Siftome Phase 3L

GSE33294

Transcriptome sequencing of human 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
2011-10-27
Last update
2019-05-15
Organization
The University of Hong Kong
Department
Centre for PanorOmic Sciences
Public date
2013-04-02
Experiment types
Expression profiling by high throughput sequencing
Platforms
GPL10999 Illumina Genome Analyzer IIx (Homo sapiens)
Series type
Series
SubSeries
Not available
BioProject
PRJNA149267
Supplementary files
TAR: GSE33294_RAW.tar
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
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 fewer than ten samples limit cohort confidence. 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 3 samples
  • Likely control group normal tissue 3 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: 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 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 fewer than ten samples limit cohort confidence. 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
GSE33294
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
GSE33294
  • 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
GSE33294
  • 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
GSE33294
  • 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: GSE33294
dataset_title: Transcriptome sequencing of human hepatocellular carcinoma
organism: Homo sapiens
assay_type: bulk RNA-seq
processed_data_available: true
raw_data_available: true
submission_date: 2011-10-27
last_update_date: 2019-05-15
organization_name: The University of Hong Kong
department: Centre for PanorOmic Sciences
public_date: 2013-04-02
experiment_types: Expression profiling by high throughput sequencing
platforms: GPL10999 Illumina Genome Analyzer IIx (Homo sapiens)
sub_series: Not available
bioproject: PRJNA149267
supplementary_files: TAR: GSE33294_RAW.tar
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.
  • 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 fewer than ten samples limit cohort confidence.
  • 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

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

Normalized Fields

14 fields
Field Value Source Origin Confidence Evidence Reason
assay_type bulk RNA-seq dataset GSE33294 Runtime Siftome inference GEO:dataset:GSE33294:543ae8119b8ec84b6beb28202ed17ba57b4b58546b0de9c12852c35b9cdbae84 high confidence bulk rna-seq dataset_accession: GSE33294 dataset_title: Transcriptome sequencing of human hepatocellular carcinoma organism: Homo sapiens assay_type: bulk RNA-seq processed_data_available: t... keyword match keyword match: bulk rna-seq
organism Homo sapiens dataset GSE33294 Runtime Siftome inference GEO:dataset:GSE33294:543ae8119b8ec84b6beb28202ed17ba57b4b58546b0de9c12852c35b9cdbae84 high confidence homo sapiens dataset_accession: GSE33294 dataset_title: Transcriptome sequencing of human hepatocellular carcinoma organism: Homo sapiens assay_type: bulk RNA-seq processed_data_available: t... keyword match keyword match: homo sapiens
sample_type normal tissue sample GSM823518 Runtime Siftome inference GEO:sample:GSM823518:a59522bb7a18831640e1ef34eb282d2e5a4ea5d1e24a8050b3bbf4ceefcf173c medium confidence non-tumor sample_accession: GSM823518 sample_title: HCC448N source_name: liver tissue, non-tumor characteristics: tissue: liver; phenotype: non-tumor HCC448N controlled vocabulary controlled vocabulary sample type match: non-tumor
sample_type tumor sample sample GSM823519 Runtime Siftome inference GEO:sample:GSM823519:d8a13ca1a5937294b729e978ce83ea23bd20e722a7cd56e7171180448bc3b766 medium confidence carcinoma sample_accession: GSM823519 sample_title: HCC448T source_name: liver tissue, cancerous characteristics: tissue: liver; phenotype: hepatocellular carcinoma HCC448T controlled vocabulary controlled vocabulary sample type match: carcinoma
sample_type normal tissue sample GSM823520 Runtime Siftome inference GEO:sample:GSM823520:e83c5853570620cf040561bb1d7b845c2b997f59211aa3ee71043e4235006361 medium confidence non-tumor sample_accession: GSM823520 sample_title: HCC473N source_name: liver tissue, non-tumor characteristics: tissue: liver; phenotype: non-tumor HCC473N controlled vocabulary controlled vocabulary sample type match: non-tumor
sample_type tumor sample sample GSM823521 Runtime Siftome inference GEO:sample:GSM823521:105fc03322d110dd2a8b03fe3fab938c6769b0e3fe51aeb3dcba98328a366677 medium confidence carcinoma sample_accession: GSM823521 sample_title: HCC473T source_name: liver tissue, cancerous characteristics: tissue: liver; phenotype: hepatocellular carcinoma HCC473T controlled vocabulary controlled vocabulary sample type match: carcinoma
sample_type normal tissue sample GSM823522 Runtime Siftome inference GEO:sample:GSM823522:8a5e6d5a9165384c4e16bb226b8ce9c3db386a6db916a5f0839b8c850fe8d2bf medium confidence non-tumor sample_accession: GSM823522 sample_title: HCC510N source_name: liver tissue, non-tumor characteristics: tissue: liver; phenotype: non-tumor HCC510N controlled vocabulary controlled vocabulary sample type match: non-tumor
sample_type tumor sample sample GSM823523 Runtime Siftome inference GEO:sample:GSM823523:022431595fd2e95ba71319aa93ceb198cb2d5902d1e7bc8cfead51811716120a medium confidence carcinoma sample_accession: GSM823523 sample_title: HCC510T source_name: liver tissue, cancerous characteristics: tissue: liver; phenotype: hepatocellular carcinoma HCC510T controlled vocabulary controlled vocabulary sample type match: carcinoma
tissue liver sample GSM823518 Runtime Siftome inference GEO:sample:GSM823518:a59522bb7a18831640e1ef34eb282d2e5a4ea5d1e24a8050b3bbf4ceefcf173c low confidence liver sample_accession: GSM823518 sample_title: HCC448N source_name: liver tissue, non-tumor characteristics: tissue: liver; phenotype: non-tumor HCC448N controlled vocabulary controlled vocabulary tissue match: liver
tissue liver sample GSM823519 Runtime Siftome inference GEO:sample:GSM823519:d8a13ca1a5937294b729e978ce83ea23bd20e722a7cd56e7171180448bc3b766 low confidence liver sample_accession: GSM823519 sample_title: HCC448T source_name: liver tissue, cancerous characteristics: tissue: liver; phenotype: hepatocellular carcinoma HCC448T controlled vocabulary controlled vocabulary tissue match: liver
tissue liver sample GSM823520 Runtime Siftome inference GEO:sample:GSM823520:e83c5853570620cf040561bb1d7b845c2b997f59211aa3ee71043e4235006361 low confidence liver sample_accession: GSM823520 sample_title: HCC473N source_name: liver tissue, non-tumor characteristics: tissue: liver; phenotype: non-tumor HCC473N controlled vocabulary controlled vocabulary tissue match: liver
tissue liver sample GSM823521 Runtime Siftome inference GEO:sample:GSM823521:105fc03322d110dd2a8b03fe3fab938c6769b0e3fe51aeb3dcba98328a366677 low confidence liver sample_accession: GSM823521 sample_title: HCC473T source_name: liver tissue, cancerous characteristics: tissue: liver; phenotype: hepatocellular carcinoma HCC473T controlled vocabulary controlled vocabulary tissue match: liver
tissue liver sample GSM823522 Runtime Siftome inference GEO:sample:GSM823522:8a5e6d5a9165384c4e16bb226b8ce9c3db386a6db916a5f0839b8c850fe8d2bf low confidence liver sample_accession: GSM823522 sample_title: HCC510N source_name: liver tissue, non-tumor characteristics: tissue: liver; phenotype: non-tumor HCC510N controlled vocabulary controlled vocabulary tissue match: liver
tissue liver sample GSM823523 Runtime Siftome inference GEO:sample:GSM823523:022431595fd2e95ba71319aa93ceb198cb2d5902d1e7bc8cfead51811716120a low confidence liver sample_accession: GSM823523 sample_title: HCC510T source_name: liver tissue, cancerous characteristics: tissue: liver; phenotype: hepatocellular carcinoma HCC510T controlled vocabulary controlled vocabulary tissue match: liver

