Siftome Phase 3L

GSE304512

Developing precision medicine for remote liver cancer patients

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
2025-08-04
Last update
2026-01-29
Organization
James Cook University
Department
Not available
Public date
2026-01-28
Experiment types
Expression profiling by high throughput sequencing
Platforms
GPL34284 Illumina NovaSeq X Plus (Homo sapiens)
Series type
Series
SubSeries
Not available
BioProject
PRJNA1301410
Supplementary files
TAR: GSE304512_RAW.tar
Organism
Homo sapiens
Assay
bulk RNA-seq
Samples
38
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 19 samples
  • Likely control group normal tissue 19 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
GSE304512
Sample records
38 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
GSE304512
  • 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
GSE304512
  • 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
GSE304512
  • 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: GSE304512
dataset_title: Developing precision medicine for remote liver cancer patients
organism: Homo sapiens
assay_type: bulk RNA-seq
processed_data_available: true
raw_data_available: true
submission_date: 2025-08-04
last_update_date: 2026-01-29
organization_name: James Cook University
department: Not available
public_date: 2026-01-28
experiment_types: Expression profiling by high throughput sequencing
platforms: GPL34284 Illumina NovaSeq X Plus (Homo sapiens)
sub_series: Not available
bioproject: PRJNA1301410
supplementary_files: TAR: GSE304512_RAW.tar
series_type: Series

Why It Matched

  • Tumor vs unmatched normal · Tissue · suitability 0%.
  • Prioritized assay: bulk RNA-seq is the active assay expectation.
  • Downgraded disease context: not a colorectal/GI cancer cohort.
  • Processed data is available for downstream review.
  • 1 warning require review.

Why It May Not Be Suitable

  • Disease or condition label could not be normalized.
  • Non-colorectal cancer context downgraded for colorectal tumor-vs-normal tissue ranking.
  • Missing or unclear metadata: Disease clarity: Disease or condition metadata was not normalized.
  • Missing or unclear metadata: Treatment clarity: No unclear treatment split detected in the sample metadata.
  • Overall score capped because comparison suitability is weak for the selected search intent.
  • Overall score capped because 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

