Siftome Phase 3L

GSE192912

Cancer-associated Fibroblast-derived SPP1 is a Potential Target for Overcoming Sorafenib and Lenvatinib Resistance 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
2022-01-03
Last update
2022-12-24
Organization
Ajou University of Korea
Department
Not available
Public date
2022-12-24
Experiment types
Expression profiling by high throughput sequencing
Platforms
GPL11154 Illumina HiSeq 2000 (Homo sapiens)
Series type
Series
SubSeries
Not available
BioProject
PRJNA793786
Supplementary files
TXT: GSE192912_Processed_data_files.txt.gz
Organism
Homo sapiens
Assay
bulk RNA-seq
Samples
19
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
85% DE readiness

Contrast completeness

25/25 pts

Both case and control groups are present in the proposed grouping.

Minimum group size

8/20 pts

A contrast exists, but at least one group is below the minimum sample count.

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

  • At least one contrast group is below the minimum sample count.

Next Steps

  • Review blockers and update sample grouping or dataset selection before 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

Blocked

At least one group has fewer than 2 samples.

Choose a larger dataset or merge only scientifically valid groups.

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

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.
  • Analysis preparation checklist contains blocked items.
  • At least one comparison group has fewer than two samples.

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 18 samples
  • Likely control group normal tissue 1 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
GSE192912
Sample records
19 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
GSE192912
  • 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
GSE192912
  • 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
GSE192912
  • 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: GSE192912
dataset_title: Cancer-associated Fibroblast-derived SPP1 is a Potential Target for Overcoming Sorafenib and Lenvatinib Resistance in Hepatocellular Carcinoma
organism: Homo sapiens
assay_type: bulk RNA-seq
processed_data_available: true
raw_data_available: true
submission_date: 2022-01-03
last_update_date: 2022-12-24
organization_name: Ajou University of Korea
department: Not available
public_date: 2022-12-24
experiment_types: Expression profiling by high throughput sequencing
platforms: GPL11154 Illumina HiSeq 2000 (Homo sapiens)
sub_series: Not available
bioproject: PRJNA793786
supplementary_files: TXT: GSE192912_Processed_data_files.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.
  • 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

