Siftome Phase 3L

GSE135631

RNA-Seq data of tumors and paired adjacent tissues from 15 HCC 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
2019-08-09
Last update
2022-12-01
Organization
Second Military Medical University
Department
Not available
Public date
2022-12-01
Experiment types
Expression profiling by high throughput sequencing
Platforms
GPL16791 Illumina HiSeq 2500 (Homo sapiens)
Series type
Series
SubSeries
Not available
BioProject
PRJNA559494
Supplementary files
TXT: GSE135631_Read_Counts_Matrix_Gene_Level.txt.gz; TXT: GSE135631_TPM_Matrix_Gene_Level.txt.gz
Organism
Homo sapiens
Assay
bulk RNA-seq
Samples
30
Study design
Tumor vs matched 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 matched 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 90% Disease or condition metadata normalized. Organism normalized. Assay type normalized.
  • comparison suitability 0% Tumor and normal sample groups detected. No excluded sample type flags detected. Matched 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 normalized. Tissue clarity: Tissue metadata was not 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 matched normal Study design remains rule-derived: Tumor vs matched normal.
  • Specimen/source Tissue Specimen/source remains rule-derived: Tissue.
  • Likely case group tumor sample 15 samples
  • Likely control group normal tissue 15 samples

Warnings

  • TISSUE_TYPE_MISSING warning Tissue or cell type 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 matched 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: colorectal/GI relevance is unclear. 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 matched normal · Tissue · suitability 0%. Contributed to match or upgrade evidence.
  • Supporting fact Prioritized for patient tissue tumor-vs-normal triage. 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: colorectal/GI relevance is unclear. 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 Tissue or cell type 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: Tissue clarity: Tissue 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: colorectal/GI relevance is unclear. Contributed to downgrade or manual-review evidence.
  • Caution fact Missing or unclear metadata: Downgraded disease context: colorectal/GI relevance is unclear. 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
GSE135631
Sample records
30 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
GSE135631
  • 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
GSE135631
  • 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
GSE135631
  • 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: GSE135631
dataset_title: RNA-Seq data of tumors and paired adjacent tissues from 15 HCC patients
organism: Homo sapiens
assay_type: bulk RNA-seq
processed_data_available: true
raw_data_available: true
submission_date: 2019-08-09
last_update_date: 2022-12-01
organization_name: Second Military Medical University
department: Not available
public_date: 2022-12-01
experiment_types: Expression profiling by high throughput sequencing
platforms: GPL16791 Illumina HiSeq 2500 (Homo sapiens)
sub_series: Not available
bioproject: PRJNA559494
supplementary_files: TXT: GSE135631_Read_Counts_Matrix_Gene_Level.txt.gz; TXT: GSE135631_TPM_Matrix_Gene_Level.txt.gz
series_type: Series

Why It Matched

  • Tumor vs matched normal · Tissue · suitability 0%.
  • Prioritized for patient tissue tumor-vs-normal triage.
  • Prioritized assay: bulk RNA-seq is the active assay expectation.
  • Downgraded disease context: colorectal/GI relevance is unclear.
  • Processed data is available for downstream review.
  • 1 warning require review.

Why It May Not Be Suitable

  • Tissue or cell type could not be normalized.
  • Non-colorectal cancer context downgraded for colorectal tumor-vs-normal tissue ranking.
  • Missing or unclear metadata: Tissue clarity: Tissue 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: colorectal/GI relevance is unclear.
  • Missing or unclear metadata: Downgraded disease context: colorectal/GI relevance is unclear.
  • Comparison suitability score is below the Phase 1 recommended threshold.

Warnings

  • warning TISSUE_TYPE_MISSING Tissue or cell type could not be normalized.

