Siftome Phase 3L

GSE241466

Transcriptomic profiling of the intermediate cell carcinoma of the primary liver cancer

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
2023-08-22
Last update
2024-08-15
Organization
Ajou University School of Medicine
Department
Not available
Public date
2024-08-14
Experiment types
Expression profiling by high throughput sequencing
Platforms
GPL24676 Illumina NovaSeq 6000 (Homo sapiens)
Series type
Series
SubSeries
Not available
BioProject
PRJNA1008226
Supplementary files
TAR: GSE241466_RAW.tar; TXT: GSE241466_Raw_data.txt.gz
Organism
Homo sapiens
Assay
bulk RNA-seq
Samples
25
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 18 samples
  • Likely control group normal tissue 7 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
GSE241466
Sample records
25 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
GSE241466
  • 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
GSE241466
  • 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
GSE241466
  • 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: GSE241466
dataset_title: Transcriptomic profiling of the intermediate cell carcinoma of the primary liver cancer
organism: Homo sapiens
assay_type: bulk RNA-seq
processed_data_available: true
raw_data_available: true
submission_date: 2023-08-22
last_update_date: 2024-08-15
organization_name: Ajou University School of Medicine
department: Not available
public_date: 2024-08-14
experiment_types: Expression profiling by high throughput sequencing
platforms: GPL24676 Illumina NovaSeq 6000 (Homo sapiens)
sub_series: Not available
bioproject: PRJNA1008226
supplementary_files: TAR: GSE241466_RAW.tar; TXT: GSE241466_Raw_data.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