41 fields
Field Value Source Origin Confidence Evidence Reason
assay_type bulk RNA-seq dataset GSE192912 Runtime Siftome inference GEO:dataset:GSE192912:872f44c058a27e438e2f3fb54166a78fa63f6b2588ed36e73508c52fac13cad4 high confidence bulk rna-seq dataset_accession: GSE192912 dataset_title: Cancer-associated Fibroblast-derived SPP1 is a Potential Target for Overcoming Sorafenib and Lenvatinib Resistance in Hepatocellular ... keyword match keyword match: bulk rna-seq
organism Homo sapiens dataset GSE192912 Runtime Siftome inference GEO:dataset:GSE192912:872f44c058a27e438e2f3fb54166a78fa63f6b2588ed36e73508c52fac13cad4 high confidence homo sapiens dataset_accession: GSE192912 dataset_title: Cancer-associated Fibroblast-derived SPP1 is a Potential Target for Overcoming Sorafenib and Lenvatinib Resistance in Hepatocellular ... keyword match keyword match: homo sapiens
sample_type normal tissue sample GSM5768805 Runtime Siftome inference GEO:sample:GSM5768805:521eabd221b975d6a2f7e258797e3f2e05401d646ea31310a0ab6d6009d15adb low confidence normal sample_accession: GSM5768805 sample_title: HWY-NF source_name: Hepatocellular carcinoma characteristics: fibroblast type: Normal fibroblasts; tissue: liver tissue; diagnosis: HC... controlled vocabulary controlled vocabulary sample type match: normal
sample_type tumor sample sample GSM5768805 Runtime Siftome inference GEO:sample:GSM5768805:521eabd221b975d6a2f7e258797e3f2e05401d646ea31310a0ab6d6009d15adb medium confidence carcinoma sample_accession: GSM5768805 sample_title: HWY-NF source_name: Hepatocellular carcinoma characteristics: fibroblast type: Normal fibroblasts; tissue: liver tissue; diagnosis: HC... controlled vocabulary controlled vocabulary sample type match: carcinoma
sample_type tumor sample sample GSM5768806 Runtime Siftome inference GEO:sample:GSM5768806:cb53d920922b003f258f73f72eb133b1d3b56e01c2e9337a9699567c48bf0f2a medium confidence carcinoma sample_accession: GSM5768806 sample_title: ASY-PAF source_name: Hepatocellular carcinoma characteristics: fibroblast type: para-cancer fibroblasts; tissue: liver tissue; diagnos... controlled vocabulary controlled vocabulary sample type match: carcinoma
sample_type tumor sample sample GSM5768807 Runtime Siftome inference GEO:sample:GSM5768807:ee72d17f53d058434ae439a29df2fa005ed9d0454fca45b715eb2db18db13097 medium confidence carcinoma sample_accession: GSM5768807 sample_title: CHI-PAF source_name: Hepatocellular carcinoma characteristics: fibroblast type: para-cancer fibroblasts; tissue: liver tissue; diagnos... controlled vocabulary controlled vocabulary sample type match: carcinoma
sample_type tumor sample sample GSM5768808 Runtime Siftome inference GEO:sample:GSM5768808:0f1bd5d1e7dde6c4b547a48aaa1923d285488e9af99447a458b21da270ba24f1 medium confidence carcinoma sample_accession: GSM5768808 sample_title: DHS-PAF source_name: Hepatocellular carcinoma characteristics: fibroblast type: para-cancer fibroblasts; tissue: liver tissue; diagnos... controlled vocabulary controlled vocabulary sample type match: carcinoma
sample_type tumor sample sample GSM5768809 Runtime Siftome inference GEO:sample:GSM5768809:4cce930f1ea45c20e18a34b8dcc08fd31830c1781dd2de938d98c8f2fac4dc7f medium confidence carcinoma sample_accession: GSM5768809 sample_title: KYS-PAF source_name: Hepatocellular carcinoma characteristics: fibroblast type: para-cancer fibroblasts; tissue: liver tissue; diagnos... controlled vocabulary controlled vocabulary sample type match: carcinoma
sample_type tumor sample sample GSM5768810 Runtime Siftome inference GEO:sample:GSM5768810:8f616bb6fc3b9ca3a1cde76507a6ed543810d9df80e4b61864ac7f1ee338f540 medium confidence carcinoma sample_accession: GSM5768810 sample_title: LKO-PAF source_name: Hepatocellular carcinoma characteristics: fibroblast type: para-cancer fibroblasts; tissue: liver tissue; diagnos... controlled vocabulary controlled vocabulary sample type match: carcinoma
sample_type tumor sample sample GSM5768811 Runtime Siftome inference GEO:sample:GSM5768811:03d82c186580b705f5df6e77ed1dbc3d95595a059b75c7e6cd9d64f2149167a7 medium confidence carcinoma sample_accession: GSM5768811 sample_title: PYS-PAF source_name: Hepatocellular carcinoma characteristics: fibroblast type: para-cancer fibroblasts; tissue: liver tissue; diagnos... controlled vocabulary controlled vocabulary sample type match: carcinoma
