Siftome Phase 3L

GSE164441

A selective HDAC8 inhibitor potentiates antitumor immunity and efficacy of immune checkpoint blockade in hepatocellular carcinoma [RNA-seq]

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
2021-01-08
Last update
2021-07-04
Organization
The Chinese University of Hong Kong
Department
School of Biomedical Sciences
Public date
2021-04-04
Experiment types
Expression profiling by high throughput sequencing
Platforms
GPL20301 Illumina HiSeq 4000 (Homo sapiens)
Series type
SubSeries
SubSeries
Not available
BioProject
PRJNA690723
Supplementary files
TXT: GSE164441_RNAseq_10Tvs10NT_cuffdiff_FPKM.txt.gz; TXT: GSE164441_RNAseq_10Tvs10NT_cuffdiff_count.txt.gz
Organism
Homo sapiens
Assay
bulk RNA-seq
Samples
20
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 10 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 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
GSE164441
Sample records
20 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
GSE164441
  • 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
GSE164441
  • 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
GSE164441
  • 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: GSE164441
dataset_title: A selective HDAC8 inhibitor potentiates antitumor immunity and efficacy of immune checkpoint blockade in hepatocellular carcinoma [RNA-seq]
organism: Homo sapiens
assay_type: bulk RNA-seq
processed_data_available: true
raw_data_available: true
submission_date: 2021-01-08
last_update_date: 2021-07-04
organization_name: The Chinese University of Hong Kong
department: School of Biomedical Sciences
public_date: 2021-04-04
experiment_types: Expression profiling by high throughput sequencing
platforms: GPL20301 Illumina HiSeq 4000 (Homo sapiens)
sub_series: Not available
bioproject: PRJNA690723
supplementary_files: TXT: GSE164441_RNAseq_10Tvs10NT_cuffdiff_FPKM.txt.gz; TXT: GSE164441_RNAseq_10Tvs10NT_cuffdiff_count.txt.gz
series_type: SubSeries

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 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