53 fields
Field Value Source Origin Confidence Evidence Reason
assay_type bulk RNA-seq dataset GSE241466 Runtime Siftome inference GEO:dataset:GSE241466:8fecf317fb49153ae6a0d004fb63b239277ea9c023b7ab52163a0e382b40a7aa high confidence bulk rna-seq dataset_accession: GSE241466 dataset_title: Transcriptomic profiling of the intermediate cell carcinoma of the primary liver cancer organism: Homo sapiens assay_type: bulk RNA-s... keyword match keyword match: bulk rna-seq
organism Homo sapiens dataset GSE241466 Runtime Siftome inference GEO:dataset:GSE241466:8fecf317fb49153ae6a0d004fb63b239277ea9c023b7ab52163a0e382b40a7aa high confidence homo sapiens dataset_accession: GSE241466 dataset_title: Transcriptomic profiling of the intermediate cell carcinoma of the primary liver cancer organism: Homo sapiens assay_type: bulk RNA-s... keyword match keyword match: homo sapiens
sample_type normal tissue sample GSM7729323 Runtime Siftome inference GEO:sample:GSM7729323:a70620e5144d6761dc19c4d67ad72a5fec2c8a4e50a9c7275c504b37c2fb13d1 medium confidence non-tumor sample_accession: GSM7729323 sample_title: YSINT2 source_name: Non-tumor characteristics: tissue: Liver; batch: batch1 YSINT2 controlled vocabulary controlled vocabulary sample type match: non-tumor
sample_type normal tissue sample GSM7729324 Runtime Siftome inference GEO:sample:GSM7729324:2d0b5f27d803c4a1b46efec48584c2d0bd9164cb9d60993d30f6252d50788a62 medium confidence non-tumor sample_accession: GSM7729324 sample_title: YSINT3 source_name: Non-tumor characteristics: tissue: Liver; batch: batch1 YSINT3 controlled vocabulary controlled vocabulary sample type match: non-tumor
sample_type normal tissue sample GSM7729325 Runtime Siftome inference GEO:sample:GSM7729325:136a8b7daba8d96ef822e0eab875e71f9079cfc50a374ef5b988924f382f68f5 medium confidence non-tumor sample_accession: GSM7729325 sample_title: YSINT4 source_name: Non-tumor characteristics: tissue: Liver; batch: batch1 YSINT4 controlled vocabulary controlled vocabulary sample type match: non-tumor
sample_type normal tissue sample GSM7729326 Runtime Siftome inference GEO:sample:GSM7729326:c5ce7de7612da2961ebecaec00581861fd9daa727fdd08550050962914225437 medium confidence non-tumor sample_accession: GSM7729326 sample_title: YSINT5 source_name: Non-tumor characteristics: tissue: Liver; batch: batch1 YSINT5 controlled vocabulary controlled vocabulary sample type match: non-tumor
sample_type normal tissue sample GSM7729327 Runtime Siftome inference GEO:sample:GSM7729327:d5953b6b7d45c99b0a065c05926a4317c3f6556ded9fcd3f4104d111b49268b9 medium confidence non-tumor sample_accession: GSM7729327 sample_title: YSINT6 source_name: Non-tumor characteristics: tissue: Liver; batch: batch1 YSINT6 controlled vocabulary controlled vocabulary sample type match: non-tumor
sample_type tumor sample sample GSM7729328 Runtime Siftome inference GEO:sample:GSM7729328:f48c2a38b4d9255d368e3be39639f2e2fb379ef89bc23e07e085144f58721092 medium confidence carcinoma sample_accession: GSM7729328 sample_title: YSINT7 source_name: Intermediate cell carcinoma characteristics: tissue: Liver; batch: batch1 YSINT7 controlled vocabulary controlled vocabulary sample type match: carcinoma
sample_type tumor sample sample GSM7729329 Runtime Siftome inference GEO:sample:GSM7729329:8add5096546afec6e22cb8a00d03a89cfc87e5043116cb6d0bb1a01f36e3c1f6 medium confidence carcinoma sample_accession: GSM7729329 sample_title: YSINT8 source_name: Intermediate cell carcinoma characteristics: tissue: Liver; batch: batch1 YSINT8 controlled vocabulary controlled vocabulary sample type match: carcinoma
sample_type tumor sample sample GSM7729330 Runtime Siftome inference GEO:sample:GSM7729330:84ab8abf14a7d0cd38333b02356fc0bb31954dc2f15fbfe21c08b91903d56a7a medium confidence carcinoma sample_accession: GSM7729330 sample_title: YSINT9 source_name: Intermediate cell carcinoma characteristics: tissue: Liver; batch: batch1 YSINT9 controlled vocabulary controlled vocabulary sample type match: carcinoma