sample_type tumor sample sample GSM5768812 Runtime Siftome inference GEO:sample:GSM5768812:a44440051a09a1833e070aaaa85ed54de0426fdc584472488248af5966fd87e8 medium confidence carcinoma sample_accession: GSM5768812 sample_title: SDH-PAF source_name: Hepatocellular carcinoma characteristics: fibroblast type: para-cancer fibroblasts; tissue: liver tissue; diagnos... controlled vocabulary controlled vocabulary sample type match: carcinoma
sample_type tumor sample sample GSM5768813 Runtime Siftome inference GEO:sample:GSM5768813:773bfffcf0a8dcbca825195a996517806850256ac17fc71b28bdc0b1add47759 medium confidence carcinoma sample_accession: GSM5768813 sample_title: SMJ-PAF source_name: Hepatocellular carcinoma characteristics: fibroblast type: para-cancer fibroblasts; tissue: liver tissue; diagnos... controlled vocabulary controlled vocabulary sample type match: carcinoma
sample_type tumor sample sample GSM5768814 Runtime Siftome inference GEO:sample:GSM5768814:3f09f4f233ad2386b5ddbe541bcbf5915f7ee2ee086b20b512da28df501d31ae medium confidence carcinoma sample_accession: GSM5768814 sample_title: YOY-PAF source_name: Hepatocellular carcinoma characteristics: fibroblast type: para-cancer fibroblasts; tissue: liver tissue; diagnos... controlled vocabulary controlled vocabulary sample type match: carcinoma
sample_type tumor sample sample GSM5768815 Runtime Siftome inference GEO:sample:GSM5768815:3bf9995a7c2c67590e6304fc80eb855c8444c0c78ae86f20658b6837a24a694c medium confidence carcinoma sample_accession: GSM5768815 sample_title: ASY-CAF source_name: Hepatocellular carcinoma characteristics: fibroblast type: cancer-associated fibroblasts; tissue: liver tissue; d... controlled vocabulary controlled vocabulary sample type match: carcinoma
sample_type tumor sample sample GSM5768816 Runtime Siftome inference GEO:sample:GSM5768816:cb6a9328cc4f90bc42b42c047f87b82b072cfdfca75b71ad060d35a9d0667141 medium confidence carcinoma sample_accession: GSM5768816 sample_title: CHI-CAF source_name: Hepatocellular carcinoma characteristics: fibroblast type: cancer-associated fibroblasts; tissue: liver tissue; d... controlled vocabulary controlled vocabulary sample type match: carcinoma
sample_type tumor sample sample GSM5768817 Runtime Siftome inference GEO:sample:GSM5768817:6ea88901aee189196a93426d3df27da123bedc1de5ea63bbf3f59f0d9fba245d medium confidence carcinoma sample_accession: GSM5768817 sample_title: DHS-CAF source_name: Hepatocellular carcinoma characteristics: fibroblast type: cancer-associated fibroblasts; tissue: liver tissue; d... controlled vocabulary controlled vocabulary sample type match: carcinoma
sample_type tumor sample sample GSM5768818 Runtime Siftome inference GEO:sample:GSM5768818:ba9bbea874cb45237a52ee84f93657780cd36bbaefae4402cd5915cc8abef254 medium confidence carcinoma sample_accession: GSM5768818 sample_title: KYS-CAF source_name: Hepatocellular carcinoma characteristics: fibroblast type: cancer-associated fibroblasts; tissue: liver tissue; d... controlled vocabulary controlled vocabulary sample type match: carcinoma
sample_type tumor sample sample GSM5768819 Runtime Siftome inference GEO:sample:GSM5768819:0b94d077b930d3be1a0d7978718bb9e7b481d5bafeb938776281482b3ed11637 medium confidence carcinoma sample_accession: GSM5768819 sample_title: LKO-CAF source_name: Hepatocellular carcinoma characteristics: fibroblast type: cancer-associated fibroblasts; tissue: liver tissue; d... controlled vocabulary controlled vocabulary sample type match: carcinoma
sample_type tumor sample sample GSM5768820 Runtime Siftome inference GEO:sample:GSM5768820:76bfa7b8baf875fcca5e9490f8b83216feb252573eb05977bec42321a738d03e medium confidence carcinoma sample_accession: GSM5768820 sample_title: PYS-CAF source_name: Hepatocellular carcinoma characteristics: fibroblast type: cancer-associated fibroblasts; tissue: liver tissue; d... controlled vocabulary controlled vocabulary sample type match: carcinoma
sample_type tumor sample sample GSM5768821 Runtime Siftome inference GEO:sample:GSM5768821:56e0ccd1f867171a1846117c16a6404872e48f04cb0e349a77121de8ae38e6e7 medium confidence carcinoma sample_accession: GSM5768821 sample_title: SDH-CAF source_name: Hepatocellular carcinoma characteristics: fibroblast type: cancer-associated fibroblasts; tissue: liver tissue; d... controlled vocabulary controlled vocabulary sample type match: carcinoma