32 fields
Field Value Source Origin Confidence Evidence Reason
assay_type bulk RNA-seq dataset GSE164441 Runtime Siftome inference GEO:dataset:GSE164441:9b5b74312ea82b99ada4c6c94bf8a898d4ea517e1b7b86a12933d49876d829f7 high confidence bulk rna-seq dataset_accession: GSE164441 dataset_title: A selective HDAC8 inhibitor potentiates antitumor immunity and efficacy of immune checkpoint blockade in hepatocellular carcinoma [RN... keyword match keyword match: bulk rna-seq
organism Homo sapiens dataset GSE164441 Runtime Siftome inference GEO:dataset:GSE164441:9b5b74312ea82b99ada4c6c94bf8a898d4ea517e1b7b86a12933d49876d829f7 high confidence homo sapiens dataset_accession: GSE164441 dataset_title: A selective HDAC8 inhibitor potentiates antitumor immunity and efficacy of immune checkpoint blockade in hepatocellular carcinoma [RN... keyword match keyword match: homo sapiens
sample_type normal tissue sample GSM5009643 Runtime Siftome inference GEO:sample:GSM5009643:b7972983d35e337b869524dca58f181d59df37048786520b3d1778ef7e664bba medium confidence non-tumor sample_accession: GSM5009643 sample_title: 651_NT_RNA-seq source_name: Adjacent non-tumor liver tissue from NAFLD-HCC patient characteristics: tissue: Adjacent non-tumor liver t... controlled vocabulary controlled vocabulary sample type match: non-tumor
sample_type tumor sample sample GSM5009644 Runtime Siftome inference GEO:sample:GSM5009644:affc81eeea345b8e6661e21d6ee1b6e6e1674f0aeaa3c9e6f96c158fd3a36ed8 low confidence tumor sample_accession: GSM5009644 sample_title: 651_T_RNA-seq source_name: Tumor tissue from NAFLD-HCC patient characteristics: ajcc stage: AJCC 1; tissue: Tumor tissue 651_T_RNA-seq controlled vocabulary controlled vocabulary sample type match: tumor
sample_type normal tissue sample GSM5009645 Runtime Siftome inference GEO:sample:GSM5009645:61015ebb3bb213cba43b8b2c0adcfd8caa08ded1834b3260406d5242c2bdc797 medium confidence non-tumor sample_accession: GSM5009645 sample_title: 678_NT_RNA-seq source_name: Adjacent non-tumor liver tissue from NAFLD-HCC patient characteristics: tissue: Adjacent non-tumor liver t... controlled vocabulary controlled vocabulary sample type match: non-tumor
sample_type tumor sample sample GSM5009646 Runtime Siftome inference GEO:sample:GSM5009646:368329d3b6729e4e49f987168ebb07b4833e98f5ec20a71164d8464add07e163 low confidence tumor sample_accession: GSM5009646 sample_title: 678_T_RNA-seq source_name: Tumor tissue from NAFLD-HCC patient characteristics: ajcc stage: AJCC 1; tissue: Tumor tissue 678_T_RNA-seq controlled vocabulary controlled vocabulary sample type match: tumor
sample_type normal tissue sample GSM5009647 Runtime Siftome inference GEO:sample:GSM5009647:511adf1069ea8722973f529beeba02505a169937677a1b0f2389a89cd525dd16 medium confidence non-tumor sample_accession: GSM5009647 sample_title: 707_NT_RNA-seq source_name: Adjacent non-tumor liver tissue from NAFLD-HCC patient characteristics: tissue: Adjacent non-tumor liver t... controlled vocabulary controlled vocabulary sample type match: non-tumor
sample_type tumor sample sample GSM5009648 Runtime Siftome inference GEO:sample:GSM5009648:ef813365ed59d36fd1161da201dab5904d68cade7050ae39567f90e4098676ac low confidence tumor sample_accession: GSM5009648 sample_title: 707_T_RNA-seq source_name: Tumor tissue from NAFLD-HCC patient characteristics: ajcc stage: AJCC 3; tissue: Tumor tissue 707_T_RNA-seq controlled vocabulary controlled vocabulary sample type match: tumor
sample_type normal tissue sample GSM5009649 Runtime Siftome inference GEO:sample:GSM5009649:d75a38fee74386d76970ad797a03bd583f09f86ad0d6fdf816f5c022c1467d5f medium confidence non-tumor sample_accession: GSM5009649 sample_title: 715_NT_RNA-seq source_name: Adjacent non-tumor liver tissue from NAFLD-HCC patient characteristics: tissue: Adjacent non-tumor liver t... controlled vocabulary controlled vocabulary sample type match: non-tumor
sample_type tumor sample sample GSM5009650 Runtime Siftome inference GEO:sample:GSM5009650:83e05c0cd34842e37100bf7f8f959b1fb1e4c302033f8a319d3fbbe09a6281ab low confidence tumor sample_accession: GSM5009650 sample_title: 715_T_RNA-seq source_name: Tumor tissue from NAFLD-HCC patient characteristics: ajcc stage: AJCC 1; tissue: Tumor tissue 715_T_RNA-seq controlled vocabulary controlled vocabulary sample type match: tumor