60 fields
Field Value Source Origin Confidence Evidence Reason
assay_type bulk RNA-seq dataset GSE304512 Runtime Siftome inference GEO:dataset:GSE304512:a9a2214f27bb50a4bbcc4badaa9a5bb026deead49536ea74ba1dff2949107635 high confidence bulk rna-seq dataset_accession: GSE304512 dataset_title: Developing precision medicine for remote liver cancer patients organism: Homo sapiens assay_type: bulk RNA-seq processed_data_availab... keyword match keyword match: bulk rna-seq
organism Homo sapiens dataset GSE304512 Runtime Siftome inference GEO:dataset:GSE304512:a9a2214f27bb50a4bbcc4badaa9a5bb026deead49536ea74ba1dff2949107635 high confidence homo sapiens dataset_accession: GSE304512 dataset_title: Developing precision medicine for remote liver cancer patients organism: Homo sapiens assay_type: bulk RNA-seq processed_data_availab... keyword match keyword match: homo sapiens
sample_type normal tissue sample GSM9151771 Runtime Siftome inference GEO:sample:GSM9151771:0ebab46a91c05718cda77066c9ee192aebf0261fb634bb05379297532eee2719 low confidence normal sample_accession: GSM9151771 sample_title: Patient 001, Normal Liver source_name: Liver characteristics: tissue: Liver Patient 001, Normal Liver controlled vocabulary controlled vocabulary sample type match: normal
sample_type normal tissue sample GSM9151772 Runtime Siftome inference GEO:sample:GSM9151772:44b91d23a3506b0ad49322d94beae1f12889dfb3433fa588feb990e57726c7b7 low confidence normal sample_accession: GSM9151772 sample_title: Patient 002, Normal Liver source_name: Liver characteristics: tissue: Liver Patient 002, Normal Liver controlled vocabulary controlled vocabulary sample type match: normal
sample_type normal tissue sample GSM9151773 Runtime Siftome inference GEO:sample:GSM9151773:13948c63f94f44fcd9eb5ba7c1f27b82636198b6b3edb18de00991988a64de1a low confidence normal sample_accession: GSM9151773 sample_title: Patient 003, Normal Liver source_name: Liver characteristics: tissue: Liver Patient 003, Normal Liver controlled vocabulary controlled vocabulary sample type match: normal
sample_type normal tissue sample GSM9151774 Runtime Siftome inference GEO:sample:GSM9151774:e46bbf985bf01ff58ef1259c5bdcfb73e2c345708f3328825f6a2ddfa3c9deb7 low confidence normal sample_accession: GSM9151774 sample_title: Patient 004, Normal Liver source_name: Liver characteristics: tissue: Liver Patient 004, Normal Liver controlled vocabulary controlled vocabulary sample type match: normal
sample_type normal tissue sample GSM9151775 Runtime Siftome inference GEO:sample:GSM9151775:d968b6706ccf74a5deb8fb5cf0f71cde1c2b77ab86ee299a060833e63085e554 low confidence normal sample_accession: GSM9151775 sample_title: Patient 005, Normal Liver source_name: Liver characteristics: tissue: Liver Patient 005, Normal Liver controlled vocabulary controlled vocabulary sample type match: normal
sample_type normal tissue sample GSM9151776 Runtime Siftome inference GEO:sample:GSM9151776:bb7f4f7c0820b522dc324499c08b066c817facb5083170ab6e52468e19790d5b low confidence normal sample_accession: GSM9151776 sample_title: Patient 006, Normal Liver source_name: Liver characteristics: tissue: Liver Patient 006, Normal Liver controlled vocabulary controlled vocabulary sample type match: normal
sample_type normal tissue sample GSM9151777 Runtime Siftome inference GEO:sample:GSM9151777:89a84943d3ff05fd169c1585c375f871b8171c45648c9617d64ad47635d614a3 low confidence normal sample_accession: GSM9151777 sample_title: Patient 007, Normal Liver source_name: Liver characteristics: tissue: Liver Patient 007, Normal Liver controlled vocabulary controlled vocabulary sample type match: normal
sample_type normal tissue sample GSM9151778 Runtime Siftome inference GEO:sample:GSM9151778:da0fd3ef6e09354fb4be295f8abbf8ec2501324c0ec54fe64344ed5623fac0de low confidence normal sample_accession: GSM9151778 sample_title: Patient 008, Normal Liver source_name: Liver characteristics: tissue: Liver Patient 008, Normal Liver controlled vocabulary controlled vocabulary sample type match: normal
sample_type normal tissue sample GSM9151779 Runtime Siftome inference GEO:sample:GSM9151779:b0f35b01941750ed4c145bf63a3d729c51a5d2d302aa130a2ee86bebde2057d8 low confidence normal sample_accession: GSM9151779 sample_title: Patient 009, Normal Liver source_name: Liver characteristics: tissue: Liver Patient 009, Normal Liver controlled vocabulary controlled vocabulary sample type match: normal
sample_type normal tissue sample GSM9151780 Runtime Siftome inference GEO:sample:GSM9151780:bed81e950b74588193cd042ceebfbde56a07132d42f441e22626774fe8ea1760 low confidence normal sample_accession: GSM9151780 sample_title: Patient 010, Normal Liver source_name: Liver characteristics: tissue: Liver Patient 010, Normal Liver controlled vocabulary controlled vocabulary sample type match: normal