sample_type tumor sample sample GSM5768822 Runtime Siftome inference GEO:sample:GSM5768822:ff083fb7308b2dbe820db65ff83b503c2d13f82416e880df55cf58bc1080a0b5 medium confidence carcinoma sample_accession: GSM5768822 sample_title: SMJ-CAF source_name: Hepatocellular carcinoma characteristics: fibroblast type: cancer-associated fibroblasts; tissue: liver tissue; d... controlled vocabulary controlled vocabulary sample type match: carcinoma
sample_type tumor sample sample GSM5768823 Runtime Siftome inference GEO:sample:GSM5768823:599948ee81e043e62f4c424817a02464477d5e6f1638337a54453b4c5b24880a medium confidence carcinoma sample_accession: GSM5768823 sample_title: YOY-CAF source_name: Hepatocellular carcinoma characteristics: fibroblast type: cancer-associated fibroblasts; tissue: liver tissue; d... controlled vocabulary controlled vocabulary sample type match: carcinoma
tissue liver sample GSM5768805 Runtime Siftome inference GEO:sample:GSM5768805:521eabd221b975d6a2f7e258797e3f2e05401d646ea31310a0ab6d6009d15adb low confidence liver sample_accession: GSM5768805 sample_title: HWY-NF source_name: Hepatocellular carcinoma characteristics: fibroblast type: Normal fibroblasts; tissue: liver tissue; diagnosis: HC... controlled vocabulary controlled vocabulary tissue match: liver
tissue liver sample GSM5768806 Runtime Siftome inference GEO:sample:GSM5768806:cb53d920922b003f258f73f72eb133b1d3b56e01c2e9337a9699567c48bf0f2a low confidence liver sample_accession: GSM5768806 sample_title: ASY-PAF source_name: Hepatocellular carcinoma characteristics: fibroblast type: para-cancer fibroblasts; tissue: liver tissue; diagnos... controlled vocabulary controlled vocabulary tissue match: liver
tissue liver sample GSM5768807 Runtime Siftome inference GEO:sample:GSM5768807:ee72d17f53d058434ae439a29df2fa005ed9d0454fca45b715eb2db18db13097 low confidence liver sample_accession: GSM5768807 sample_title: CHI-PAF source_name: Hepatocellular carcinoma characteristics: fibroblast type: para-cancer fibroblasts; tissue: liver tissue; diagnos... controlled vocabulary controlled vocabulary tissue match: liver
tissue liver sample GSM5768808 Runtime Siftome inference GEO:sample:GSM5768808:0f1bd5d1e7dde6c4b547a48aaa1923d285488e9af99447a458b21da270ba24f1 low confidence liver sample_accession: GSM5768808 sample_title: DHS-PAF source_name: Hepatocellular carcinoma characteristics: fibroblast type: para-cancer fibroblasts; tissue: liver tissue; diagnos... controlled vocabulary controlled vocabulary tissue match: liver
tissue liver sample GSM5768809 Runtime Siftome inference GEO:sample:GSM5768809:4cce930f1ea45c20e18a34b8dcc08fd31830c1781dd2de938d98c8f2fac4dc7f low confidence liver sample_accession: GSM5768809 sample_title: KYS-PAF source_name: Hepatocellular carcinoma characteristics: fibroblast type: para-cancer fibroblasts; tissue: liver tissue; diagnos... controlled vocabulary controlled vocabulary tissue match: liver
tissue liver sample GSM5768810 Runtime Siftome inference GEO:sample:GSM5768810:8f616bb6fc3b9ca3a1cde76507a6ed543810d9df80e4b61864ac7f1ee338f540 low confidence liver sample_accession: GSM5768810 sample_title: LKO-PAF source_name: Hepatocellular carcinoma characteristics: fibroblast type: para-cancer fibroblasts; tissue: liver tissue; diagnos... controlled vocabulary controlled vocabulary tissue match: liver
tissue liver sample GSM5768811 Runtime Siftome inference GEO:sample:GSM5768811:03d82c186580b705f5df6e77ed1dbc3d95595a059b75c7e6cd9d64f2149167a7 low confidence liver sample_accession: GSM5768811 sample_title: PYS-PAF source_name: Hepatocellular carcinoma characteristics: fibroblast type: para-cancer fibroblasts; tissue: liver tissue; diagnos... controlled vocabulary controlled vocabulary tissue match: liver
tissue liver sample GSM5768812 Runtime Siftome inference GEO:sample:GSM5768812:a44440051a09a1833e070aaaa85ed54de0426fdc584472488248af5966fd87e8 low confidence liver sample_accession: GSM5768812 sample_title: SDH-PAF source_name: Hepatocellular carcinoma characteristics: fibroblast type: para-cancer fibroblasts; tissue: liver tissue; diagnos... controlled vocabulary controlled vocabulary tissue match: liver