Normalized Fields

48 fields
Field Value Source Origin Confidence Evidence Reason
assay_type bulk RNA-seq dataset GSE135631 Runtime Siftome inference GEO:dataset:GSE135631:a5a3a8033de823dc21dfd5207baaceb4ba4b74c772c6b65eb461d3b2c058fb77 high confidence bulk rna-seq dataset_accession: GSE135631 dataset_title: RNA-Seq data of tumors and paired adjacent tissues from 15 HCC patients organism: Homo sapiens assay_type: bulk RNA-seq processed_dat... keyword match keyword match: bulk rna-seq
disease colorectal cancer dataset GSE135631 Runtime Siftome inference GEO:dataset:GSE135631:a5a3a8033de823dc21dfd5207baaceb4ba4b74c772c6b65eb461d3b2c058fb77 medium confidence read dataset_accession: GSE135631 dataset_title: RNA-Seq data of tumors and paired adjacent tissues from 15 HCC patients organism: Homo sapiens assay_type: bulk RNA-seq processed_dat... controlled vocabulary controlled vocabulary disease match: read
normal_tissue_type adjacent normal sample GSM4023793 Runtime Siftome inference GEO:sample:GSM4023793:6e25a2d06cf04b51c7a67f305b132f1950b81e07b0753b6aa47fd18e6130bf05 high confidence adjacent normal sample_accession: GSM4023793 sample_title: Sample_067754N source_name: Adjacent tissue characteristics: individual: 67754; disease state: HCC; tissue: Adjacent normal Sample_067... controlled vocabulary controlled vocabulary normal tissue type match: adjacent normal
normal_tissue_type adjacent normal sample GSM4023795 Runtime Siftome inference GEO:sample:GSM4023795:07ffcbf8bc06acc4d700c28d936bfe9f35ad056e5e29ed04ce96d9ebdd46388f high confidence adjacent normal sample_accession: GSM4023795 sample_title: Sample_070103N source_name: Adjacent tissue characteristics: individual: 70103; disease state: HCC; tissue: Adjacent normal Sample_070... controlled vocabulary controlled vocabulary normal tissue type match: adjacent normal
normal_tissue_type adjacent normal sample GSM4023797 Runtime Siftome inference GEO:sample:GSM4023797:02a5195c92eca1f8c0ff2f399deaf5e4b658dfcdf124cd9b238e2e6424fcff23 high confidence adjacent normal sample_accession: GSM4023797 sample_title: Sample_070785N source_name: Adjacent tissue characteristics: individual: 70785; disease state: HCC; tissue: Adjacent normal Sample_070... controlled vocabulary controlled vocabulary normal tissue type match: adjacent normal
normal_tissue_type adjacent normal sample GSM4023799 Runtime Siftome inference GEO:sample:GSM4023799:15dce18ea5db1801e1966cf1332427cbc15e902b8192a3554bccfd0a6c23e9bc high confidence adjacent normal sample_accession: GSM4023799 sample_title: Sample_070880N source_name: Adjacent tissue characteristics: individual: 70880; disease state: HCC; tissue: Adjacent normal Sample_070... controlled vocabulary controlled vocabulary normal tissue type match: adjacent normal
normal_tissue_type adjacent normal sample GSM4023801 Runtime Siftome inference GEO:sample:GSM4023801:6afe68fbcc2a2cd9fb7414caf8f4fd99ff74983abf0d510176d7d58ddf678e55 high confidence adjacent normal sample_accession: GSM4023801 sample_title: Sample_074607N source_name: Adjacent tissue characteristics: individual: 74607; disease state: HCC; tissue: Adjacent normal Sample_074... controlled vocabulary controlled vocabulary normal tissue type match: adjacent normal
normal_tissue_type adjacent normal sample GSM4023803 Runtime Siftome inference GEO:sample:GSM4023803:2dcc0d0ba8fa435943a89cda7d09002474f0563a7a550e07ded15bffe6264b2f high confidence adjacent normal sample_accession: GSM4023803 sample_title: Sample_074720N source_name: Adjacent tissue characteristics: individual: 74720; disease state: HCC; tissue: Adjacent normal Sample_074... controlled vocabulary controlled vocabulary normal tissue type match: adjacent normal
normal_tissue_type adjacent normal sample GSM4023805 Runtime Siftome inference GEO:sample:GSM4023805:1eab899acec02377636c1e88f6fdf7d5cbc51970965d3bce6da5445603c1b685 high confidence adjacent normal sample_accession: GSM4023805 sample_title: Sample_074848N source_name: Adjacent tissue characteristics: individual: 74848; disease state: HCC; tissue: Adjacent normal Sample_074... controlled vocabulary controlled vocabulary normal tissue type match: adjacent normal
