatocellular carcinoma (HCC); tissue: liver tumor; differentiation: Poorly; tumor stage: A3(BCLC); patient id: P17
  • GSM2559751 Highly differentiated P21T liver, tumor disease state: hepatocellular carcinoma (HCC); tissue: liver tumor; differentiation: Highly; tumor stage: 0(BCLC); patient id: P21
  • GSM2559753 Highly differentiated P24T liver, tumor disease state: hepatocellular carcinoma (HCC); tissue: liver tumor; differentiation: Highly; tumor stage: B(BCLC); patient id: P24
  • GSM2559755 Highly differentiated P40T liver, tumor disease state: hepatocellular carcinoma (HCC); tissue: liver tumor; differentiation: Highly; tumor stage: A1(BCLC); patient id: P40

excluded: animal sample in human dataset

6 samples
  • GSM2559744 Moderately differentiated P26N liver, non-tumor disease state: hepatocellular carcinoma (HCC); tissue: adjacent non-tumorous liver; differentiation: Moderately; tumor stage: B(BCLC); patient id: P26
  • GSM2559745 Moderately differentiated P26T liver, tumor disease state: hepatocellular carcinoma (HCC); tissue: liver tumor; differentiation: Moderately; tumor stage: B(BCLC); patient id: P26
  • GSM2559746 Moderately differentiated P29N liver, non-tumor disease state: hepatocellular carcinoma (HCC); tissue: adjacent non-tumorous liver; differentiation: Moderately; tumor stage: A2(BCLC); patient id: P29
  • GSM2559747 Moderately differentiated P29T liver, tumor disease state: hepatocellular carcinoma (HCC); tissue: liver tumor; differentiation: Moderately; tumor stage: A2(BCLC); patient id: P29
  • GSM2559748 Moderately differentiated P36N liver, non-tumor disease state: hepatocellular carcinoma (HCC); tissue: adjacent non-tumorous liver; differentiation: Moderately; tumor stage: B(BCLC); patient id: P36
  • GSM2559749 Moderately differentiated P36T liver, tumor disease state: hepatocellular carcinoma (HCC); tissue: liver tumor; differentiation: Moderately; tumor stage: B(BCLC); patient id: P36

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.
  • Animal sample markers downgraded because this is a human dataset 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

18 samples

Review Audit Trail

0 decisions

No review decisions have been stored for this dataset.