sample_type normal tissue sample GSM9151781 Runtime Siftome inference GEO:sample:GSM9151781:dd7655c6a4e51c77658ace86e95e0fb406544ce0d90acea9bc917ca218dbcbd8 low confidence normal sample_accession: GSM9151781 sample_title: Patient 012, Normal Liver source_name: Liver characteristics: tissue: Liver Patient 012, Normal Liver controlled vocabulary controlled vocabulary sample type match: normal
sample_type normal tissue sample GSM9151782 Runtime Siftome inference GEO:sample:GSM9151782:04f4823299bcbbc634d225128078d9328344b218582e600dd0ff7a8ffb3c1041 low confidence normal sample_accession: GSM9151782 sample_title: Patient 014, Normal Liver source_name: Liver characteristics: tissue: Liver Patient 014, Normal Liver controlled vocabulary controlled vocabulary sample type match: normal
sample_type normal tissue sample GSM9151783 Runtime Siftome inference GEO:sample:GSM9151783:d6884cd6f3544b5da209cb567499c486e471a71498945b576524764dc28ded4f low confidence normal sample_accession: GSM9151783 sample_title: Patient 015, Normal Liver source_name: Liver characteristics: tissue: Liver Patient 015, Normal Liver controlled vocabulary controlled vocabulary sample type match: normal
sample_type normal tissue sample GSM9151784 Runtime Siftome inference GEO:sample:GSM9151784:46ee02e1f4e3a31f4b95d249795179c29e227e8bbfe7ea3c6d3e586f80bf1e9a low confidence normal sample_accession: GSM9151784 sample_title: Patient 017, Normal Liver source_name: Liver characteristics: tissue: Liver Patient 017, Normal Liver controlled vocabulary controlled vocabulary sample type match: normal
sample_type normal tissue sample GSM9151785 Runtime Siftome inference GEO:sample:GSM9151785:59256d51dbe003f22d62ac40ac29e4dde6f61d756a884e4865343fc44fbf46b1 low confidence normal sample_accession: GSM9151785 sample_title: Patient 018, Normal Liver source_name: Liver characteristics: tissue: Liver Patient 018, Normal Liver controlled vocabulary controlled vocabulary sample type match: normal
sample_type normal tissue sample GSM9151786 Runtime Siftome inference GEO:sample:GSM9151786:1d481954523130f22151e3898ef6aaefd18dab653a2fa2c1ec62d15c52a632dd low confidence normal sample_accession: GSM9151786 sample_title: Patient 019, Normal Liver source_name: Liver characteristics: tissue: Liver Patient 019, Normal Liver controlled vocabulary controlled vocabulary sample type match: normal
sample_type normal tissue sample GSM9151787 Runtime Siftome inference GEO:sample:GSM9151787:4e8d31afe7a2e18b4c0d3fdb0b174d9b32753b089db85eefb53be3a89df0198b low confidence normal sample_accession: GSM9151787 sample_title: Patient 020, Normal Liver source_name: Liver characteristics: tissue: Liver Patient 020, Normal Liver controlled vocabulary controlled vocabulary sample type match: normal
sample_type normal tissue sample GSM9151788 Runtime Siftome inference GEO:sample:GSM9151788:de4cec5586e65e221717cda848516283e831fb1373ab3e61eef0d4c65897fdf8 low confidence normal sample_accession: GSM9151788 sample_title: Patient 021, Normal Liver source_name: Liver characteristics: tissue: Liver Patient 021, Normal Liver controlled vocabulary controlled vocabulary sample type match: normal
sample_type normal tissue sample GSM9151789 Runtime Siftome inference GEO:sample:GSM9151789:00719977402fd899570fd60fcdc622136c2bb69eae119104b44f3fca81a626e1 low confidence normal sample_accession: GSM9151789 sample_title: Patient 022, Normal Liver source_name: Liver characteristics: tissue: Liver Patient 022, Normal Liver controlled vocabulary controlled vocabulary sample type match: normal
sample_type tumor sample sample GSM9151790 Runtime Siftome inference GEO:sample:GSM9151790:1b0a478487db627ad4b0dd4b81ae2a9c730552cc03edce2fbecf154dfcedeb05 low confidence tumour sample_accession: GSM9151790 sample_title: Patient 001, Tumour Tissue source_name: Hepatocellular Carcinoma characteristics: tissue: Hepatocellular Carcinoma Patient 001, Tumour... controlled vocabulary controlled vocabulary sample type match: tumour
sample_type tumor sample sample GSM9151791 Runtime Siftome inference GEO:sample:GSM9151791:2123ff6b600036308052b556c41ae7ea3a09d194d6c733af353cd709a92153fb low confidence tumour sample_accession: GSM9151791 sample_title: Patient 002, Tumour Tissue source_name: Hepatocellular Carcinoma characteristics: tissue: Hepatocellular Carcinoma Patient 002, Tumour... controlled vocabulary controlled vocabulary sample type match: tumour
sample_type tumor sample sample GSM9151792 Runtime Siftome inference GEO:sample:GSM9151792:810f9d30794c9721bfa9587142857210ba6665d8fd7a2c54e262b586bdf35faf low confidence tumour sample_accession: GSM9151792 sample_title: Patient 003, Tumour Tissue source_name: Hepatocellular Carcinoma characteristics: tissue: Hepatocellular Carcinoma Patient 003, Tumour... controlled vocabulary controlled vocabulary sample type match: tumour