sample_type tumor sample sample GSM7729331 Runtime Siftome inference GEO:sample:GSM7729331:abe8d79144998f33812cdba28533a48b226a4a940067171d624064951f5ac1e1 medium confidence carcinoma sample_accession: GSM7729331 sample_title: YSINT10 source_name: Intermediate cell carcinoma characteristics: tissue: Liver; batch: batch1 YSINT10 controlled vocabulary controlled vocabulary sample type match: carcinoma
sample_type tumor sample sample GSM7729332 Runtime Siftome inference GEO:sample:GSM7729332:c37325a8d982aa5ea6df7d3096fb71134af0a32b3e60fc22968d5054bccd699d medium confidence carcinoma sample_accession: GSM7729332 sample_title: YSINT11 source_name: Intermediate cell carcinoma characteristics: tissue: Liver; batch: batch1 YSINT11 controlled vocabulary controlled vocabulary sample type match: carcinoma
sample_type tumor sample sample GSM7729333 Runtime Siftome inference GEO:sample:GSM7729333:863e1873a4c87761d1ad8fd0ed9f75b01305e4b60bc8e1dfc0c919164a31f0ec medium confidence carcinoma sample_accession: GSM7729333 sample_title: YSINT12 source_name: Intermediate cell carcinoma characteristics: tissue: Liver; batch: batch1 YSINT12 controlled vocabulary controlled vocabulary sample type match: carcinoma
sample_type tumor sample sample GSM7729334 Runtime Siftome inference GEO:sample:GSM7729334:ac5faebf34efbd12a5f19a72e13cf1c0a792494d6d65e1305e05d40cd243f99b medium confidence carcinoma sample_accession: GSM7729334 sample_title: YSINT13 source_name: Hepatocellular carcinoma characteristics: tissue: Liver; batch: batch1 YSINT13 controlled vocabulary controlled vocabulary sample type match: carcinoma
sample_type tumor sample sample GSM7729335 Runtime Siftome inference GEO:sample:GSM7729335:773810245dd2b957571f3091f6af23c6fb7f4f3d0d5e685b44174cbcdbb764dd medium confidence carcinoma sample_accession: GSM7729335 sample_title: YSINT14 source_name: Hepatocellular carcinoma characteristics: tissue: Liver; batch: batch1 YSINT14 controlled vocabulary controlled vocabulary sample type match: carcinoma
sample_type tumor sample sample GSM7729336 Runtime Siftome inference GEO:sample:GSM7729336:8a2230a91177c123a40be0f58aef326f2d244f3158be96e8cd169746eb587acb medium confidence carcinoma sample_accession: GSM7729336 sample_title: YSINT15 source_name: Hepatocellular carcinoma characteristics: tissue: Liver; batch: batch1 YSINT15 controlled vocabulary controlled vocabulary sample type match: carcinoma
sample_type tumor sample sample GSM7729337 Runtime Siftome inference GEO:sample:GSM7729337:cf1c70fbcb2e8b022eec074824eebb3ab4292f33402acb42c0d08e97ecf1100b medium confidence carcinoma sample_accession: GSM7729337 sample_title: YSINT16 source_name: Hepatocellular carcinoma characteristics: tissue: Liver; batch: batch1 YSINT16 controlled vocabulary controlled vocabulary sample type match: carcinoma
sample_type tumor sample sample GSM7729338 Runtime Siftome inference GEO:sample:GSM7729338:dd49b75efe8fdb3257f706b2649c43ec137a84953ea4621eb63f44e160082069 medium confidence carcinoma sample_accession: GSM7729338 sample_title: YSINT17 source_name: Hepatocellular carcinoma characteristics: tissue: Liver; batch: batch1 YSINT17 controlled vocabulary controlled vocabulary sample type match: carcinoma
sample_type tumor sample sample GSM7729339 Runtime Siftome inference GEO:sample:GSM7729339:11affa58665cdf4d3d543b1ca4236e42677b98ad6ecdde1f20f54a8abf55e485 medium confidence carcinoma sample_accession: GSM7729339 sample_title: YSINT18 source_name: Intrahepatic cholangiocarcinoma characteristics: tissue: Liver; batch: batch1 YSINT18 controlled vocabulary controlled vocabulary sample type match: carcinoma
sample_type tumor sample sample GSM7729340 Runtime Siftome inference GEO:sample:GSM7729340:35c4f9ee80d1dbd339192743230642d3b34ba87a3ec645e630dd1bbd50f72648 medium confidence carcinoma sample_accession: GSM7729340 sample_title: YSINT19 source_name: Intrahepatic cholangiocarcinoma characteristics: tissue: Liver; batch: batch1 YSINT19 controlled vocabulary controlled vocabulary sample type match: carcinoma