Sample Group Preview

Possible case samples

Samples currently treated as the comparison case group.

3
  • GSM823519 HCC448T tumor sample Case marker detected. liver tissue, cancerous tissue: liver; phenotype: hepatocellular carcinoma
  • GSM823521 HCC473T tumor sample Case marker detected. liver tissue, cancerous tissue: liver; phenotype: hepatocellular carcinoma
  • GSM823523 HCC510T tumor sample Case marker detected. liver tissue, cancerous tissue: liver; phenotype: hepatocellular carcinoma

Possible control samples

Samples currently treated as controls or baseline.

3
  • GSM823518 HCC448N normal tissue Control marker detected. liver tissue, non-tumor tissue: liver; phenotype: non-tumor
  • GSM823520 HCC473N normal tissue Control marker detected. liver tissue, non-tumor tissue: liver; phenotype: non-tumor
  • GSM823522 HCC510N normal tissue Control marker detected. liver tissue, non-tumor tissue: liver; phenotype: non-tumor

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

3 samples
  • GSM823518 HCC448N liver tissue, non-tumor tissue: liver; phenotype: non-tumor
  • GSM823520 HCC473N liver tissue, non-tumor tissue: liver; phenotype: non-tumor
  • GSM823522 HCC510N liver tissue, non-tumor tissue: liver; phenotype: non-tumor

tumor sample

3 samples
  • GSM823519 HCC448T liver tissue, cancerous tissue: liver; phenotype: hepatocellular carcinoma
  • GSM823521 HCC473T liver tissue, cancerous tissue: liver; phenotype: hepatocellular carcinoma
  • GSM823523 HCC510T liver tissue, cancerous tissue: liver; phenotype: hepatocellular carcinoma

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 fewer than ten samples limit cohort confidence.
  • Overall score capped because tumor/normal grouping is from a non-colorectal cancer context.

Sample Links

6 samples

Review Audit Trail

0 decisions

No review decisions have been stored for this dataset.