sample_type tumor sample sample GSM9151793 Runtime Siftome inference GEO:sample:GSM9151793:a969e71a7ec928e740e27acdbbf37c55d2fb47e52626a8d5f4816d7e4e21559f low confidence tumour sample_accession: GSM9151793 sample_title: Patient 004, Tumour Tissue source_name: Hepatocellular Carcinoma characteristics: tissue: Hepatocellular Carcinoma Patient 004, Tumour... controlled vocabulary controlled vocabulary sample type match: tumour
sample_type tumor sample sample GSM9151794 Runtime Siftome inference GEO:sample:GSM9151794:ef24978d13b2e424d1ee055ae5d8a86d07e7cb6236d65392338560f6c24c7ab1 low confidence tumour sample_accession: GSM9151794 sample_title: Patient 005, Tumour Tissue source_name: Hepatocellular Carcinoma characteristics: tissue: Hepatocellular Carcinoma Patient 005, Tumour... controlled vocabulary controlled vocabulary sample type match: tumour
sample_type tumor sample sample GSM9151795 Runtime Siftome inference GEO:sample:GSM9151795:59bffeabe48d90f59d90950d0acae4c8861c9fcf587502f7ea784927beb20114 low confidence tumour sample_accession: GSM9151795 sample_title: Patient 006, Tumour Tissue source_name: Hepatocellular Carcinoma characteristics: tissue: Hepatocellular Carcinoma Patient 006, Tumour... controlled vocabulary controlled vocabulary sample type match: tumour
sample_type tumor sample sample GSM9151796 Runtime Siftome inference GEO:sample:GSM9151796:2613269d4eaacd7680a9dc32ca9a3808eff208e931f03b58a22640ac2873ec8f low confidence tumour sample_accession: GSM9151796 sample_title: Patient 007, Tumour Tissue source_name: Hepatocellular Carcinoma characteristics: tissue: Hepatocellular Carcinoma Patient 007, Tumour... controlled vocabulary controlled vocabulary sample type match: tumour
sample_type tumor sample sample GSM9151797 Runtime Siftome inference GEO:sample:GSM9151797:442b0fd05bcd1f1e2b4adb45657afd4a9890334012dc4e9126a0b9b6e2cf6751 low confidence tumour sample_accession: GSM9151797 sample_title: Patient 008, Tumour Tissue source_name: Hepatocellular Carcinoma characteristics: tissue: Hepatocellular Carcinoma Patient 008, Tumour... controlled vocabulary controlled vocabulary sample type match: tumour
sample_type tumor sample sample GSM9151798 Runtime Siftome inference GEO:sample:GSM9151798:0c3b04ca2dc53a2c7aa65a5c2f7b743f752d525cdfc4d16225b5ced5d69269bf low confidence tumour sample_accession: GSM9151798 sample_title: Patient 009, Tumour Tissue source_name: Hepatocellular Carcinoma characteristics: tissue: Hepatocellular Carcinoma Patient 009, Tumour... controlled vocabulary controlled vocabulary sample type match: tumour
sample_type tumor sample sample GSM9151799 Runtime Siftome inference GEO:sample:GSM9151799:2535f82187b6341dd5724ee4a014055a552a0395ddba5d97efcd094a2404dc0e low confidence tumour sample_accession: GSM9151799 sample_title: Patient 010, Tumour Tissue source_name: Hepatocellular Carcinoma characteristics: tissue: Hepatocellular Carcinoma Patient 010, Tumour... controlled vocabulary controlled vocabulary sample type match: tumour
sample_type tumor sample sample GSM9151800 Runtime Siftome inference GEO:sample:GSM9151800:b974e39cf7edd9fcd03320be902447679167d10a471149d01c6c8976a526dfc3 low confidence tumour sample_accession: GSM9151800 sample_title: Patient 012, Tumour Tissue source_name: Hepatocellular Carcinoma characteristics: tissue: Hepatocellular Carcinoma Patient 012, Tumour... controlled vocabulary controlled vocabulary sample type match: tumour
sample_type tumor sample sample GSM9151801 Runtime Siftome inference GEO:sample:GSM9151801:3d64e8a1fd7e5cc7e99b7f4f09c607d1c8cea64b2704a7f31bfb65f080821a38 low confidence tumour sample_accession: GSM9151801 sample_title: Patient 014, Tumour Tissue source_name: Hepatocellular Carcinoma characteristics: tissue: Hepatocellular Carcinoma Patient 014, Tumour... controlled vocabulary controlled vocabulary sample type match: tumour
sample_type tumor sample sample GSM9151802 Runtime Siftome inference GEO:sample:GSM9151802:dda257385a261816bba60e232c33648b093f4c62f22944df8bff3a3619fb1904 low confidence tumour sample_accession: GSM9151802 sample_title: Patient 015, Tumour Tissue source_name: Hepatocellular Carcinoma characteristics: tissue: Hepatocellular Carcinoma Patient 015, Tumour... controlled vocabulary controlled vocabulary sample type match: tumour
sample_type tumor sample sample GSM9151803 Runtime Siftome inference GEO:sample:GSM9151803:f6cc1afe76b8878a4f2648c2b286f42e64294a18ea7291550e5e5378b8655ac3 low confidence tumour sample_accession: GSM9151803 sample_title: Patient 017, Tumour Tissue source_name: Hepatocellular Carcinoma characteristics: tissue: Hepatocellular Carcinoma Patient 017, Tumour... controlled vocabulary controlled vocabulary sample type match: tumour