sample_type tumor sample sample GSM7729341 Runtime Siftome inference GEO:sample:GSM7729341:1c80cc80a45254507f3af4254a94acd36260da0f0e6bed6856bed8525340396b medium confidence carcinoma sample_accession: GSM7729341 sample_title: YSINT20 source_name: Intrahepatic cholangiocarcinoma characteristics: tissue: Liver; batch: batch1 YSINT20 controlled vocabulary controlled vocabulary sample type match: carcinoma
sample_type tumor sample sample GSM7729342 Runtime Siftome inference GEO:sample:GSM7729342:d06e4703ca0af279c57231c661f0cd522fcbf0b8a8f78fe3ab51180b799f52f5 medium confidence carcinoma sample_accession: GSM7729342 sample_title: YSINT21 source_name: Intrahepatic cholangiocarcinoma characteristics: tissue: Liver; batch: batch1 YSINT21 controlled vocabulary controlled vocabulary sample type match: carcinoma
sample_type tumor sample sample GSM7729343 Runtime Siftome inference GEO:sample:GSM7729343:e98bc67b278f6bc52eb26e760cb586c9ac56461f87d3f9828bc4d8246c15b167 medium confidence carcinoma sample_accession: GSM7729343 sample_title: YSINT22 source_name: Intrahepatic cholangiocarcinoma characteristics: tissue: Liver; batch: batch1 YSINT22 controlled vocabulary controlled vocabulary sample type match: carcinoma
sample_type normal tissue sample GSM7729344 Runtime Siftome inference GEO:sample:GSM7729344:ab29db59f10637f128114f867e83ad68930a43ffc2646a8ad845e71b54e3f268 medium confidence non-tumor sample_accession: GSM7729344 sample_title: YSINT23 source_name: Non-tumor characteristics: tissue: Liver; batch: batch2 YSINT23 controlled vocabulary controlled vocabulary sample type match: non-tumor
sample_type normal tissue sample GSM7729345 Runtime Siftome inference GEO:sample:GSM7729345:61bfbbfb789035ae97ceec4a8318e939538c40b3e00adf6675fdc3dca2fc807d medium confidence non-tumor sample_accession: GSM7729345 sample_title: YSINT24 source_name: Non-tumor characteristics: tissue: Liver; batch: batch2 YSINT24 controlled vocabulary controlled vocabulary sample type match: non-tumor
sample_type tumor sample sample GSM7729346 Runtime Siftome inference GEO:sample:GSM7729346:6cdb19e7e1e50f43ca77485ac476df16f84b8d743169068459815a570a469654 medium confidence carcinoma sample_accession: GSM7729346 sample_title: YSINT25 source_name: Intermediate cell carcinoma characteristics: tissue: Liver; batch: batch2 YSINT25 controlled vocabulary controlled vocabulary sample type match: carcinoma
sample_type tumor sample sample GSM7729347 Runtime Siftome inference GEO:sample:GSM7729347:33e8f78d0099526485d3fad3b30b8acb0fa1a7ac2ecd5d73f146f519e63ae901 medium confidence carcinoma sample_accession: GSM7729347 sample_title: YSINT26 source_name: Intermediate cell carcinoma characteristics: tissue: Liver; batch: batch2 YSINT26 controlled vocabulary controlled vocabulary sample type match: carcinoma
tissue liver dataset GSE241466 Runtime Siftome inference GEO:dataset:GSE241466:8fecf317fb49153ae6a0d004fb63b239277ea9c023b7ab52163a0e382b40a7aa low confidence liver dataset_accession: GSE241466 dataset_title: Transcriptomic profiling of the intermediate cell carcinoma of the primary liver cancer organism: Homo sapiens assay_type: bulk RNA-s... controlled vocabulary controlled vocabulary tissue match: liver
tissue liver sample GSM7729323 Runtime Siftome inference GEO:sample:GSM7729323:a70620e5144d6761dc19c4d67ad72a5fec2c8a4e50a9c7275c504b37c2fb13d1 low confidence liver sample_accession: GSM7729323 sample_title: YSINT2 source_name: Non-tumor characteristics: tissue: Liver; batch: batch1 YSINT2 controlled vocabulary controlled vocabulary tissue match: liver
tissue liver sample GSM7729324 Runtime Siftome inference GEO:sample:GSM7729324:2d0b5f27d803c4a1b46efec48584c2d0bd9164cb9d60993d30f6252d50788a62 low confidence liver sample_accession: GSM7729324 sample_title: YSINT3 source_name: Non-tumor characteristics: tissue: Liver; batch: batch1 YSINT3 controlled vocabulary controlled vocabulary tissue match: liver
tissue liver sample GSM7729325 Runtime Siftome inference GEO:sample:GSM7729325:136a8b7daba8d96ef822e0eab875e71f9079cfc50a374ef5b988924f382f68f5 low confidence liver sample_accession: GSM7729325 sample_title: YSINT4 source_name: Non-tumor characteristics: tissue: Liver; batch: batch1 YSINT4 controlled vocabulary controlled vocabulary tissue match: liver