tissue liver sample GSM5768813 Runtime Siftome inference GEO:sample:GSM5768813:773bfffcf0a8dcbca825195a996517806850256ac17fc71b28bdc0b1add47759 low confidence liver sample_accession: GSM5768813 sample_title: SMJ-PAF source_name: Hepatocellular carcinoma characteristics: fibroblast type: para-cancer fibroblasts; tissue: liver tissue; diagnos... controlled vocabulary controlled vocabulary tissue match: liver
tissue liver sample GSM5768814 Runtime Siftome inference GEO:sample:GSM5768814:3f09f4f233ad2386b5ddbe541bcbf5915f7ee2ee086b20b512da28df501d31ae low confidence liver sample_accession: GSM5768814 sample_title: YOY-PAF source_name: Hepatocellular carcinoma characteristics: fibroblast type: para-cancer fibroblasts; tissue: liver tissue; diagnos... controlled vocabulary controlled vocabulary tissue match: liver
tissue liver sample GSM5768815 Runtime Siftome inference GEO:sample:GSM5768815:3bf9995a7c2c67590e6304fc80eb855c8444c0c78ae86f20658b6837a24a694c low confidence liver sample_accession: GSM5768815 sample_title: ASY-CAF source_name: Hepatocellular carcinoma characteristics: fibroblast type: cancer-associated fibroblasts; tissue: liver tissue; d... controlled vocabulary controlled vocabulary tissue match: liver
tissue liver sample GSM5768816 Runtime Siftome inference GEO:sample:GSM5768816:cb6a9328cc4f90bc42b42c047f87b82b072cfdfca75b71ad060d35a9d0667141 low confidence liver sample_accession: GSM5768816 sample_title: CHI-CAF source_name: Hepatocellular carcinoma characteristics: fibroblast type: cancer-associated fibroblasts; tissue: liver tissue; d... controlled vocabulary controlled vocabulary tissue match: liver
tissue liver sample GSM5768817 Runtime Siftome inference GEO:sample:GSM5768817:6ea88901aee189196a93426d3df27da123bedc1de5ea63bbf3f59f0d9fba245d low confidence liver sample_accession: GSM5768817 sample_title: DHS-CAF source_name: Hepatocellular carcinoma characteristics: fibroblast type: cancer-associated fibroblasts; tissue: liver tissue; d... controlled vocabulary controlled vocabulary tissue match: liver
tissue liver sample GSM5768818 Runtime Siftome inference GEO:sample:GSM5768818:ba9bbea874cb45237a52ee84f93657780cd36bbaefae4402cd5915cc8abef254 low confidence liver sample_accession: GSM5768818 sample_title: KYS-CAF source_name: Hepatocellular carcinoma characteristics: fibroblast type: cancer-associated fibroblasts; tissue: liver tissue; d... controlled vocabulary controlled vocabulary tissue match: liver
tissue liver sample GSM5768819 Runtime Siftome inference GEO:sample:GSM5768819:0b94d077b930d3be1a0d7978718bb9e7b481d5bafeb938776281482b3ed11637 low confidence liver sample_accession: GSM5768819 sample_title: LKO-CAF source_name: Hepatocellular carcinoma characteristics: fibroblast type: cancer-associated fibroblasts; tissue: liver tissue; d... controlled vocabulary controlled vocabulary tissue match: liver
tissue liver sample GSM5768820 Runtime Siftome inference GEO:sample:GSM5768820:76bfa7b8baf875fcca5e9490f8b83216feb252573eb05977bec42321a738d03e low confidence liver sample_accession: GSM5768820 sample_title: PYS-CAF source_name: Hepatocellular carcinoma characteristics: fibroblast type: cancer-associated fibroblasts; tissue: liver tissue; d... controlled vocabulary controlled vocabulary tissue match: liver
tissue liver sample GSM5768821 Runtime Siftome inference GEO:sample:GSM5768821:56e0ccd1f867171a1846117c16a6404872e48f04cb0e349a77121de8ae38e6e7 low confidence liver sample_accession: GSM5768821 sample_title: SDH-CAF source_name: Hepatocellular carcinoma characteristics: fibroblast type: cancer-associated fibroblasts; tissue: liver tissue; d... controlled vocabulary controlled vocabulary tissue match: liver
tissue liver sample GSM5768822 Runtime Siftome inference GEO:sample:GSM5768822:ff083fb7308b2dbe820db65ff83b503c2d13f82416e880df55cf58bc1080a0b5 low confidence liver sample_accession: GSM5768822 sample_title: SMJ-CAF source_name: Hepatocellular carcinoma characteristics: fibroblast type: cancer-associated fibroblasts; tissue: liver tissue; d... controlled vocabulary controlled vocabulary tissue match: liver
tissue liver sample GSM5768823 Runtime Siftome inference GEO:sample:GSM5768823:599948ee81e043e62f4c424817a02464477d5e6f1638337a54453b4c5b24880a low confidence liver sample_accession: GSM5768823 sample_title: YOY-CAF source_name: Hepatocellular carcinoma characteristics: fibroblast type: cancer-associated fibroblasts; tissue: liver tissue; d... controlled vocabulary controlled vocabulary tissue match: liver