sample_type tumor sample sample GSM9151804 Runtime Siftome inference GEO:sample:GSM9151804:50ab0b87ee05546a2b6614b0e380ba7abb0a119fb3dec7e020ae345c4f85e010 low confidence tumour sample_accession: GSM9151804 sample_title: Patient 018, Tumour Tissue source_name: Hepatocellular Carcinoma characteristics: tissue: Hepatocellular Carcinoma Patient 018, Tumour... controlled vocabulary controlled vocabulary sample type match: tumour
sample_type tumor sample sample GSM9151805 Runtime Siftome inference GEO:sample:GSM9151805:e29b8303ee488e5e4573b03e38e7249d3aea7b1f0a340a2030ebc986c1382305 low confidence tumour sample_accession: GSM9151805 sample_title: Patient 019, Tumour Tissue source_name: Hepatocellular Carcinoma characteristics: tissue: Hepatocellular Carcinoma Patient 019, Tumour... controlled vocabulary controlled vocabulary sample type match: tumour
sample_type tumor sample sample GSM9151806 Runtime Siftome inference GEO:sample:GSM9151806:ee8414156ddabd1e572ee86bd389aed317b16c337e108ff7232c90b1530c793a low confidence tumour sample_accession: GSM9151806 sample_title: Patient 020, Tumour Tissue source_name: Hepatocellular Carcinoma characteristics: tissue: Hepatocellular Carcinoma Patient 020, Tumour... controlled vocabulary controlled vocabulary sample type match: tumour
sample_type tumor sample sample GSM9151807 Runtime Siftome inference GEO:sample:GSM9151807:d86253f74ccb71e1da2172461448af3ce508e21d1c0c4f61fe7519f19059f721 low confidence tumour sample_accession: GSM9151807 sample_title: Patient 021, Tumour Tissue source_name: Hepatocellular Carcinoma characteristics: tissue: Hepatocellular Carcinoma Patient 021, Tumour... controlled vocabulary controlled vocabulary sample type match: tumour
sample_type tumor sample sample GSM9151808 Runtime Siftome inference GEO:sample:GSM9151808:bbebb7fb8a4d7e6c0668f59d3012101934a755f955627e086a129d9a3716d09e low confidence tumour sample_accession: GSM9151808 sample_title: Patient 022, Tumour Tissue source_name: Hepatocellular Carcinoma characteristics: tissue: Hepatocellular Carcinoma Patient 022, Tumour... controlled vocabulary controlled vocabulary sample type match: tumour
tissue liver dataset GSE304512 Runtime Siftome inference GEO:dataset:GSE304512:a9a2214f27bb50a4bbcc4badaa9a5bb026deead49536ea74ba1dff2949107635 low confidence liver dataset_accession: GSE304512 dataset_title: Developing precision medicine for remote liver cancer patients organism: Homo sapiens assay_type: bulk RNA-seq processed_data_availab... controlled vocabulary controlled vocabulary tissue match: liver
tissue liver sample GSM9151771 Runtime Siftome inference GEO:sample:GSM9151771:0ebab46a91c05718cda77066c9ee192aebf0261fb634bb05379297532eee2719 low confidence liver sample_accession: GSM9151771 sample_title: Patient 001, Normal Liver source_name: Liver characteristics: tissue: Liver Patient 001, Normal Liver controlled vocabulary controlled vocabulary tissue match: liver
tissue liver sample GSM9151772 Runtime Siftome inference GEO:sample:GSM9151772:44b91d23a3506b0ad49322d94beae1f12889dfb3433fa588feb990e57726c7b7 low confidence liver sample_accession: GSM9151772 sample_title: Patient 002, Normal Liver source_name: Liver characteristics: tissue: Liver Patient 002, Normal Liver controlled vocabulary controlled vocabulary tissue match: liver
tissue liver sample GSM9151773 Runtime Siftome inference GEO:sample:GSM9151773:13948c63f94f44fcd9eb5ba7c1f27b82636198b6b3edb18de00991988a64de1a low confidence liver sample_accession: GSM9151773 sample_title: Patient 003, Normal Liver source_name: Liver characteristics: tissue: Liver Patient 003, Normal Liver controlled vocabulary controlled vocabulary tissue match: liver
tissue liver sample GSM9151774 Runtime Siftome inference GEO:sample:GSM9151774:e46bbf985bf01ff58ef1259c5bdcfb73e2c345708f3328825f6a2ddfa3c9deb7 low confidence liver sample_accession: GSM9151774 sample_title: Patient 004, Normal Liver source_name: Liver characteristics: tissue: Liver Patient 004, Normal Liver controlled vocabulary controlled vocabulary tissue match: liver
tissue liver sample GSM9151775 Runtime Siftome inference GEO:sample:GSM9151775:d968b6706ccf74a5deb8fb5cf0f71cde1c2b77ab86ee299a060833e63085e554 low confidence liver sample_accession: GSM9151775 sample_title: Patient 005, Normal Liver source_name: Liver characteristics: tissue: Liver Patient 005, Normal Liver controlled vocabulary controlled vocabulary tissue match: liver
tissue liver sample GSM9151776 Runtime Siftome inference GEO:sample:GSM9151776:bb7f4f7c0820b522dc324499c08b066c817facb5083170ab6e52468e19790d5b low confidence liver sample_accession: GSM9151776 sample_title: Patient 006, Normal Liver source_name: Liver characteristics: tissue: Liver Patient 006, Normal Liver controlled vocabulary controlled vocabulary tissue match: liver