tissue liver sample GSM7729326 Runtime Siftome inference GEO:sample:GSM7729326:c5ce7de7612da2961ebecaec00581861fd9daa727fdd08550050962914225437 low confidence liver sample_accession: GSM7729326 sample_title: YSINT5 source_name: Non-tumor characteristics: tissue: Liver; batch: batch1 YSINT5 controlled vocabulary controlled vocabulary tissue match: liver
tissue liver sample GSM7729327 Runtime Siftome inference GEO:sample:GSM7729327:d5953b6b7d45c99b0a065c05926a4317c3f6556ded9fcd3f4104d111b49268b9 low confidence liver sample_accession: GSM7729327 sample_title: YSINT6 source_name: Non-tumor characteristics: tissue: Liver; batch: batch1 YSINT6 controlled vocabulary controlled vocabulary tissue match: liver
tissue liver sample GSM7729328 Runtime Siftome inference GEO:sample:GSM7729328:f48c2a38b4d9255d368e3be39639f2e2fb379ef89bc23e07e085144f58721092 low confidence liver sample_accession: GSM7729328 sample_title: YSINT7 source_name: Intermediate cell carcinoma characteristics: tissue: Liver; batch: batch1 YSINT7 controlled vocabulary controlled vocabulary tissue match: liver
tissue liver sample GSM7729329 Runtime Siftome inference GEO:sample:GSM7729329:8add5096546afec6e22cb8a00d03a89cfc87e5043116cb6d0bb1a01f36e3c1f6 low confidence liver sample_accession: GSM7729329 sample_title: YSINT8 source_name: Intermediate cell carcinoma characteristics: tissue: Liver; batch: batch1 YSINT8 controlled vocabulary controlled vocabulary tissue match: liver
tissue liver sample GSM7729330 Runtime Siftome inference GEO:sample:GSM7729330:84ab8abf14a7d0cd38333b02356fc0bb31954dc2f15fbfe21c08b91903d56a7a low confidence liver sample_accession: GSM7729330 sample_title: YSINT9 source_name: Intermediate cell carcinoma characteristics: tissue: Liver; batch: batch1 YSINT9 controlled vocabulary controlled vocabulary tissue match: liver
tissue liver sample GSM7729331 Runtime Siftome inference GEO:sample:GSM7729331:abe8d79144998f33812cdba28533a48b226a4a940067171d624064951f5ac1e1 low confidence liver sample_accession: GSM7729331 sample_title: YSINT10 source_name: Intermediate cell carcinoma characteristics: tissue: Liver; batch: batch1 YSINT10 controlled vocabulary controlled vocabulary tissue match: liver
tissue liver sample GSM7729332 Runtime Siftome inference GEO:sample:GSM7729332:c37325a8d982aa5ea6df7d3096fb71134af0a32b3e60fc22968d5054bccd699d low confidence liver sample_accession: GSM7729332 sample_title: YSINT11 source_name: Intermediate cell carcinoma characteristics: tissue: Liver; batch: batch1 YSINT11 controlled vocabulary controlled vocabulary tissue match: liver
tissue liver sample GSM7729333 Runtime Siftome inference GEO:sample:GSM7729333:863e1873a4c87761d1ad8fd0ed9f75b01305e4b60bc8e1dfc0c919164a31f0ec low confidence liver sample_accession: GSM7729333 sample_title: YSINT12 source_name: Intermediate cell carcinoma characteristics: tissue: Liver; batch: batch1 YSINT12 controlled vocabulary controlled vocabulary tissue match: liver
tissue liver sample GSM7729334 Runtime Siftome inference GEO:sample:GSM7729334:ac5faebf34efbd12a5f19a72e13cf1c0a792494d6d65e1305e05d40cd243f99b low confidence liver sample_accession: GSM7729334 sample_title: YSINT13 source_name: Hepatocellular carcinoma characteristics: tissue: Liver; batch: batch1 YSINT13 controlled vocabulary controlled vocabulary tissue match: liver
tissue liver sample GSM7729335 Runtime Siftome inference GEO:sample:GSM7729335:773810245dd2b957571f3091f6af23c6fb7f4f3d0d5e685b44174cbcdbb764dd low confidence liver sample_accession: GSM7729335 sample_title: YSINT14 source_name: Hepatocellular carcinoma characteristics: tissue: Liver; batch: batch1 YSINT14 controlled vocabulary controlled vocabulary tissue match: liver
tissue liver sample GSM7729336 Runtime Siftome inference GEO:sample:GSM7729336:8a2230a91177c123a40be0f58aef326f2d244f3158be96e8cd169746eb587acb low confidence liver sample_accession: GSM7729336 sample_title: YSINT15 source_name: Hepatocellular carcinoma characteristics: tissue: Liver; batch: batch1 YSINT15 controlled vocabulary controlled vocabulary tissue match: liver