sample_type normal tissue sample GSM5009651 Runtime Siftome inference GEO:sample:GSM5009651:a1e215cf696aeb05ba49acd64c35b51baa42a72e5d9f6a86c6a21ba0554c91b2 medium confidence non-tumor sample_accession: GSM5009651 sample_title: 717_NT_RNA-seq source_name: Adjacent non-tumor liver tissue from NAFLD-HCC patient characteristics: tissue: Adjacent non-tumor liver t... controlled vocabulary controlled vocabulary sample type match: non-tumor
sample_type tumor sample sample GSM5009652 Runtime Siftome inference GEO:sample:GSM5009652:ea4d55be1942ef61ed9a44bda61c8521da370ea89a5af295ef34c6aa97df1b8f low confidence tumor sample_accession: GSM5009652 sample_title: 717_T_RNA-seq source_name: Tumor tissue from NAFLD-HCC patient characteristics: ajcc stage: AJCC 1; tissue: Tumor tissue 717_T_RNA-seq controlled vocabulary controlled vocabulary sample type match: tumor
sample_type normal tissue sample GSM5009653 Runtime Siftome inference GEO:sample:GSM5009653:3156b5c58e00f4bba2816753478c5b854931e7a56bfbbf26cc3ca07c9bb97966 medium confidence non-tumor sample_accession: GSM5009653 sample_title: 754_NT_RNA-seq source_name: Adjacent non-tumor liver tissue from NAFLD-HCC patient characteristics: tissue: Adjacent non-tumor liver t... controlled vocabulary controlled vocabulary sample type match: non-tumor
sample_type tumor sample sample GSM5009654 Runtime Siftome inference GEO:sample:GSM5009654:bd7a0d9905a9d432f1e6bfbf0c973624b922e4febe1398ff7035dd6b4868b40b low confidence tumor sample_accession: GSM5009654 sample_title: 754_T_RNA-seq source_name: Tumor tissue from NAFLD-HCC patient characteristics: ajcc stage: AJCC 1; tissue: Tumor tissue 754_T_RNA-seq controlled vocabulary controlled vocabulary sample type match: tumor
sample_type normal tissue sample GSM5009655 Runtime Siftome inference GEO:sample:GSM5009655:995fb046b12bc2c03ea5635bf2eb37962b188a6bdafb3622af93397d6e0c9c74 medium confidence non-tumor sample_accession: GSM5009655 sample_title: 796_NT_RNA-seq source_name: Adjacent non-tumor liver tissue from NAFLD-HCC patient characteristics: tissue: Adjacent non-tumor liver t... controlled vocabulary controlled vocabulary sample type match: non-tumor
sample_type tumor sample sample GSM5009656 Runtime Siftome inference GEO:sample:GSM5009656:cdcad27aa7ca105281fb65ba33493916a534d30300b1e7c6c2e5ee081ba7b7dd low confidence tumor sample_accession: GSM5009656 sample_title: 796_T_RNA-seq source_name: Tumor tissue from NAFLD-HCC patient characteristics: ajcc stage: AJCC 1; tissue: Tumor tissue 796_T_RNA-seq controlled vocabulary controlled vocabulary sample type match: tumor
sample_type normal tissue sample GSM5009657 Runtime Siftome inference GEO:sample:GSM5009657:15c51617410e3d4ea256cb82accc40af2ece4930ba174f77f96a94912c6d069e medium confidence non-tumor sample_accession: GSM5009657 sample_title: 705_NT_RNA-seq source_name: Adjacent non-tumor liver tissue from NAFLD-HCC patient characteristics: tissue: Adjacent non-tumor liver t... controlled vocabulary controlled vocabulary sample type match: non-tumor
sample_type tumor sample sample GSM5009658 Runtime Siftome inference GEO:sample:GSM5009658:22cdd9bc5e52dac1f6ab1994a6a263c205ba5fa547dbb220e10f015d973cb9ee low confidence tumor sample_accession: GSM5009658 sample_title: 705_T_RNA-seq source_name: Tumor tissue from NAFLD-HCC patient characteristics: ajcc stage: AJCC 3; tissue: Tumor tissue 705_T_RNA-seq controlled vocabulary controlled vocabulary sample type match: tumor
sample_type normal tissue sample GSM5009659 Runtime Siftome inference GEO:sample:GSM5009659:3f165aca30b3e79e55ea0a01becdee0467c6a8eabbcfd867ba9d58817cf38495 medium confidence non-tumor sample_accession: GSM5009659 sample_title: 741_NT_RNA-seq source_name: Adjacent non-tumor liver tissue from NAFLD-HCC patient characteristics: tissue: Adjacent non-tumor liver t... controlled vocabulary controlled vocabulary sample type match: non-tumor
sample_type tumor sample sample GSM5009660 Runtime Siftome inference GEO:sample:GSM5009660:e1058b2bb0603c32618c2d007e21f424efc6b437ec5aa62384d0a6ce5ddd4de6 low confidence tumor sample_accession: GSM5009660 sample_title: 741_T_RNA-seq source_name: Tumor tissue from NAFLD-HCC patient characteristics: ajcc stage: AJCC 3; tissue: Tumor tissue 741_T_RNA-seq controlled vocabulary controlled vocabulary sample type match: tumor
sample_type normal tissue sample GSM5009661 Runtime Siftome inference GEO:sample:GSM5009661:61d9a6fe8c8f78068b5430d50cd1f84a7430fe7e314be4ba4f160426b8c8e08a medium confidence non-tumor sample_accession: GSM5009661 sample_title: 768_NT_RNA-seq source_name: Adjacent non-tumor liver tissue from NAFLD-HCC patient characteristics: tissue: Adjacent non-tumor liver t... controlled vocabulary controlled vocabulary sample type match: non-tumor