normal_tissue_type adjacent normal sample GSM4023807 Runtime Siftome inference GEO:sample:GSM4023807:a5b75a201e12995e3d8e8d168b90752395033a5cab574bf7fcd528f369c016ff high confidence adjacent normal sample_accession: GSM4023807 sample_title: Sample_075199N source_name: Adjacent tissue characteristics: individual: 75199; disease state: HCC; tissue: Adjacent normal Sample_075... controlled vocabulary controlled vocabulary normal tissue type match: adjacent normal
normal_tissue_type adjacent normal sample GSM4023809 Runtime Siftome inference GEO:sample:GSM4023809:c82ae47e57ca27c78bd4934f17154966c66d1baea0e13138844943b61e3b795f high confidence adjacent normal sample_accession: GSM4023809 sample_title: Sample_P070913N source_name: Adjacent tissue characteristics: individual: P070913; disease state: HCC; tissue: Adjacent normal Sample_... controlled vocabulary controlled vocabulary normal tissue type match: adjacent normal
normal_tissue_type adjacent normal sample GSM4023811 Runtime Siftome inference GEO:sample:GSM4023811:450768828f6831579bf5862ba7fa34e0870c3c8c53ca995ad605b2664ca0c5e7 high confidence adjacent normal sample_accession: GSM4023811 sample_title: Sample_P079741N source_name: Adjacent tissue characteristics: individual: P079741; disease state: HCC; tissue: Adjacent normal Sample_... controlled vocabulary controlled vocabulary normal tissue type match: adjacent normal
normal_tissue_type adjacent normal sample GSM4023813 Runtime Siftome inference GEO:sample:GSM4023813:aa7588f4ab6723a2f34b8627058e12f57e580c43ffe4006b74e4412ac18a5eb5 high confidence adjacent normal sample_accession: GSM4023813 sample_title: Sample_P079779N source_name: Adjacent tissue characteristics: individual: P079779; disease state: HCC; tissue: Adjacent normal Sample_... controlled vocabulary controlled vocabulary normal tissue type match: adjacent normal
normal_tissue_type adjacent normal sample GSM4023815 Runtime Siftome inference GEO:sample:GSM4023815:9087680e3a34005b332f2c9e3e2e2d798b2fb40b908ab3fb325fc9d634480256 high confidence adjacent normal sample_accession: GSM4023815 sample_title: Sample_P116019N source_name: Adjacent tissue characteristics: individual: P116019; disease state: HCC; tissue: Adjacent normal Sample_... controlled vocabulary controlled vocabulary normal tissue type match: adjacent normal
normal_tissue_type adjacent normal sample GSM4023817 Runtime Siftome inference GEO:sample:GSM4023817:b5103d99de9ca27d28845736a6b7c8e75303478da99f4cb78a3f271cd16535c4 high confidence adjacent normal sample_accession: GSM4023817 sample_title: Sample_R079741N source_name: Adjacent tissue characteristics: individual: R079741; disease state: HCC; tissue: Adjacent normal Sample_... controlled vocabulary controlled vocabulary normal tissue type match: adjacent normal
normal_tissue_type adjacent normal sample GSM4023819 Runtime Siftome inference GEO:sample:GSM4023819:84a7a8a8626ac42d2b6b61953d14b7704f55500c412f466eb948d49458832db0 high confidence adjacent normal sample_accession: GSM4023819 sample_title: Sample_R079779N source_name: Adjacent tissue characteristics: individual: R079779; disease state: HCC; tissue: Adjacent normal Sample_... controlled vocabulary controlled vocabulary normal tissue type match: adjacent normal
normal_tissue_type adjacent normal sample GSM4023821 Runtime Siftome inference GEO:sample:GSM4023821:a5818d87d9851a063e8d3b5416da2662d438feb6c11b850804c69302ca832fc3 high confidence adjacent normal sample_accession: GSM4023821 sample_title: Sample_R116019N source_name: Adjacent tissue characteristics: individual: R116019; disease state: HCC; tissue: Adjacent normal Sample_... controlled vocabulary controlled vocabulary normal tissue type match: adjacent normal
organism Homo sapiens dataset GSE135631 Runtime Siftome inference GEO:dataset:GSE135631:a5a3a8033de823dc21dfd5207baaceb4ba4b74c772c6b65eb461d3b2c058fb77 high confidence homo sapiens dataset_accession: GSE135631 dataset_title: RNA-Seq data of tumors and paired adjacent tissues from 15 HCC patients organism: Homo sapiens assay_type: bulk RNA-seq processed_dat... keyword match keyword match: homo sapiens