tissue liver sample GSM7729337 Runtime Siftome inference GEO:sample:GSM7729337:cf1c70fbcb2e8b022eec074824eebb3ab4292f33402acb42c0d08e97ecf1100b low confidence liver sample_accession: GSM7729337 sample_title: YSINT16 source_name: Hepatocellular carcinoma characteristics: tissue: Liver; batch: batch1 YSINT16 controlled vocabulary controlled vocabulary tissue match: liver
tissue liver sample GSM7729338 Runtime Siftome inference GEO:sample:GSM7729338:dd49b75efe8fdb3257f706b2649c43ec137a84953ea4621eb63f44e160082069 low confidence liver sample_accession: GSM7729338 sample_title: YSINT17 source_name: Hepatocellular carcinoma characteristics: tissue: Liver; batch: batch1 YSINT17 controlled vocabulary controlled vocabulary tissue match: liver
tissue liver sample GSM7729339 Runtime Siftome inference GEO:sample:GSM7729339:11affa58665cdf4d3d543b1ca4236e42677b98ad6ecdde1f20f54a8abf55e485 low confidence liver sample_accession: GSM7729339 sample_title: YSINT18 source_name: Intrahepatic cholangiocarcinoma characteristics: tissue: Liver; batch: batch1 YSINT18 controlled vocabulary controlled vocabulary tissue match: liver
tissue liver sample GSM7729340 Runtime Siftome inference GEO:sample:GSM7729340:35c4f9ee80d1dbd339192743230642d3b34ba87a3ec645e630dd1bbd50f72648 low confidence liver sample_accession: GSM7729340 sample_title: YSINT19 source_name: Intrahepatic cholangiocarcinoma characteristics: tissue: Liver; batch: batch1 YSINT19 controlled vocabulary controlled vocabulary tissue match: liver
tissue liver sample GSM7729341 Runtime Siftome inference GEO:sample:GSM7729341:1c80cc80a45254507f3af4254a94acd36260da0f0e6bed6856bed8525340396b low confidence liver sample_accession: GSM7729341 sample_title: YSINT20 source_name: Intrahepatic cholangiocarcinoma characteristics: tissue: Liver; batch: batch1 YSINT20 controlled vocabulary controlled vocabulary tissue match: liver
tissue liver sample GSM7729342 Runtime Siftome inference GEO:sample:GSM7729342:d06e4703ca0af279c57231c661f0cd522fcbf0b8a8f78fe3ab51180b799f52f5 low confidence liver sample_accession: GSM7729342 sample_title: YSINT21 source_name: Intrahepatic cholangiocarcinoma characteristics: tissue: Liver; batch: batch1 YSINT21 controlled vocabulary controlled vocabulary tissue match: liver
tissue liver sample GSM7729343 Runtime Siftome inference GEO:sample:GSM7729343:e98bc67b278f6bc52eb26e760cb586c9ac56461f87d3f9828bc4d8246c15b167 low confidence liver sample_accession: GSM7729343 sample_title: YSINT22 source_name: Intrahepatic cholangiocarcinoma characteristics: tissue: Liver; batch: batch1 YSINT22 controlled vocabulary controlled vocabulary tissue match: liver
tissue liver sample GSM7729344 Runtime Siftome inference GEO:sample:GSM7729344:ab29db59f10637f128114f867e83ad68930a43ffc2646a8ad845e71b54e3f268 low confidence liver sample_accession: GSM7729344 sample_title: YSINT23 source_name: Non-tumor characteristics: tissue: Liver; batch: batch2 YSINT23 controlled vocabulary controlled vocabulary tissue match: liver
tissue liver sample GSM7729345 Runtime Siftome inference GEO:sample:GSM7729345:61bfbbfb789035ae97ceec4a8318e939538c40b3e00adf6675fdc3dca2fc807d low confidence liver sample_accession: GSM7729345 sample_title: YSINT24 source_name: Non-tumor characteristics: tissue: Liver; batch: batch2 YSINT24 controlled vocabulary controlled vocabulary tissue match: liver
tissue liver sample GSM7729346 Runtime Siftome inference GEO:sample:GSM7729346:6cdb19e7e1e50f43ca77485ac476df16f84b8d743169068459815a570a469654 low confidence liver sample_accession: GSM7729346 sample_title: YSINT25 source_name: Intermediate cell carcinoma characteristics: tissue: Liver; batch: batch2 YSINT25 controlled vocabulary controlled vocabulary tissue match: liver
tissue liver sample GSM7729347 Runtime Siftome inference GEO:sample:GSM7729347:33e8f78d0099526485d3fad3b30b8acb0fa1a7ac2ecd5d73f146f519e63ae901 low confidence liver sample_accession: GSM7729347 sample_title: YSINT26 source_name: Intermediate cell carcinoma characteristics: tissue: Liver; batch: batch2 YSINT26 controlled vocabulary controlled vocabulary tissue match: liver