Sample Group Preview

Possible case samples

Samples currently treated as the comparison case group.

18
  • GSM5768806 ASY-PAF tumor sample Case marker detected. Hepatocellular carcinoma fibroblast type: para-cancer fibroblasts; tissue: liver tissue; diagnosis: HCC
  • GSM5768807 CHI-PAF tumor sample Case marker detected. Hepatocellular carcinoma fibroblast type: para-cancer fibroblasts; tissue: liver tissue; diagnosis: HCC
  • GSM5768808 DHS-PAF tumor sample Case marker detected. Hepatocellular carcinoma fibroblast type: para-cancer fibroblasts; tissue: liver tissue; diagnosis: HCC
  • GSM5768809 KYS-PAF tumor sample Case marker detected. Hepatocellular carcinoma fibroblast type: para-cancer fibroblasts; tissue: liver tissue; diagnosis: HCC
  • GSM5768810 LKO-PAF tumor sample Case marker detected. Hepatocellular carcinoma fibroblast type: para-cancer fibroblasts; tissue: liver tissue; diagnosis: HCC
  • GSM5768811 PYS-PAF tumor sample Case marker detected. Hepatocellular carcinoma fibroblast type: para-cancer fibroblasts; tissue: liver tissue; diagnosis: HCC
  • GSM5768812 SDH-PAF tumor sample Case marker detected. Hepatocellular carcinoma fibroblast type: para-cancer fibroblasts; tissue: liver tissue; diagnosis: HCC
  • GSM5768813 SMJ-PAF tumor sample Case marker detected. Hepatocellular carcinoma fibroblast type: para-cancer fibroblasts; tissue: liver tissue; diagnosis: HCC
  • GSM5768814 YOY-PAF tumor sample Case marker detected. Hepatocellular carcinoma fibroblast type: para-cancer fibroblasts; tissue: liver tissue; diagnosis: HCC
  • GSM5768815 ASY-CAF tumor sample Case marker detected. Hepatocellular carcinoma fibroblast type: cancer-associated fibroblasts; tissue: liver tissue; diagnosis: HCC
  • GSM5768816 CHI-CAF tumor sample Case marker detected. Hepatocellular carcinoma fibroblast type: cancer-associated fibroblasts; tissue: liver tissue; diagnosis: HCC
  • GSM5768817 DHS-CAF tumor sample Case marker detected. Hepatocellular carcinoma fibroblast type: cancer-associated fibroblasts; tissue: liver tissue; diagnosis: HCC
  • GSM5768818 KYS-CAF tumor sample Case marker detected. Hepatocellular carcinoma fibroblast type: cancer-associated fibroblasts; tissue: liver tissue; diagnosis: HCC
  • GSM5768819 LKO-CAF tumor sample Case marker detected. Hepatocellular carcinoma fibroblast type: cancer-associated fibroblasts; tissue: liver tissue; diagnosis: HCC
  • GSM5768820 PYS-CAF tumor sample Case marker detected. Hepatocellular carcinoma fibroblast type: cancer-associated fibroblasts; tissue: liver tissue; diagnosis: HCC
  • GSM5768821 SDH-CAF tumor sample Case marker detected. Hepatocellular carcinoma fibroblast type: cancer-associated fibroblasts; tissue: liver tissue; diagnosis: HCC
  • GSM5768822 SMJ-CAF tumor sample Case marker detected. Hepatocellular carcinoma fibroblast type: cancer-associated fibroblasts; tissue: liver tissue; diagnosis: HCC
  • GSM5768823 YOY-CAF tumor sample Case marker detected. Hepatocellular carcinoma fibroblast type: cancer-associated fibroblasts; tissue: liver tissue; diagnosis: HCC