sample_type normal tissue sample GSM4023793 Runtime Siftome inference GEO:sample:GSM4023793:6e25a2d06cf04b51c7a67f305b132f1950b81e07b0753b6aa47fd18e6130bf05 high confidence adjacent normal sample_accession: GSM4023793 sample_title: Sample_067754N source_name: Adjacent tissue characteristics: individual: 67754; disease state: HCC; tissue: Adjacent normal Sample_067... controlled vocabulary controlled vocabulary sample type match: adjacent normal
sample_type tumor sample sample GSM4023794 Runtime Siftome inference GEO:sample:GSM4023794:c4dbe5c7c65d12aae79fe2be55850bb33999187274e136817c5688a9068d046c low confidence tumor sample_accession: GSM4023794 sample_title: Sample_067754T source_name: tumor characteristics: individual: 67754; disease state: HCC; tissue: tumor Sample_067754T controlled vocabulary controlled vocabulary sample type match: tumor
sample_type normal tissue sample GSM4023795 Runtime Siftome inference GEO:sample:GSM4023795:07ffcbf8bc06acc4d700c28d936bfe9f35ad056e5e29ed04ce96d9ebdd46388f high confidence adjacent normal sample_accession: GSM4023795 sample_title: Sample_070103N source_name: Adjacent tissue characteristics: individual: 70103; disease state: HCC; tissue: Adjacent normal Sample_070... controlled vocabulary controlled vocabulary sample type match: adjacent normal
sample_type tumor sample sample GSM4023796 Runtime Siftome inference GEO:sample:GSM4023796:fcc73e07b95173d5c01962962c3659ffb96d8395d3c3362c6d4cd599efdf78de low confidence tumor sample_accession: GSM4023796 sample_title: Sample_070103T source_name: tumor characteristics: individual: 70103; disease state: HCC; tissue: tumor Sample_070103T controlled vocabulary controlled vocabulary sample type match: tumor
sample_type normal tissue sample GSM4023797 Runtime Siftome inference GEO:sample:GSM4023797:02a5195c92eca1f8c0ff2f399deaf5e4b658dfcdf124cd9b238e2e6424fcff23 high confidence adjacent normal sample_accession: GSM4023797 sample_title: Sample_070785N source_name: Adjacent tissue characteristics: individual: 70785; disease state: HCC; tissue: Adjacent normal Sample_070... controlled vocabulary controlled vocabulary sample type match: adjacent normal
sample_type tumor sample sample GSM4023798 Runtime Siftome inference GEO:sample:GSM4023798:e85d25b7b73c4e88993512d1ad5d25cf0e0cf40938aa5b5e4415482126873bfb low confidence tumor sample_accession: GSM4023798 sample_title: Sample_070785T source_name: tumor characteristics: individual: 70785; disease state: HCC; tissue: tumor Sample_070785T controlled vocabulary controlled vocabulary sample type match: tumor
sample_type normal tissue sample GSM4023799 Runtime Siftome inference GEO:sample:GSM4023799:15dce18ea5db1801e1966cf1332427cbc15e902b8192a3554bccfd0a6c23e9bc high confidence adjacent normal sample_accession: GSM4023799 sample_title: Sample_070880N source_name: Adjacent tissue characteristics: individual: 70880; disease state: HCC; tissue: Adjacent normal Sample_070... controlled vocabulary controlled vocabulary sample type match: adjacent normal
sample_type tumor sample sample GSM4023800 Runtime Siftome inference GEO:sample:GSM4023800:8b3e5de0dd79219f00f3a750ee7e6a6ef560a7f095e46cba74ffbe561200e899 low confidence tumor sample_accession: GSM4023800 sample_title: Sample_070880T source_name: tumor characteristics: individual: 70880; disease state: HCC; tissue: tumor Sample_070880T controlled vocabulary controlled vocabulary sample type match: tumor
sample_type normal tissue sample GSM4023801 Runtime Siftome inference GEO:sample:GSM4023801:6afe68fbcc2a2cd9fb7414caf8f4fd99ff74983abf0d510176d7d58ddf678e55 high confidence adjacent normal sample_accession: GSM4023801 sample_title: Sample_074607N source_name: Adjacent tissue characteristics: individual: 74607; disease state: HCC; tissue: Adjacent normal Sample_074... controlled vocabulary controlled vocabulary sample type match: adjacent normal
sample_type tumor sample sample GSM4023802 Runtime Siftome inference GEO:sample:GSM4023802:09c25ca02d4f7f3dfeb3634e19893fc47b2f6a596a72ac190ad507fce19ca99d low confidence tumor sample_accession: GSM4023802 sample_title: Sample_074607T source_name: tumor characteristics: individual: 74607; disease state: HCC; tissue: tumor Sample_074607T controlled vocabulary controlled vocabulary sample type match: tumor