Sample Group Preview

Possible case samples

Samples currently treated as the comparison case group.

18
  • GSM7729328 YSINT7 tumor sample Case marker detected. Intermediate cell carcinoma tissue: Liver; batch: batch1
  • GSM7729329 YSINT8 tumor sample Case marker detected. Intermediate cell carcinoma tissue: Liver; batch: batch1
  • GSM7729330 YSINT9 tumor sample Case marker detected. Intermediate cell carcinoma tissue: Liver; batch: batch1
  • GSM7729331 YSINT10 tumor sample Case marker detected. Intermediate cell carcinoma tissue: Liver; batch: batch1
  • GSM7729332 YSINT11 tumor sample Case marker detected. Intermediate cell carcinoma tissue: Liver; batch: batch1
  • GSM7729333 YSINT12 tumor sample Case marker detected. Intermediate cell carcinoma tissue: Liver; batch: batch1
  • GSM7729334 YSINT13 tumor sample Case marker detected. Hepatocellular carcinoma tissue: Liver; batch: batch1
  • GSM7729335 YSINT14 tumor sample Case marker detected. Hepatocellular carcinoma tissue: Liver; batch: batch1
  • GSM7729336 YSINT15 tumor sample Case marker detected. Hepatocellular carcinoma tissue: Liver; batch: batch1
  • GSM7729337 YSINT16 tumor sample Case marker detected. Hepatocellular carcinoma tissue: Liver; batch: batch1
  • GSM7729338 YSINT17 tumor sample Case marker detected. Hepatocellular carcinoma tissue: Liver; batch: batch1
  • GSM7729339 YSINT18 tumor sample Case marker detected. Intrahepatic cholangiocarcinoma tissue: Liver; batch: batch1
  • GSM7729340 YSINT19 tumor sample Case marker detected. Intrahepatic cholangiocarcinoma tissue: Liver; batch: batch1
  • GSM7729341 YSINT20 tumor sample Case marker detected. Intrahepatic cholangiocarcinoma tissue: Liver; batch: batch1
  • GSM7729342 YSINT21 tumor sample Case marker detected. Intrahepatic cholangiocarcinoma tissue: Liver; batch: batch1
  • GSM7729343 YSINT22 tumor sample Case marker detected. Intrahepatic cholangiocarcinoma tissue: Liver; batch: batch1
  • GSM7729346 YSINT25 tumor sample Case marker detected. Intermediate cell carcinoma tissue: Liver; batch: batch2
  • GSM7729347 YSINT26 tumor sample Case marker detected. Intermediate cell carcinoma tissue: Liver; batch: batch2

Possible control samples

Samples currently treated as controls or baseline.

