Siftome Phase 3L

GSE252600

Apolipoprotein L1 is a tumor suppressor in clear cell renal cell carcinoma metastasis [RNA-Seq]

Not suitable Dataset does not meet the current suitability threshold.
Sample grouping CSV Contrast CSV DESeq2 metadata CSV R handoff notes Handoff report Download instructions Open GEO dataset
Source
GEO
Search intent
Patient tissue tumor-vs-normal
Intent behavior
search-intent-behavior-v1
Submission date
2024-01-05
Last update
2024-05-17
Organization
Soonchunhyang University
Department
Not available
Public date
2024-04-10
Experiment types
Expression profiling by high throughput sequencing
Platforms
GPL16791 Illumina HiSeq 2500 (Homo sapiens)
Series type
SubSeries
SubSeries
Not available
BioProject
PRJNA1061486
Supplementary files
XLSX: GSE252600_data3-mRNA.xlsx
Organism
Homo sapiens
Assay
bulk RNA-seq
Samples
18
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
94% 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

7/10 pts

Metadata quality is usable, but still deserves review.

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 50% Organism normalized. Assay type 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 70% 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 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 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 9 samples
  • Likely control group normal tissue 9 samples

Warnings

  • DISEASE_LABEL_UNCLEAR warning Disease or condition label could not be normalized.
  • 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 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 2 active warnings 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 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: 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 2 warnings 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 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: Disease clarity: Disease or condition metadata was not normalized. 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
GSE252600
Sample records
18 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
GSE252600
  • 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
GSE252600
  • 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
GSE252600
  • 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: GSE252600
dataset_title: Apolipoprotein L1 is a tumor suppressor in clear cell renal cell carcinoma metastasis [RNA-Seq]
organism: Homo sapiens
assay_type: bulk RNA-seq
processed_data_available: true
raw_data_available: true
submission_date: 2024-01-05
last_update_date: 2024-05-17
organization_name: Soonchunhyang University
department: Not available
public_date: 2024-04-10
experiment_types: Expression profiling by high throughput sequencing
platforms: GPL16791 Illumina HiSeq 2500 (Homo sapiens)
sub_series: Not available
bioproject: PRJNA1061486
supplementary_files: XLSX: GSE252600_data3-mRNA.xlsx
series_type: SubSeries

Why It Matched

  • Tumor vs unmatched normal · Tissue · suitability 0%.
  • Prioritized assay: bulk RNA-seq is the active assay expectation.
  • Downgraded disease context: colorectal/GI relevance is unclear.
  • Processed data is available for downstream review.
  • 2 warnings require review.

Why It May Not Be Suitable

  • Disease or condition label could not be normalized.
  • Tissue or cell type 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: 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 DISEASE_LABEL_UNCLEAR Disease or condition label could not be normalized.
  • warning TISSUE_TYPE_MISSING Tissue or cell type could not be normalized.

