Siftome Phase 3L

GSE81550

RNA-Seq expression profiling of hepatocellular carcinoma and adjacent non-tumor liver tissues

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
2016-05-18
Last update
2019-05-15
Organization
Tulane University
Department
Pathology
Public date
2016-11-18
Experiment types
Expression profiling by high throughput sequencing
Platforms
GPL11154 Illumina HiSeq 2000 (Homo sapiens)
Series type
Series
SubSeries
Not available
BioProject
PRJNA321974
Supplementary files
TAR: GSE81550_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
GSE81550
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
GSE81550
  • 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
GSE81550
  • 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
GSE81550
  • 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: GSE81550
dataset_title: RNA-Seq expression profiling of hepatocellular carcinoma and adjacent non-tumor liver tissues
organism: Homo sapiens
assay_type: bulk RNA-seq
processed_data_available: true
raw_data_available: true
submission_date: 2016-05-18
last_update_date: 2019-05-15
organization_name: Tulane University
department: Pathology
public_date: 2016-11-18
experiment_types: Expression profiling by high throughput sequencing
platforms: GPL11154 Illumina HiSeq 2000 (Homo sapiens)
sub_series: Not available
bioproject: PRJNA321974
supplementary_files: TAR: GSE81550_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

12 fields
Field Value Source Origin Confidence Evidence Reason
assay_type bulk RNA-seq dataset GSE81550 Runtime Siftome inference GEO:dataset:GSE81550:60a2886c1d50b2c5edb78388574144d28451c54362a345c12a8c129bd43ed09b high confidence bulk rna-seq dataset_accession: GSE81550 dataset_title: RNA-Seq expression profiling of hepatocellular carcinoma and adjacent non-tumor liver tissues organism: Homo sapiens assay_type: bulk ... keyword match keyword match: bulk rna-seq
organism Homo sapiens dataset GSE81550 Runtime Siftome inference GEO:dataset:GSE81550:60a2886c1d50b2c5edb78388574144d28451c54362a345c12a8c129bd43ed09b high confidence homo sapiens dataset_accession: GSE81550 dataset_title: RNA-Seq expression profiling of hepatocellular carcinoma and adjacent non-tumor liver tissues organism: Homo sapiens assay_type: bulk ... keyword match keyword match: homo sapiens
sample_type tumor sample sample GSM2157097 Runtime Siftome inference GEO:sample:GSM2157097:2a0acfb45a9d5c62f4946adc78e238e3a576c7da83c07a1e07a1a86f5986c104 low confidence tumor sample_accession: GSM2157097 sample_title: HCC tissue_p1 [0FU_t] source_name: HCC tissue characteristics: tissue type: hepatocellular carcinoma (HCC); tumor stage: stage II HCC ... controlled vocabulary controlled vocabulary sample type match: tumor
sample_type normal tissue sample GSM2157098 Runtime Siftome inference GEO:sample:GSM2157098:656893ff2f7c4182450141ed19e8b4d8f06c69a044599eed6157d0157c45a756 medium confidence non-tumor sample_accession: GSM2157098 sample_title: Adjacent liver tissue_p1 [0FU_nt] source_name: Adjacent liver tissue characteristics: tissue type: adjacent non-tumor tissue; tumor st... controlled vocabulary controlled vocabulary sample type match: non-tumor
sample_type tumor sample sample GSM2157099 Runtime Siftome inference GEO:sample:GSM2157099:9f7bfddf0f148e00abc596b7bac258ef901967180dbb778b213e79a0d1f92c85 low confidence tumor sample_accession: GSM2157099 sample_title: HCC tissue_p2 [0MB_t] source_name: HCC tissue characteristics: tissue type: hepatocellular carcinoma (HCC); tumor stage: stage II HCC ... controlled vocabulary controlled vocabulary sample type match: tumor
sample_type normal tissue sample GSM2157100 Runtime Siftome inference GEO:sample:GSM2157100:9f21d91b5be06e72d279894c864d430414df01ef946bf765fcd938313f22aa79 medium confidence non-tumor sample_accession: GSM2157100 sample_title: Adjacent liver tissue_p2 [0MB_nt] source_name: Adjacent liver tissue characteristics: tissue type: adjacent non-tumor tissue; tumor st... controlled vocabulary controlled vocabulary sample type match: non-tumor
sample_type tumor sample sample GSM2157101 Runtime Siftome inference GEO:sample:GSM2157101:78728fef4c057e14c1ffd9fadb9ca09c9fe2a1ba45bb3d83d501d009fd2c5886 low confidence tumor sample_accession: GSM2157101 sample_title: HCC tissue_p3 [00Q_t] source_name: HCC tissue characteristics: tissue type: hepatocellular carcinoma (HCC); tumor stage: stage I HCC t... controlled vocabulary controlled vocabulary sample type match: tumor
sample_type normal tissue sample GSM2157102 Runtime Siftome inference GEO:sample:GSM2157102:718e9a085c424d76f9a245346f610cc6441f98bfa5b41efa345af6f9b8bddf1e medium confidence non-tumor sample_accession: GSM2157102 sample_title: Adjacent liver tissue_p3 [00Q_nt] source_name: Adjacent liver tissue characteristics: tissue type: adjacent non-tumor tissue; tumor st... controlled vocabulary controlled vocabulary sample type match: non-tumor
tissue liver dataset GSE81550 Runtime Siftome inference GEO:dataset:GSE81550:60a2886c1d50b2c5edb78388574144d28451c54362a345c12a8c129bd43ed09b low confidence liver dataset_accession: GSE81550 dataset_title: RNA-Seq expression profiling of hepatocellular carcinoma and adjacent non-tumor liver tissues organism: Homo sapiens assay_type: bulk ... controlled vocabulary controlled vocabulary tissue match: liver
tissue liver sample GSM2157098 Runtime Siftome inference GEO:sample:GSM2157098:656893ff2f7c4182450141ed19e8b4d8f06c69a044599eed6157d0157c45a756 low confidence liver sample_accession: GSM2157098 sample_title: Adjacent liver tissue_p1 [0FU_nt] source_name: Adjacent liver tissue characteristics: tissue type: adjacent non-tumor tissue; tumor st... controlled vocabulary controlled vocabulary tissue match: liver
tissue liver sample GSM2157100 Runtime Siftome inference GEO:sample:GSM2157100:9f21d91b5be06e72d279894c864d430414df01ef946bf765fcd938313f22aa79 low confidence liver sample_accession: GSM2157100 sample_title: Adjacent liver tissue_p2 [0MB_nt] source_name: Adjacent liver tissue characteristics: tissue type: adjacent non-tumor tissue; tumor st... controlled vocabulary controlled vocabulary tissue match: liver
tissue liver sample GSM2157102 Runtime Siftome inference GEO:sample:GSM2157102:718e9a085c424d76f9a245346f610cc6441f98bfa5b41efa345af6f9b8bddf1e low confidence liver sample_accession: GSM2157102 sample_title: Adjacent liver tissue_p3 [00Q_nt] source_name: Adjacent liver tissue characteristics: tissue type: adjacent non-tumor tissue; tumor st... controlled vocabulary controlled vocabulary tissue match: liver