tissue liver sample GSM9151777 Runtime Siftome inference GEO:sample:GSM9151777:89a84943d3ff05fd169c1585c375f871b8171c45648c9617d64ad47635d614a3 low confidence liver sample_accession: GSM9151777 sample_title: Patient 007, Normal Liver source_name: Liver characteristics: tissue: Liver Patient 007, Normal Liver controlled vocabulary controlled vocabulary tissue match: liver
tissue liver sample GSM9151778 Runtime Siftome inference GEO:sample:GSM9151778:da0fd3ef6e09354fb4be295f8abbf8ec2501324c0ec54fe64344ed5623fac0de low confidence liver sample_accession: GSM9151778 sample_title: Patient 008, Normal Liver source_name: Liver characteristics: tissue: Liver Patient 008, Normal Liver controlled vocabulary controlled vocabulary tissue match: liver
tissue liver sample GSM9151779 Runtime Siftome inference GEO:sample:GSM9151779:b0f35b01941750ed4c145bf63a3d729c51a5d2d302aa130a2ee86bebde2057d8 low confidence liver sample_accession: GSM9151779 sample_title: Patient 009, Normal Liver source_name: Liver characteristics: tissue: Liver Patient 009, Normal Liver controlled vocabulary controlled vocabulary tissue match: liver
tissue liver sample GSM9151780 Runtime Siftome inference GEO:sample:GSM9151780:bed81e950b74588193cd042ceebfbde56a07132d42f441e22626774fe8ea1760 low confidence liver sample_accession: GSM9151780 sample_title: Patient 010, Normal Liver source_name: Liver characteristics: tissue: Liver Patient 010, Normal Liver controlled vocabulary controlled vocabulary tissue match: liver
tissue liver sample GSM9151781 Runtime Siftome inference GEO:sample:GSM9151781:dd7655c6a4e51c77658ace86e95e0fb406544ce0d90acea9bc917ca218dbcbd8 low confidence liver sample_accession: GSM9151781 sample_title: Patient 012, Normal Liver source_name: Liver characteristics: tissue: Liver Patient 012, Normal Liver controlled vocabulary controlled vocabulary tissue match: liver
tissue liver sample GSM9151782 Runtime Siftome inference GEO:sample:GSM9151782:04f4823299bcbbc634d225128078d9328344b218582e600dd0ff7a8ffb3c1041 low confidence liver sample_accession: GSM9151782 sample_title: Patient 014, Normal Liver source_name: Liver characteristics: tissue: Liver Patient 014, Normal Liver controlled vocabulary controlled vocabulary tissue match: liver
tissue liver sample GSM9151783 Runtime Siftome inference GEO:sample:GSM9151783:d6884cd6f3544b5da209cb567499c486e471a71498945b576524764dc28ded4f low confidence liver sample_accession: GSM9151783 sample_title: Patient 015, Normal Liver source_name: Liver characteristics: tissue: Liver Patient 015, Normal Liver controlled vocabulary controlled vocabulary tissue match: liver
tissue liver sample GSM9151784 Runtime Siftome inference GEO:sample:GSM9151784:46ee02e1f4e3a31f4b95d249795179c29e227e8bbfe7ea3c6d3e586f80bf1e9a low confidence liver sample_accession: GSM9151784 sample_title: Patient 017, Normal Liver source_name: Liver characteristics: tissue: Liver Patient 017, Normal Liver controlled vocabulary controlled vocabulary tissue match: liver
tissue liver sample GSM9151785 Runtime Siftome inference GEO:sample:GSM9151785:59256d51dbe003f22d62ac40ac29e4dde6f61d756a884e4865343fc44fbf46b1 low confidence liver sample_accession: GSM9151785 sample_title: Patient 018, Normal Liver source_name: Liver characteristics: tissue: Liver Patient 018, Normal Liver controlled vocabulary controlled vocabulary tissue match: liver
tissue liver sample GSM9151786 Runtime Siftome inference GEO:sample:GSM9151786:1d481954523130f22151e3898ef6aaefd18dab653a2fa2c1ec62d15c52a632dd low confidence liver sample_accession: GSM9151786 sample_title: Patient 019, Normal Liver source_name: Liver characteristics: tissue: Liver Patient 019, Normal Liver controlled vocabulary controlled vocabulary tissue match: liver
tissue liver sample GSM9151787 Runtime Siftome inference GEO:sample:GSM9151787:4e8d31afe7a2e18b4c0d3fdb0b174d9b32753b089db85eefb53be3a89df0198b low confidence liver sample_accession: GSM9151787 sample_title: Patient 020, Normal Liver source_name: Liver characteristics: tissue: Liver Patient 020, Normal Liver controlled vocabulary controlled vocabulary tissue match: liver
tissue liver sample GSM9151788 Runtime Siftome inference GEO:sample:GSM9151788:de4cec5586e65e221717cda848516283e831fb1373ab3e61eef0d4c65897fdf8 low confidence liver sample_accession: GSM9151788 sample_title: Patient 021, Normal Liver source_name: Liver characteristics: tissue: Liver Patient 021, Normal Liver controlled vocabulary controlled vocabulary tissue match: liver
tissue liver sample GSM9151789 Runtime Siftome inference GEO:sample:GSM9151789:00719977402fd899570fd60fcdc622136c2bb69eae119104b44f3fca81a626e1 low confidence liver sample_accession: GSM9151789 sample_title: Patient 022, Normal Liver source_name: Liver characteristics: tissue: Liver Patient 022, Normal Liver controlled vocabulary controlled vocabulary tissue match: liver