sample_type normal tissue sample GSM4023803 Runtime Siftome inference GEO:sample:GSM4023803:2dcc0d0ba8fa435943a89cda7d09002474f0563a7a550e07ded15bffe6264b2f high confidence adjacent normal sample_accession: GSM4023803 sample_title: Sample_074720N source_name: Adjacent tissue characteristics: individual: 74720; disease state: HCC; tissue: Adjacent normal Sample_074... controlled vocabulary controlled vocabulary sample type match: adjacent normal
sample_type tumor sample sample GSM4023804 Runtime Siftome inference GEO:sample:GSM4023804:0e4102e7dcf563d1130555755c38cb86d67f6b11259aa4b82fd2510ea72b1876 low confidence tumor sample_accession: GSM4023804 sample_title: Sample_074720T source_name: tumor characteristics: individual: 74720; disease state: HCC; tissue: tumor Sample_074720T controlled vocabulary controlled vocabulary sample type match: tumor
sample_type normal tissue sample GSM4023805 Runtime Siftome inference GEO:sample:GSM4023805:1eab899acec02377636c1e88f6fdf7d5cbc51970965d3bce6da5445603c1b685 high confidence adjacent normal sample_accession: GSM4023805 sample_title: Sample_074848N source_name: Adjacent tissue characteristics: individual: 74848; disease state: HCC; tissue: Adjacent normal Sample_074... controlled vocabulary controlled vocabulary sample type match: adjacent normal
sample_type tumor sample sample GSM4023806 Runtime Siftome inference GEO:sample:GSM4023806:7c3e41d31b78bfec1c97f763d79cd6a2f9c8484fd8c001a27cfcff0970c594c8 low confidence tumor sample_accession: GSM4023806 sample_title: Sample_074848T source_name: tumor characteristics: individual: 74848; disease state: HCC; tissue: tumor Sample_074848T controlled vocabulary controlled vocabulary sample type match: tumor
sample_type normal tissue sample GSM4023807 Runtime Siftome inference GEO:sample:GSM4023807:a5b75a201e12995e3d8e8d168b90752395033a5cab574bf7fcd528f369c016ff high confidence adjacent normal sample_accession: GSM4023807 sample_title: Sample_075199N source_name: Adjacent tissue characteristics: individual: 75199; disease state: HCC; tissue: Adjacent normal Sample_075... controlled vocabulary controlled vocabulary sample type match: adjacent normal
sample_type tumor sample sample GSM4023808 Runtime Siftome inference GEO:sample:GSM4023808:7f4df55e504887151138e83e35b027f541fb9ef48a775cb53dac7d655ca405cd low confidence tumor sample_accession: GSM4023808 sample_title: Sample_075199T source_name: tumor characteristics: individual: 75199; disease state: HCC; tissue: tumor Sample_075199T controlled vocabulary controlled vocabulary sample type match: tumor
sample_type normal tissue sample GSM4023809 Runtime Siftome inference GEO:sample:GSM4023809:c82ae47e57ca27c78bd4934f17154966c66d1baea0e13138844943b61e3b795f high confidence adjacent normal sample_accession: GSM4023809 sample_title: Sample_P070913N source_name: Adjacent tissue characteristics: individual: P070913; disease state: HCC; tissue: Adjacent normal Sample_... controlled vocabulary controlled vocabulary sample type match: adjacent normal
sample_type tumor sample sample GSM4023810 Runtime Siftome inference GEO:sample:GSM4023810:35b1a9657f61fe1cf04c21aaabb421110008ced9d862327614042dbf462e38c7 low confidence tumor sample_accession: GSM4023810 sample_title: Sample_P070913T source_name: tumor characteristics: individual: P070913; disease state: HCC; tissue: tumor Sample_P070913T controlled vocabulary controlled vocabulary sample type match: tumor
sample_type normal tissue sample GSM4023811 Runtime Siftome inference GEO:sample:GSM4023811:450768828f6831579bf5862ba7fa34e0870c3c8c53ca995ad605b2664ca0c5e7 high confidence adjacent normal sample_accession: GSM4023811 sample_title: Sample_P079741N source_name: Adjacent tissue characteristics: individual: P079741; disease state: HCC; tissue: Adjacent normal Sample_... controlled vocabulary controlled vocabulary sample type match: adjacent normal
sample_type tumor sample sample GSM4023812 Runtime Siftome inference GEO:sample:GSM4023812:83659301aebdc9ffd71db5044d78e369814fea65a126f626d99e5a8b54625b79 low confidence tumor sample_accession: GSM4023812 sample_title: Sample_P079741T source_name: tumor characteristics: individual: P079741; disease state: HCC; tissue: tumor Sample_P079741T controlled vocabulary controlled vocabulary sample type match: tumor