Sample Group Preview

Possible case samples

Samples currently treated as the comparison case group.

3
  • GSM2157097 HCC tissue_p1 [0FU_t] tumor sample Case marker detected. HCC tissue tissue type: hepatocellular carcinoma (HCC); tumor stage: stage II
  • GSM2157099 HCC tissue_p2 [0MB_t] tumor sample Case marker detected. HCC tissue tissue type: hepatocellular carcinoma (HCC); tumor stage: stage II
  • GSM2157101 HCC tissue_p3 [00Q_t] tumor sample Case marker detected. HCC tissue tissue type: hepatocellular carcinoma (HCC); tumor stage: stage I

Possible control samples

Samples currently treated as controls or baseline.

3
  • GSM2157098 Adjacent liver tissue_p1 [0FU_nt] normal tissue Control marker detected. Adjacent liver tissue tissue type: adjacent non-tumor tissue; tumor stage: stage II
  • GSM2157100 Adjacent liver tissue_p2 [0MB_nt] normal tissue Control marker detected. Adjacent liver tissue tissue type: adjacent non-tumor tissue; tumor stage: stage II
  • GSM2157102 Adjacent liver tissue_p3 [00Q_nt] normal tissue Control marker detected. Adjacent liver tissue tissue type: adjacent non-tumor tissue; tumor stage: stage I

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

tumor sample

3 samples
  • GSM2157097 HCC tissue_p1 [0FU_t] HCC tissue tissue type: hepatocellular carcinoma (HCC); tumor stage: stage II
  • GSM2157099 HCC tissue_p2 [0MB_t] HCC tissue tissue type: hepatocellular carcinoma (HCC); tumor stage: stage II
  • GSM2157101 HCC tissue_p3 [00Q_t] HCC tissue tissue type: hepatocellular carcinoma (HCC); tumor stage: stage I

normal tissue

3 samples
  • GSM2157098 Adjacent liver tissue_p1 [0FU_nt] Adjacent liver tissue tissue type: adjacent non-tumor tissue; tumor stage: stage II
  • GSM2157100 Adjacent liver tissue_p2 [0MB_nt] Adjacent liver tissue tissue type: adjacent non-tumor tissue; tumor stage: stage II
  • GSM2157102 Adjacent liver tissue_p3 [00Q_nt] Adjacent liver tissue tissue type: adjacent non-tumor tissue; tumor stage: stage I

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.