Sample Group Preview

Possible case samples

Samples currently treated as the comparison case group.

19
  • GSM9151790 Patient 001, Tumour Tissue tumor sample Case marker detected. Hepatocellular Carcinoma tissue: Hepatocellular Carcinoma
  • GSM9151791 Patient 002, Tumour Tissue tumor sample Case marker detected. Hepatocellular Carcinoma tissue: Hepatocellular Carcinoma
  • GSM9151792 Patient 003, Tumour Tissue tumor sample Case marker detected. Hepatocellular Carcinoma tissue: Hepatocellular Carcinoma
  • GSM9151793 Patient 004, Tumour Tissue tumor sample Case marker detected. Hepatocellular Carcinoma tissue: Hepatocellular Carcinoma
  • GSM9151794 Patient 005, Tumour Tissue tumor sample Case marker detected. Hepatocellular Carcinoma tissue: Hepatocellular Carcinoma
  • GSM9151795 Patient 006, Tumour Tissue tumor sample Case marker detected. Hepatocellular Carcinoma tissue: Hepatocellular Carcinoma
  • GSM9151796 Patient 007, Tumour Tissue tumor sample Case marker detected. Hepatocellular Carcinoma tissue: Hepatocellular Carcinoma
  • GSM9151797 Patient 008, Tumour Tissue tumor sample Case marker detected. Hepatocellular Carcinoma tissue: Hepatocellular Carcinoma
  • GSM9151798 Patient 009, Tumour Tissue tumor sample Case marker detected. Hepatocellular Carcinoma tissue: Hepatocellular Carcinoma
  • GSM9151799 Patient 010, Tumour Tissue tumor sample Case marker detected. Hepatocellular Carcinoma tissue: Hepatocellular Carcinoma
  • GSM9151800 Patient 012, Tumour Tissue tumor sample Case marker detected. Hepatocellular Carcinoma tissue: Hepatocellular Carcinoma
  • GSM9151801 Patient 014, Tumour Tissue tumor sample Case marker detected. Hepatocellular Carcinoma tissue: Hepatocellular Carcinoma
  • GSM9151802 Patient 015, Tumour Tissue tumor sample Case marker detected. Hepatocellular Carcinoma tissue: Hepatocellular Carcinoma
  • GSM9151803 Patient 017, Tumour Tissue tumor sample Case marker detected. Hepatocellular Carcinoma tissue: Hepatocellular Carcinoma
  • GSM9151804 Patient 018, Tumour Tissue tumor sample Case marker detected. Hepatocellular Carcinoma tissue: Hepatocellular Carcinoma
  • GSM9151805 Patient 019, Tumour Tissue tumor sample Case marker detected. Hepatocellular Carcinoma tissue: Hepatocellular Carcinoma
  • GSM9151806 Patient 020, Tumour Tissue tumor sample Case marker detected. Hepatocellular Carcinoma tissue: Hepatocellular Carcinoma
  • GSM9151807 Patient 021, Tumour Tissue tumor sample Case marker detected. Hepatocellular Carcinoma tissue: Hepatocellular Carcinoma
  • GSM9151808 Patient 022, Tumour Tissue tumor sample Case marker detected. Hepatocellular Carcinoma tissue: Hepatocellular Carcinoma

Possible control samples

Samples currently treated as controls or baseline.

19
  • GSM9151771 Patient 001, Normal Liver normal tissue Control marker detected. Liver tissue: Liver
  • GSM9151772 Patient 002, Normal Liver normal tissue Control marker detected. Liver tissue: Liver
  • GSM9151773 Patient 003, Normal Liver normal tissue Control marker detected. Liver tissue: Liver
  • GSM9151774 Patient 004, Normal Liver normal tissue Control marker detected. Liver tissue: Liver
  • GSM9151775 Patient 005, Normal Liver normal tissue Control marker detected. Liver tissue: Liver
  • GSM9151776 Patient 006, Normal Liver normal tissue Control marker detected. Liver tissue: Liver
  • GSM9151777 Patient 007, Normal Liver normal tissue Control marker detected. Liver tissue: Liver
  • GSM9151778 Patient 008, Normal Liver normal tissue Control marker detected. Liver tissue: Liver
  • GSM9151779 Patient 009, Normal Liver normal tissue Control marker detected. Liver tissue: Liver
  • GSM9151780 Patient 010, Normal Liver normal tissue Control marker detected. Liver tissue: Liver
  • GSM9151781 Patient 012, Normal Liver normal tissue Control marker detected. Liver tissue: Liver
  • GSM9151782 Patient 014, Normal Liver normal tissue Control marker detected. Liver tissue: Liver
  • GSM9151783 Patient 015, Normal Liver normal tissue Control marker detected. Liver tissue: Liver
  • GSM9151784 Patient 017, Normal Liver normal tissue Control marker detected. Liver tissue: Liver
  • GSM9151785 Patient 018, Normal Liver normal tissue Control marker detected. Liver tissue: Liver
  • GSM9151786 Patient 019, Normal Liver normal tissue Control marker detected. Liver tissue: Liver
  • GSM9151787 Patient 020, Normal Liver normal tissue Control marker detected. Liver tissue: Liver
  • GSM9151788 Patient 021, Normal Liver normal tissue Control marker detected. Liver tissue: Liver
  • GSM9151789 Patient 022, Normal Liver normal tissue Control marker detected. Liver tissue: Liver