sample_type normal tissue sample GSM4023813 Runtime Siftome inference GEO:sample:GSM4023813:aa7588f4ab6723a2f34b8627058e12f57e580c43ffe4006b74e4412ac18a5eb5 high confidence adjacent normal sample_accession: GSM4023813 sample_title: Sample_P079779N source_name: Adjacent tissue characteristics: individual: P079779; disease state: HCC; tissue: Adjacent normal Sample_... controlled vocabulary controlled vocabulary sample type match: adjacent normal
sample_type tumor sample sample GSM4023814 Runtime Siftome inference GEO:sample:GSM4023814:773e2c542cd5947765e26d63f5d86417190926ab4cb7d2b746c2ea45f52280f2 low confidence tumor sample_accession: GSM4023814 sample_title: Sample_P079779T source_name: tumor characteristics: individual: P079779; disease state: HCC; tissue: tumor Sample_P079779T controlled vocabulary controlled vocabulary sample type match: tumor
sample_type normal tissue sample GSM4023815 Runtime Siftome inference GEO:sample:GSM4023815:9087680e3a34005b332f2c9e3e2e2d798b2fb40b908ab3fb325fc9d634480256 high confidence adjacent normal sample_accession: GSM4023815 sample_title: Sample_P116019N source_name: Adjacent tissue characteristics: individual: P116019; disease state: HCC; tissue: Adjacent normal Sample_... controlled vocabulary controlled vocabulary sample type match: adjacent normal
sample_type tumor sample sample GSM4023816 Runtime Siftome inference GEO:sample:GSM4023816:f7c29d41faefad0582300d1f94cf4520b8dc3ddbf71572d95d17fc237e1b7ddb low confidence tumor sample_accession: GSM4023816 sample_title: Sample_P116019T source_name: tumor characteristics: individual: P116019; disease state: HCC; tissue: tumor Sample_P116019T controlled vocabulary controlled vocabulary sample type match: tumor
sample_type normal tissue sample GSM4023817 Runtime Siftome inference GEO:sample:GSM4023817:b5103d99de9ca27d28845736a6b7c8e75303478da99f4cb78a3f271cd16535c4 high confidence adjacent normal sample_accession: GSM4023817 sample_title: Sample_R079741N source_name: Adjacent tissue characteristics: individual: R079741; disease state: HCC; tissue: Adjacent normal Sample_... controlled vocabulary controlled vocabulary sample type match: adjacent normal
sample_type tumor sample sample GSM4023818 Runtime Siftome inference GEO:sample:GSM4023818:1a7a237bbd9ea70523e45e1fb7451a0c77372abf91cde1a36cd3ea74071ef70e low confidence tumor sample_accession: GSM4023818 sample_title: Sample_R079741T source_name: tumor characteristics: individual: R079741; disease state: HCC; tissue: tumor Sample_R079741T controlled vocabulary controlled vocabulary sample type match: tumor
sample_type normal tissue sample GSM4023819 Runtime Siftome inference GEO:sample:GSM4023819:84a7a8a8626ac42d2b6b61953d14b7704f55500c412f466eb948d49458832db0 high confidence adjacent normal sample_accession: GSM4023819 sample_title: Sample_R079779N source_name: Adjacent tissue characteristics: individual: R079779; disease state: HCC; tissue: Adjacent normal Sample_... controlled vocabulary controlled vocabulary sample type match: adjacent normal
sample_type tumor sample sample GSM4023820 Runtime Siftome inference GEO:sample:GSM4023820:be99a54090b12b7db73e44d922386505f5fbfd273b11b4eae42367020a5c698c low confidence tumor sample_accession: GSM4023820 sample_title: Sample_R079779T source_name: tumor characteristics: individual: R079779; disease state: HCC; tissue: tumor Sample_R079779T controlled vocabulary controlled vocabulary sample type match: tumor
sample_type normal tissue sample GSM4023821 Runtime Siftome inference GEO:sample:GSM4023821:a5818d87d9851a063e8d3b5416da2662d438feb6c11b850804c69302ca832fc3 high confidence adjacent normal sample_accession: GSM4023821 sample_title: Sample_R116019N source_name: Adjacent tissue characteristics: individual: R116019; disease state: HCC; tissue: Adjacent normal Sample_... controlled vocabulary controlled vocabulary sample type match: adjacent normal
sample_type tumor sample sample GSM4023822 Runtime Siftome inference GEO:sample:GSM4023822:6270008776416def53e41585dc4c74722d304d25d099c3969bd988e2dcbf2f89 low confidence tumor sample_accession: GSM4023822 sample_title: Sample_R116019T source_name: tumor characteristics: individual: R116019; disease state: HCC; tissue: tumor Sample_R116019T controlled vocabulary controlled vocabulary sample type match: tumor