Normalized Fields

29 fields
Field Value Source Origin Confidence Evidence Reason
assay_type bulk RNA-seq dataset GSE252600 Runtime Siftome inference GEO:dataset:GSE252600:a8a71076d548a61fd0d26a6322fb9cac1873be0f97f1b40309cefdd077a48cdc high confidence bulk rna-seq dataset_accession: GSE252600 dataset_title: Apolipoprotein L1 is a tumor suppressor in clear cell renal cell carcinoma metastasis [RNA-Seq] organism: Homo sapiens assay_type: bu... keyword match keyword match: bulk rna-seq
organism Homo sapiens dataset GSE252600 Runtime Siftome inference GEO:dataset:GSE252600:a8a71076d548a61fd0d26a6322fb9cac1873be0f97f1b40309cefdd077a48cdc high confidence homo sapiens dataset_accession: GSE252600 dataset_title: Apolipoprotein L1 is a tumor suppressor in clear cell renal cell carcinoma metastasis [RNA-Seq] organism: Homo sapiens assay_type: bu... keyword match keyword match: homo sapiens
sample_type tumor sample sample GSM8003764 Runtime Siftome inference GEO:sample:GSM8003764:346079042881e5ba190b61927e4f28c09d86b8e3e4afcf1efa65de6d809a0ee7 low confidence tumor sample_accession: GSM8003764 sample_title: human sample 1, stage 2 source_name: kidney characteristics: tissue: kidney; tumor stage: tumor stage 2; disease: clear cell renal cel... controlled vocabulary controlled vocabulary sample type match: tumor
sample_type tumor sample sample GSM8003765 Runtime Siftome inference GEO:sample:GSM8003765:cb09b557d5f95e2bf9b891f77f13f33d6da1f6369355e13aeb1774065fec6a42 low confidence tumor sample_accession: GSM8003765 sample_title: human sample 2, stage 1 source_name: kidney characteristics: tissue: kidney; tumor stage: tumor stage 1; disease: clear cell renal cel... controlled vocabulary controlled vocabulary sample type match: tumor
sample_type tumor sample sample GSM8003766 Runtime Siftome inference GEO:sample:GSM8003766:17045b7ed645177092819870548ec2aa926156db4304473edcf20cca549fc55f low confidence tumor sample_accession: GSM8003766 sample_title: human sample 3, stage 3 source_name: kidney characteristics: tissue: kidney; tumor stage: tumor stage 3; disease: clear cell renal cel... controlled vocabulary controlled vocabulary sample type match: tumor
sample_type tumor sample sample GSM8003767 Runtime Siftome inference GEO:sample:GSM8003767:d5ee82695a0b388d724499b1f96fcc3903858edc9bae9d78819da6c08ff49e2f low confidence tumor sample_accession: GSM8003767 sample_title: human sample 4, stage 1 source_name: kidney characteristics: tissue: kidney; tumor stage: tumor stage 1; disease: clear cell renal cel... controlled vocabulary controlled vocabulary sample type match: tumor
sample_type tumor sample sample GSM8003768 Runtime Siftome inference GEO:sample:GSM8003768:e2a63a48fc45dd784343840c5ef34da344ea113af9d399c647d43eb794e418ed low confidence tumor sample_accession: GSM8003768 sample_title: human sample 5, stage 1 source_name: kidney characteristics: tissue: kidney; tumor stage: tumor stage 1; disease: clear cell renal cel... controlled vocabulary controlled vocabulary sample type match: tumor
sample_type tumor sample sample GSM8003769 Runtime Siftome inference GEO:sample:GSM8003769:954375b875270e69d6c0378b92ccdfa7ae43d2098a06d67ed3009651a6b4b078 low confidence tumor sample_accession: GSM8003769 sample_title: human sample 8, stage 3 source_name: kidney characteristics: tissue: kidney; tumor stage: tumor stage 3; disease: clear cell renal cel... controlled vocabulary controlled vocabulary sample type match: tumor
sample_type tumor sample sample GSM8003770 Runtime Siftome inference GEO:sample:GSM8003770:0a8828c58622b1c6633ac1c2c263cd648c02096521dc2f2f08083ba68fb45c4e low confidence tumor sample_accession: GSM8003770 sample_title: human sample 9, stage 4 source_name: kidney characteristics: tissue: kidney; tumor stage: tumor stage 4; disease: clear cell renal cel... controlled vocabulary controlled vocabulary sample type match: tumor
sample_type tumor sample sample GSM8003771 Runtime Siftome inference GEO:sample:GSM8003771:1c923d7428f8eaf61efda6ce2f11cba010b1f05cb070f360950b02227419c079 low confidence tumor sample_accession: GSM8003771 sample_title: human sample 10, stage 2 source_name: kidney characteristics: tissue: kidney; tumor stage: tumor stage 2; disease: clear cell renal ce... controlled vocabulary controlled vocabulary sample type match: tumor
sample_type tumor sample sample GSM8003772 Runtime Siftome inference GEO:sample:GSM8003772:02b35bf84c6223afc5d6f42b6c4104b32e35c0644b70c939a254825191f51d87 low confidence tumor sample_accession: GSM8003772 sample_title: human sample 12, stage 4 source_name: kidney characteristics: tissue: kidney; tumor stage: tumor stage 4; disease: clear cell renal ce... controlled vocabulary controlled vocabulary sample type match: tumor
sample_type normal tissue sample GSM8003773 Runtime Siftome inference GEO:sample:GSM8003773:34617e99c40d74610d08f7a01176516bcf6c41825410c6e074b076ca10a3eb18 low confidence normal sample_accession: GSM8003773 sample_title: human sample 1s source_name: kidney characteristics: tissue: kidney; tumor stage: normal human sample 1s controlled vocabulary controlled vocabulary sample type match: normal