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

19 samples
  • GSM9151771 Patient 001, Normal Liver Liver tissue: Liver
  • GSM9151772 Patient 002, Normal Liver Liver tissue: Liver
  • GSM9151773 Patient 003, Normal Liver Liver tissue: Liver
  • GSM9151774 Patient 004, Normal Liver Liver tissue: Liver
  • GSM9151775 Patient 005, Normal Liver Liver tissue: Liver
  • GSM9151776 Patient 006, Normal Liver Liver tissue: Liver
  • GSM9151777 Patient 007, Normal Liver Liver tissue: Liver
  • GSM9151778 Patient 008, Normal Liver Liver tissue: Liver
  • GSM9151779 Patient 009, Normal Liver Liver tissue: Liver
  • GSM9151780 Patient 010, Normal Liver Liver tissue: Liver
  • GSM9151781 Patient 012, Normal Liver Liver tissue: Liver
  • GSM9151782 Patient 014, Normal Liver Liver tissue: Liver
  • GSM9151783 Patient 015, Normal Liver Liver tissue: Liver
  • GSM9151784 Patient 017, Normal Liver Liver tissue: Liver
  • GSM9151785 Patient 018, Normal Liver Liver tissue: Liver
  • GSM9151786 Patient 019, Normal Liver Liver tissue: Liver
  • GSM9151787 Patient 020, Normal Liver Liver tissue: Liver
  • GSM9151788 Patient 021, Normal Liver Liver tissue: Liver
  • GSM9151789 Patient 022, Normal Liver Liver tissue: Liver

tumor sample

19 samples
  • GSM9151790 Patient 001, Tumour Tissue Hepatocellular Carcinoma tissue: Hepatocellular Carcinoma
  • GSM9151791 Patient 002, Tumour Tissue Hepatocellular Carcinoma tissue: Hepatocellular Carcinoma
  • GSM9151792 Patient 003, Tumour Tissue Hepatocellular Carcinoma tissue: Hepatocellular Carcinoma
  • GSM9151793 Patient 004, Tumour Tissue Hepatocellular Carcinoma tissue: Hepatocellular Carcinoma
  • GSM9151794 Patient 005, Tumour Tissue Hepatocellular Carcinoma tissue: Hepatocellular Carcinoma
  • GSM9151795 Patient 006, Tumour Tissue Hepatocellular Carcinoma tissue: Hepatocellular Carcinoma
  • GSM9151796 Patient 007, Tumour Tissue Hepatocellular Carcinoma tissue: Hepatocellular Carcinoma
  • GSM9151797 Patient 008, Tumour Tissue Hepatocellular Carcinoma tissue: Hepatocellular Carcinoma
  • GSM9151798 Patient 009, Tumour Tissue Hepatocellular Carcinoma tissue: Hepatocellular Carcinoma
  • GSM9151799 Patient 010, Tumour Tissue Hepatocellular Carcinoma tissue: Hepatocellular Carcinoma
  • GSM9151800 Patient 012, Tumour Tissue Hepatocellular Carcinoma tissue: Hepatocellular Carcinoma
  • GSM9151801 Patient 014, Tumour Tissue Hepatocellular Carcinoma tissue: Hepatocellular Carcinoma
  • GSM9151802 Patient 015, Tumour Tissue Hepatocellular Carcinoma tissue: Hepatocellular Carcinoma
  • GSM9151803 Patient 017, Tumour Tissue Hepatocellular Carcinoma tissue: Hepatocellular Carcinoma
  • GSM9151804 Patient 018, Tumour Tissue Hepatocellular Carcinoma tissue: Hepatocellular Carcinoma
  • GSM9151805 Patient 019, Tumour Tissue Hepatocellular Carcinoma tissue: Hepatocellular Carcinoma
  • GSM9151806 Patient 020, Tumour Tissue Hepatocellular Carcinoma tissue: Hepatocellular Carcinoma
  • GSM9151807 Patient 021, Tumour Tissue Hepatocellular Carcinoma tissue: Hepatocellular Carcinoma
  • GSM9151808 Patient 022, Tumour Tissue Hepatocellular Carcinoma tissue: Hepatocellular Carcinoma

Score Breakdown

60%

relevance

  • Organism normalized.
  • Assay type normalized.
  • Tissue metadata normalized.
0%

comparison suitability

  • Tumor and normal sample groups detected.
  • No excluded sample type flags detected.
  • Tumor/normal design boosted for colorectal tumor-vs-normal tissue triage.
  • Patient tissue or biopsy specimens boosted for tissue comparison triage.
  • Non-colorectal cancer context downgraded for colorectal tumor-vs-normal tissue ranking.
85%

metadata quality

  • Sample source clarity: All samples have source metadata and clear GSE/GSM accessions.
  • Group clarity: Rule-based grouping found both case and control samples.
  • Disease clarity: Disease or condition metadata was not normalized.
  • Tissue clarity: Tissue metadata normalized.
  • Treatment clarity: No unclear treatment split detected in the sample metadata.
  • Replicate clarity: No pooled sample or technical replicate flags detected.
  • Data availability clarity: Dataset-level processed or raw data availability is explicit.
100%

data availability

  • Processed data available.
  • Raw data available.
34%

overall

  • Weighted score: 30% relevance, 30% comparison suitability, 25% metadata quality, 15% data availability.
  • Overall score capped because comparison suitability is weak for the selected search intent.
  • Overall score capped because tumor/normal grouping is from a non-colorectal cancer context.

Sample Links

38 samples

Review Audit Trail

0 decisions

No review decisions have been stored for this dataset.