sample_type tumor sample sample GSM5009662 Runtime Siftome inference GEO:sample:GSM5009662:8a2a0347975b76c6be093e01000ba4745f356b467bd8ec156c23e240c00e9f26 low confidence tumor sample_accession: GSM5009662 sample_title: 768_T_RNA-seq source_name: Tumor tissue from NAFLD-HCC patient characteristics: ajcc stage: AJCC 3; tissue: Tumor tissue 768_T_RNA-seq controlled vocabulary controlled vocabulary sample type match: tumor
tissue liver sample GSM5009643 Runtime Siftome inference GEO:sample:GSM5009643:b7972983d35e337b869524dca58f181d59df37048786520b3d1778ef7e664bba low confidence liver sample_accession: GSM5009643 sample_title: 651_NT_RNA-seq source_name: Adjacent non-tumor liver tissue from NAFLD-HCC patient characteristics: tissue: Adjacent non-tumor liver t... controlled vocabulary controlled vocabulary tissue match: liver
tissue liver sample GSM5009645 Runtime Siftome inference GEO:sample:GSM5009645:61015ebb3bb213cba43b8b2c0adcfd8caa08ded1834b3260406d5242c2bdc797 low confidence liver sample_accession: GSM5009645 sample_title: 678_NT_RNA-seq source_name: Adjacent non-tumor liver tissue from NAFLD-HCC patient characteristics: tissue: Adjacent non-tumor liver t... controlled vocabulary controlled vocabulary tissue match: liver
tissue liver sample GSM5009647 Runtime Siftome inference GEO:sample:GSM5009647:511adf1069ea8722973f529beeba02505a169937677a1b0f2389a89cd525dd16 low confidence liver sample_accession: GSM5009647 sample_title: 707_NT_RNA-seq source_name: Adjacent non-tumor liver tissue from NAFLD-HCC patient characteristics: tissue: Adjacent non-tumor liver t... controlled vocabulary controlled vocabulary tissue match: liver
tissue liver sample GSM5009649 Runtime Siftome inference GEO:sample:GSM5009649:d75a38fee74386d76970ad797a03bd583f09f86ad0d6fdf816f5c022c1467d5f low confidence liver sample_accession: GSM5009649 sample_title: 715_NT_RNA-seq source_name: Adjacent non-tumor liver tissue from NAFLD-HCC patient characteristics: tissue: Adjacent non-tumor liver t... controlled vocabulary controlled vocabulary tissue match: liver
tissue liver sample GSM5009651 Runtime Siftome inference GEO:sample:GSM5009651:a1e215cf696aeb05ba49acd64c35b51baa42a72e5d9f6a86c6a21ba0554c91b2 low confidence liver sample_accession: GSM5009651 sample_title: 717_NT_RNA-seq source_name: Adjacent non-tumor liver tissue from NAFLD-HCC patient characteristics: tissue: Adjacent non-tumor liver t... controlled vocabulary controlled vocabulary tissue match: liver
tissue liver sample GSM5009653 Runtime Siftome inference GEO:sample:GSM5009653:3156b5c58e00f4bba2816753478c5b854931e7a56bfbbf26cc3ca07c9bb97966 low confidence liver sample_accession: GSM5009653 sample_title: 754_NT_RNA-seq source_name: Adjacent non-tumor liver tissue from NAFLD-HCC patient characteristics: tissue: Adjacent non-tumor liver t... controlled vocabulary controlled vocabulary tissue match: liver
tissue liver sample GSM5009655 Runtime Siftome inference GEO:sample:GSM5009655:995fb046b12bc2c03ea5635bf2eb37962b188a6bdafb3622af93397d6e0c9c74 low confidence liver sample_accession: GSM5009655 sample_title: 796_NT_RNA-seq source_name: Adjacent non-tumor liver tissue from NAFLD-HCC patient characteristics: tissue: Adjacent non-tumor liver t... controlled vocabulary controlled vocabulary tissue match: liver
tissue liver sample GSM5009657 Runtime Siftome inference GEO:sample:GSM5009657:15c51617410e3d4ea256cb82accc40af2ece4930ba174f77f96a94912c6d069e low confidence liver sample_accession: GSM5009657 sample_title: 705_NT_RNA-seq source_name: Adjacent non-tumor liver tissue from NAFLD-HCC patient characteristics: tissue: Adjacent non-tumor liver t... controlled vocabulary controlled vocabulary tissue match: liver
tissue liver sample GSM5009659 Runtime Siftome inference GEO:sample:GSM5009659:3f165aca30b3e79e55ea0a01becdee0467c6a8eabbcfd867ba9d58817cf38495 low confidence liver sample_accession: GSM5009659 sample_title: 741_NT_RNA-seq source_name: Adjacent non-tumor liver tissue from NAFLD-HCC patient characteristics: tissue: Adjacent non-tumor liver t... controlled vocabulary controlled vocabulary tissue match: liver
tissue liver sample GSM5009661 Runtime Siftome inference GEO:sample:GSM5009661:61d9a6fe8c8f78068b5430d50cd1f84a7430fe7e314be4ba4f160426b8c8e08a low confidence liver sample_accession: GSM5009661 sample_title: 768_NT_RNA-seq source_name: Adjacent non-tumor liver tissue from NAFLD-HCC patient characteristics: tissue: Adjacent non-tumor liver t... controlled vocabulary controlled vocabulary tissue match: liver