Sample Group Preview

Possible case samples

Samples currently treated as the comparison case group.

15
  • GSM4023794 Sample_067754T tumor sample Case marker detected. tumor individual: 67754; disease state: HCC; tissue: tumor
  • GSM4023796 Sample_070103T tumor sample Case marker detected. tumor individual: 70103; disease state: HCC; tissue: tumor
  • GSM4023798 Sample_070785T tumor sample Case marker detected. tumor individual: 70785; disease state: HCC; tissue: tumor
  • GSM4023800 Sample_070880T tumor sample Case marker detected. tumor individual: 70880; disease state: HCC; tissue: tumor
  • GSM4023802 Sample_074607T tumor sample Case marker detected. tumor individual: 74607; disease state: HCC; tissue: tumor
  • GSM4023804 Sample_074720T tumor sample Case marker detected. tumor individual: 74720; disease state: HCC; tissue: tumor
  • GSM4023806 Sample_074848T tumor sample Case marker detected. tumor individual: 74848; disease state: HCC; tissue: tumor
  • GSM4023808 Sample_075199T tumor sample Case marker detected. tumor individual: 75199; disease state: HCC; tissue: tumor
  • GSM4023810 Sample_P070913T tumor sample Case marker detected. tumor individual: P070913; disease state: HCC; tissue: tumor
  • GSM4023812 Sample_P079741T tumor sample Case marker detected. tumor individual: P079741; disease state: HCC; tissue: tumor
  • GSM4023814 Sample_P079779T tumor sample Case marker detected. tumor individual: P079779; disease state: HCC; tissue: tumor
  • GSM4023816 Sample_P116019T tumor sample Case marker detected. tumor individual: P116019; disease state: HCC; tissue: tumor
  • GSM4023818 Sample_R079741T tumor sample Case marker detected. tumor individual: R079741; disease state: HCC; tissue: tumor
  • GSM4023820 Sample_R079779T tumor sample Case marker detected. tumor individual: R079779; disease state: HCC; tissue: tumor
  • GSM4023822 Sample_R116019T tumor sample Case marker detected. tumor individual: R116019; disease state: HCC; tissue: tumor

Possible control samples

Samples currently treated as controls or baseline.

15
  • GSM4023793 Sample_067754N normal tissue Control marker detected. Adjacent tissue individual: 67754; disease state: HCC; tissue: Adjacent normal
  • GSM4023795 Sample_070103N normal tissue Control marker detected. Adjacent tissue individual: 70103; disease state: HCC; tissue: Adjacent normal
  • GSM4023797 Sample_070785N normal tissue Control marker detected. Adjacent tissue individual: 70785; disease state: HCC; tissue: Adjacent normal
  • GSM4023799 Sample_070880N normal tissue Control marker detected. Adjacent tissue individual: 70880; disease state: HCC; tissue: Adjacent normal
  • GSM4023801 Sample_074607N normal tissue Control marker detected. Adjacent tissue individual: 74607; disease state: HCC; tissue: Adjacent normal
  • GSM4023803 Sample_074720N normal tissue Control marker detected. Adjacent tissue individual: 74720; disease state: HCC; tissue: Adjacent normal
  • GSM4023805 Sample_074848N normal tissue Control marker detected. Adjacent tissue individual: 74848; disease state: HCC; tissue: Adjacent normal
  • GSM4023807 Sample_075199N normal tissue Control marker detected. Adjacent tissue individual: 75199; disease state: HCC; tissue: Adjacent normal
  • GSM4023809 Sample_P070913N normal tissue Control marker detected. Adjacent tissue individual: P070913; disease state: HCC; tissue: Adjacent normal
  • GSM4023811 Sample_P079741N normal tissue Control marker detected. Adjacent tissue individual: P079741; disease state: HCC; tissue: Adjacent normal
  • GSM4023813 Sample_P079779N normal tissue Control marker detected. Adjacent tissue individual: P079779; disease state: HCC; tissue: Adjacent normal
  • GSM4023815 Sample_P116019N normal tissue Control marker detected. Adjacent tissue individual: P116019; disease state: HCC; tissue: Adjacent normal
  • GSM4023817 Sample_R079741N normal tissue Control marker detected. Adjacent tissue individual: R079741; disease state: HCC; tissue: Adjacent normal
  • GSM4023819 Sample_R079779N normal tissue Control marker detected. Adjacent tissue individual: R079779; disease state: HCC; tissue: Adjacent normal
  • GSM4023821 Sample_R116019N normal tissue Control marker detected. Adjacent tissue individual: R116019; disease state: HCC; tissue: Adjacent normal