Possible control samples

Samples currently treated as controls or baseline.

1
  • GSM5768805 HWY-NF normal tissue Control marker detected. Hepatocellular carcinoma fibroblast type: Normal fibroblasts; tissue: liver tissue; diagnosis: HCC

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

1 sample
  • GSM5768805 HWY-NF Hepatocellular carcinoma fibroblast type: Normal fibroblasts; tissue: liver tissue; diagnosis: HCC

tumor sample

18 samples
  • GSM5768806 ASY-PAF Hepatocellular carcinoma fibroblast type: para-cancer fibroblasts; tissue: liver tissue; diagnosis: HCC
  • GSM5768807 CHI-PAF Hepatocellular carcinoma fibroblast type: para-cancer fibroblasts; tissue: liver tissue; diagnosis: HCC
  • GSM5768808 DHS-PAF Hepatocellular carcinoma fibroblast type: para-cancer fibroblasts; tissue: liver tissue; diagnosis: HCC
  • GSM5768809 KYS-PAF Hepatocellular carcinoma fibroblast type: para-cancer fibroblasts; tissue: liver tissue; diagnosis: HCC
  • GSM5768810 LKO-PAF Hepatocellular carcinoma fibroblast type: para-cancer fibroblasts; tissue: liver tissue; diagnosis: HCC
  • GSM5768811 PYS-PAF Hepatocellular carcinoma fibroblast type: para-cancer fibroblasts; tissue: liver tissue; diagnosis: HCC
  • GSM5768812 SDH-PAF Hepatocellular carcinoma fibroblast type: para-cancer fibroblasts; tissue: liver tissue; diagnosis: HCC
  • GSM5768813 SMJ-PAF Hepatocellular carcinoma fibroblast type: para-cancer fibroblasts; tissue: liver tissue; diagnosis: HCC
  • GSM5768814 YOY-PAF Hepatocellular carcinoma fibroblast type: para-cancer fibroblasts; tissue: liver tissue; diagnosis: HCC
  • GSM5768815 ASY-CAF Hepatocellular carcinoma fibroblast type: cancer-associated fibroblasts; tissue: liver tissue; diagnosis: HCC
  • GSM5768816 CHI-CAF Hepatocellular carcinoma fibroblast type: cancer-associated fibroblasts; tissue: liver tissue; diagnosis: HCC
  • GSM5768817 DHS-CAF Hepatocellular carcinoma fibroblast type: cancer-associated fibroblasts; tissue: liver tissue; diagnosis: HCC
  • GSM5768818 KYS-CAF Hepatocellular carcinoma fibroblast type: cancer-associated fibroblasts; tissue: liver tissue; diagnosis: HCC
  • GSM5768819 LKO-CAF Hepatocellular carcinoma fibroblast type: cancer-associated fibroblasts; tissue: liver tissue; diagnosis: HCC
  • GSM5768820 PYS-CAF Hepatocellular carcinoma fibroblast type: cancer-associated fibroblasts; tissue: liver tissue; diagnosis: HCC
  • GSM5768821 SDH-CAF Hepatocellular carcinoma fibroblast type: cancer-associated fibroblasts; tissue: liver tissue; diagnosis: HCC
  • GSM5768822 SMJ-CAF Hepatocellular carcinoma fibroblast type: cancer-associated fibroblasts; tissue: liver tissue; diagnosis: HCC
  • GSM5768823 YOY-CAF Hepatocellular carcinoma fibroblast type: cancer-associated fibroblasts; tissue: liver tissue; diagnosis: HCC

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

19 samples

Review Audit Trail

0 decisions

No review decisions have been stored for this dataset.