Sample Group Preview

Possible case samples

Samples currently treated as the comparison case group.

10
  • GSM5009644 651_T_RNA-seq tumor sample Case marker detected. Tumor tissue from NAFLD-HCC patient ajcc stage: AJCC 1; tissue: Tumor tissue
  • GSM5009646 678_T_RNA-seq tumor sample Case marker detected. Tumor tissue from NAFLD-HCC patient ajcc stage: AJCC 1; tissue: Tumor tissue
  • GSM5009648 707_T_RNA-seq tumor sample Case marker detected. Tumor tissue from NAFLD-HCC patient ajcc stage: AJCC 3; tissue: Tumor tissue
  • GSM5009650 715_T_RNA-seq tumor sample Case marker detected. Tumor tissue from NAFLD-HCC patient ajcc stage: AJCC 1; tissue: Tumor tissue
  • GSM5009652 717_T_RNA-seq tumor sample Case marker detected. Tumor tissue from NAFLD-HCC patient ajcc stage: AJCC 1; tissue: Tumor tissue
  • GSM5009654 754_T_RNA-seq tumor sample Case marker detected. Tumor tissue from NAFLD-HCC patient ajcc stage: AJCC 1; tissue: Tumor tissue
  • GSM5009656 796_T_RNA-seq tumor sample Case marker detected. Tumor tissue from NAFLD-HCC patient ajcc stage: AJCC 1; tissue: Tumor tissue
  • GSM5009658 705_T_RNA-seq tumor sample Case marker detected. Tumor tissue from NAFLD-HCC patient ajcc stage: AJCC 3; tissue: Tumor tissue
  • GSM5009660 741_T_RNA-seq tumor sample Case marker detected. Tumor tissue from NAFLD-HCC patient ajcc stage: AJCC 3; tissue: Tumor tissue
  • GSM5009662 768_T_RNA-seq tumor sample Case marker detected. Tumor tissue from NAFLD-HCC patient ajcc stage: AJCC 3; tissue: Tumor tissue

Possible control samples

Samples currently treated as controls or baseline.

10
  • GSM5009643 651_NT_RNA-seq normal tissue Control marker detected. Adjacent non-tumor liver tissue from NAFLD-HCC patient tissue: Adjacent non-tumor liver tissue
  • GSM5009645 678_NT_RNA-seq normal tissue Control marker detected. Adjacent non-tumor liver tissue from NAFLD-HCC patient tissue: Adjacent non-tumor liver tissue
  • GSM5009647 707_NT_RNA-seq normal tissue Control marker detected. Adjacent non-tumor liver tissue from NAFLD-HCC patient tissue: Adjacent non-tumor liver tissue
  • GSM5009649 715_NT_RNA-seq normal tissue Control marker detected. Adjacent non-tumor liver tissue from NAFLD-HCC patient tissue: Adjacent non-tumor liver tissue
  • GSM5009651 717_NT_RNA-seq normal tissue Control marker detected. Adjacent non-tumor liver tissue from NAFLD-HCC patient tissue: Adjacent non-tumor liver tissue
  • GSM5009653 754_NT_RNA-seq normal tissue Control marker detected. Adjacent non-tumor liver tissue from NAFLD-HCC patient tissue: Adjacent non-tumor liver tissue
  • GSM5009655 796_NT_RNA-seq normal tissue Control marker detected. Adjacent non-tumor liver tissue from NAFLD-HCC patient tissue: Adjacent non-tumor liver tissue
  • GSM5009657 705_NT_RNA-seq normal tissue Control marker detected. Adjacent non-tumor liver tissue from NAFLD-HCC patient tissue: Adjacent non-tumor liver tissue
  • GSM5009659 741_NT_RNA-seq normal tissue Control marker detected. Adjacent non-tumor liver tissue from NAFLD-HCC patient tissue: Adjacent non-tumor liver tissue
  • GSM5009661 768_NT_RNA-seq normal tissue Control marker detected. Adjacent non-tumor liver tissue from NAFLD-HCC patient tissue: Adjacent non-tumor liver 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