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 normalized. Tissue clarity: Tissue metadata was not 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

15 samples
  • GSM4023793 Sample_067754N Adjacent tissue individual: 67754; disease state: HCC; tissue: Adjacent normal
  • GSM4023795 Sample_070103N Adjacent tissue individual: 70103; disease state: HCC; tissue: Adjacent normal
  • GSM4023797 Sample_070785N Adjacent tissue individual: 70785; disease state: HCC; tissue: Adjacent normal
  • GSM4023799 Sample_070880N Adjacent tissue individual: 70880; disease state: HCC; tissue: Adjacent normal
  • GSM4023801 Sample_074607N Adjacent tissue individual: 74607; disease state: HCC; tissue: Adjacent normal
  • GSM4023803 Sample_074720N Adjacent tissue individual: 74720; disease state: HCC; tissue: Adjacent normal
  • GSM4023805 Sample_074848N Adjacent tissue individual: 74848; disease state: HCC; tissue: Adjacent normal
  • GSM4023807 Sample_075199N Adjacent tissue individual: 75199; disease state: HCC; tissue: Adjacent normal
  • GSM4023809 Sample_P070913N Adjacent tissue individual: P070913; disease state: HCC; tissue: Adjacent normal
  • GSM4023811 Sample_P079741N Adjacent tissue individual: P079741; disease state: HCC; tissue: Adjacent normal
  • GSM4023813 Sample_P079779N Adjacent tissue individual: P079779; disease state: HCC; tissue: Adjacent normal
  • GSM4023815 Sample_P116019N Adjacent tissue individual: P116019; disease state: HCC; tissue: Adjacent normal
  • GSM4023817 Sample_R079741N Adjacent tissue individual: R079741; disease state: HCC; tissue: Adjacent normal
  • GSM4023819 Sample_R079779N Adjacent tissue individual: R079779; disease state: HCC; tissue: Adjacent normal
  • GSM4023821 Sample_R116019N Adjacent tissue individual: R116019; disease state: HCC; tissue: Adjacent normal

tumor sample

15 samples
  • GSM4023794 Sample_067754T tumor individual: 67754; disease state: HCC; tissue: tumor
  • GSM4023796 Sample_070103T tumor individual: 70103; disease state: HCC; tissue: tumor
  • GSM4023798 Sample_070785T tumor individual: 70785; disease state: HCC; tissue: tumor
  • GSM4023800 Sample_070880T tumor individual: 70880; disease state: HCC; tissue: tumor
  • GSM4023802 Sample_074607T tumor individual: 74607; disease state: HCC; tissue: tumor
  • GSM4023804 Sample_074720T tumor individual: 74720; disease state: HCC; tissue: tumor
  • GSM4023806 Sample_074848T tumor individual: 74848; disease state: HCC; tissue: tumor
  • GSM4023808 Sample_075199T tumor individual: 75199; disease state: HCC; tissue: tumor
  • GSM4023810 Sample_P070913T tumor individual: P070913; disease state: HCC; tissue: tumor
  • GSM4023812 Sample_P079741T tumor individual: P079741; disease state: HCC; tissue: tumor
  • GSM4023814 Sample_P079779T tumor individual: P079779; disease state: HCC; tissue: tumor
  • GSM4023816 Sample_P116019T tumor individual: P116019; disease state: HCC; tissue: tumor
  • GSM4023818 Sample_R079741T tumor individual: R079741; disease state: HCC; tissue: tumor
  • GSM4023820 Sample_R079779T tumor individual: R079779; disease state: HCC; tissue: tumor
  • GSM4023822 Sample_R116019T tumor individual: R116019; disease state: HCC; tissue: tumor

Score Breakdown

90%

relevance

  • Disease or condition metadata normalized.
  • Organism normalized.
  • Assay type normalized.
0%

comparison suitability

  • Tumor and normal sample groups detected.
  • No excluded sample type flags detected.
  • Matched 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 normalized.
  • Tissue clarity: Tissue metadata was not 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

30 samples

Review Audit Trail

0 decisions

No review decisions have been stored for this dataset.