7
  • GSM7729323 YSINT2 normal tissue Control marker detected. Non-tumor tissue: Liver; batch: batch1
  • GSM7729324 YSINT3 normal tissue Control marker detected. Non-tumor tissue: Liver; batch: batch1
  • GSM7729325 YSINT4 normal tissue Control marker detected. Non-tumor tissue: Liver; batch: batch1
  • GSM7729326 YSINT5 normal tissue Control marker detected. Non-tumor tissue: Liver; batch: batch1
  • GSM7729327 YSINT6 normal tissue Control marker detected. Non-tumor tissue: Liver; batch: batch1
  • GSM7729344 YSINT23 normal tissue Control marker detected. Non-tumor tissue: Liver; batch: batch2
  • GSM7729345 YSINT24 normal tissue Control marker detected. Non-tumor tissue: Liver; batch: batch2

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

7 samples
  • GSM7729323 YSINT2 Non-tumor tissue: Liver; batch: batch1
  • GSM7729324 YSINT3 Non-tumor tissue: Liver; batch: batch1
  • GSM7729325 YSINT4 Non-tumor tissue: Liver; batch: batch1
  • GSM7729326 YSINT5 Non-tumor tissue: Liver; batch: batch1
  • GSM7729327 YSINT6 Non-tumor tissue: Liver; batch: batch1
  • GSM7729344 YSINT23 Non-tumor tissue: Liver; batch: batch2
  • GSM7729345 YSINT24 Non-tumor tissue: Liver; batch: batch2

tumor sample

18 samples
  • GSM7729328 YSINT7 Intermediate cell carcinoma tissue: Liver; batch: batch1
  • GSM7729329 YSINT8 Intermediate cell carcinoma tissue: Liver; batch: batch1
  • GSM7729330 YSINT9 Intermediate cell carcinoma tissue: Liver; batch: batch1
  • GSM7729331 YSINT10 Intermediate cell carcinoma tissue: Liver; batch: batch1
  • GSM7729332 YSINT11 Intermediate cell carcinoma tissue: Liver; batch: batch1
  • GSM7729333 YSINT12 Intermediate cell carcinoma tissue: Liver; batch: batch1
  • GSM7729334 YSINT13 Hepatocellular carcinoma tissue: Liver; batch: batch1
  • GSM7729335 YSINT14 Hepatocellular carcinoma tissue: Liver; batch: batch1
  • GSM7729336 YSINT15 Hepatocellular carcinoma tissue: Liver; batch: batch1
  • GSM7729337 YSINT16 Hepatocellular carcinoma tissue: Liver; batch: batch1
  • GSM7729338 YSINT17 Hepatocellular carcinoma tissue: Liver; batch: batch1
  • GSM7729339 YSINT18 Intrahepatic cholangiocarcinoma tissue: Liver; batch: batch1
  • GSM7729340 YSINT19 Intrahepatic cholangiocarcinoma tissue: Liver; batch: batch1
  • GSM7729341 YSINT20 Intrahepatic cholangiocarcinoma tissue: Liver; batch: batch1
  • GSM7729342 YSINT21 Intrahepatic cholangiocarcinoma tissue: Liver; batch: batch1
  • GSM7729343 YSINT22 Intrahepatic cholangiocarcinoma tissue: Liver; batch: batch1
  • GSM7729346 YSINT25 Intermediate cell carcinoma tissue: Liver; batch: batch2
  • GSM7729347 YSINT26 Intermediate cell carcinoma tissue: Liver; batch: batch2

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

25 samples

Review Audit Trail

0 decisions

No review decisions have been stored for this dataset.