10 samples
  • GSM5009643 651_NT_RNA-seq Adjacent non-tumor liver tissue from NAFLD-HCC patient tissue: Adjacent non-tumor liver tissue
  • GSM5009645 678_NT_RNA-seq Adjacent non-tumor liver tissue from NAFLD-HCC patient tissue: Adjacent non-tumor liver tissue
  • GSM5009647 707_NT_RNA-seq Adjacent non-tumor liver tissue from NAFLD-HCC patient tissue: Adjacent non-tumor liver tissue
  • GSM5009649 715_NT_RNA-seq Adjacent non-tumor liver tissue from NAFLD-HCC patient tissue: Adjacent non-tumor liver tissue
  • GSM5009651 717_NT_RNA-seq Adjacent non-tumor liver tissue from NAFLD-HCC patient tissue: Adjacent non-tumor liver tissue
  • GSM5009653 754_NT_RNA-seq Adjacent non-tumor liver tissue from NAFLD-HCC patient tissue: Adjacent non-tumor liver tissue
  • GSM5009655 796_NT_RNA-seq Adjacent non-tumor liver tissue from NAFLD-HCC patient tissue: Adjacent non-tumor liver tissue
  • GSM5009657 705_NT_RNA-seq Adjacent non-tumor liver tissue from NAFLD-HCC patient tissue: Adjacent non-tumor liver tissue
  • GSM5009659 741_NT_RNA-seq Adjacent non-tumor liver tissue from NAFLD-HCC patient tissue: Adjacent non-tumor liver tissue
  • GSM5009661 768_NT_RNA-seq Adjacent non-tumor liver tissue from NAFLD-HCC patient tissue: Adjacent non-tumor liver tissue

tumor sample

10 samples
  • GSM5009644 651_T_RNA-seq Tumor tissue from NAFLD-HCC patient ajcc stage: AJCC 1; tissue: Tumor tissue
  • GSM5009646 678_T_RNA-seq Tumor tissue from NAFLD-HCC patient ajcc stage: AJCC 1; tissue: Tumor tissue
  • GSM5009648 707_T_RNA-seq Tumor tissue from NAFLD-HCC patient ajcc stage: AJCC 3; tissue: Tumor tissue
  • GSM5009650 715_T_RNA-seq Tumor tissue from NAFLD-HCC patient ajcc stage: AJCC 1; tissue: Tumor tissue
  • GSM5009652 717_T_RNA-seq Tumor tissue from NAFLD-HCC patient ajcc stage: AJCC 1; tissue: Tumor tissue
  • GSM5009654 754_T_RNA-seq Tumor tissue from NAFLD-HCC patient ajcc stage: AJCC 1; tissue: Tumor tissue
  • GSM5009656 796_T_RNA-seq Tumor tissue from NAFLD-HCC patient ajcc stage: AJCC 1; tissue: Tumor tissue
  • GSM5009658 705_T_RNA-seq Tumor tissue from NAFLD-HCC patient ajcc stage: AJCC 3; tissue: Tumor tissue
  • GSM5009660 741_T_RNA-seq Tumor tissue from NAFLD-HCC patient ajcc stage: AJCC 3; tissue: Tumor tissue
  • GSM5009662 768_T_RNA-seq Tumor tissue from NAFLD-HCC patient ajcc stage: AJCC 3; tissue: 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

20 samples

Review Audit Trail

0 decisions

No review decisions have been stored for this dataset.