sample_type tumor sample sample GSM8003773 Runtime Siftome inference GEO:sample:GSM8003773:34617e99c40d74610d08f7a01176516bcf6c41825410c6e074b076ca10a3eb18 low confidence tumor sample_accession: GSM8003773 sample_title: human sample 1s source_name: kidney characteristics: tissue: kidney; tumor stage: normal human sample 1s controlled vocabulary controlled vocabulary sample type match: tumor
sample_type normal tissue sample GSM8003774 Runtime Siftome inference GEO:sample:GSM8003774:d6d4c0e78ef1892870d96f3d3566096a925a79326dc173236bddc7e642aa53f3 low confidence normal sample_accession: GSM8003774 sample_title: human sample 2s source_name: kidney characteristics: tissue: kidney; tumor stage: normal human sample 2s controlled vocabulary controlled vocabulary sample type match: normal
sample_type tumor sample sample GSM8003774 Runtime Siftome inference GEO:sample:GSM8003774:d6d4c0e78ef1892870d96f3d3566096a925a79326dc173236bddc7e642aa53f3 low confidence tumor sample_accession: GSM8003774 sample_title: human sample 2s source_name: kidney characteristics: tissue: kidney; tumor stage: normal human sample 2s controlled vocabulary controlled vocabulary sample type match: tumor
sample_type normal tissue sample GSM8003775 Runtime Siftome inference GEO:sample:GSM8003775:9c56cd1725a9415bb03782dae51a21250fe7a5fa3a3be46ef78d0f988c0cd1a0 low confidence normal sample_accession: GSM8003775 sample_title: human sample 3s source_name: kidney characteristics: tissue: kidney; tumor stage: normal human sample 3s controlled vocabulary controlled vocabulary sample type match: normal
sample_type tumor sample sample GSM8003775 Runtime Siftome inference GEO:sample:GSM8003775:9c56cd1725a9415bb03782dae51a21250fe7a5fa3a3be46ef78d0f988c0cd1a0 low confidence tumor sample_accession: GSM8003775 sample_title: human sample 3s source_name: kidney characteristics: tissue: kidney; tumor stage: normal human sample 3s controlled vocabulary controlled vocabulary sample type match: tumor
sample_type normal tissue sample GSM8003776 Runtime Siftome inference GEO:sample:GSM8003776:61504806287707afa2cd194075f748ae72a3b26c04ef92753d3d9197ceaccb53 low confidence normal sample_accession: GSM8003776 sample_title: human sample 4s source_name: kidney characteristics: tissue: kidney; tumor stage: normal human sample 4s controlled vocabulary controlled vocabulary sample type match: normal
sample_type tumor sample sample GSM8003776 Runtime Siftome inference GEO:sample:GSM8003776:61504806287707afa2cd194075f748ae72a3b26c04ef92753d3d9197ceaccb53 low confidence tumor sample_accession: GSM8003776 sample_title: human sample 4s source_name: kidney characteristics: tissue: kidney; tumor stage: normal human sample 4s controlled vocabulary controlled vocabulary sample type match: tumor
sample_type normal tissue sample GSM8003777 Runtime Siftome inference GEO:sample:GSM8003777:9ce9d6737000e93fbfde923bd193417e9655034af4cbdbbbd071020a7cd55584 low confidence normal sample_accession: GSM8003777 sample_title: human sample 5s source_name: kidney characteristics: tissue: kidney; tumor stage: normal human sample 5s controlled vocabulary controlled vocabulary sample type match: normal
sample_type tumor sample sample GSM8003777 Runtime Siftome inference GEO:sample:GSM8003777:9ce9d6737000e93fbfde923bd193417e9655034af4cbdbbbd071020a7cd55584 low confidence tumor sample_accession: GSM8003777 sample_title: human sample 5s source_name: kidney characteristics: tissue: kidney; tumor stage: normal human sample 5s controlled vocabulary controlled vocabulary sample type match: tumor
sample_type normal tissue sample GSM8003778 Runtime Siftome inference GEO:sample:GSM8003778:2e0e33981338e9cd22a5fb81e8230a6e360d5d0baa8158f9143ba4f23ba3b6fa low confidence normal sample_accession: GSM8003778 sample_title: human sample 8s source_name: kidney characteristics: tissue: kidney; tumor stage: normal human sample 8s controlled vocabulary controlled vocabulary sample type match: normal
sample_type tumor sample sample GSM8003778 Runtime Siftome inference GEO:sample:GSM8003778:2e0e33981338e9cd22a5fb81e8230a6e360d5d0baa8158f9143ba4f23ba3b6fa low confidence tumor sample_accession: GSM8003778 sample_title: human sample 8s source_name: kidney characteristics: tissue: kidney; tumor stage: normal human sample 8s controlled vocabulary controlled vocabulary sample type match: tumor
sample_type normal tissue sample GSM8003779 Runtime Siftome inference GEO:sample:GSM8003779:c13f66ef03fb1c32b60f19ba18e329f4f624b1246f0d04505b20bb7ae3409224 low confidence normal sample_accession: GSM8003779 sample_title: human sample 9s source_name: kidney characteristics: tissue: kidney; tumor stage: normal human sample 9s controlled vocabulary controlled vocabulary sample type match: normal
sample_type tumor sample sample GSM8003779 Runtime Siftome inference GEO:sample:GSM8003779:c13f66ef03fb1c32b60f19ba18e329f4f624b1246f0d04505b20bb7ae3409224 low confidence tumor sample_accession: GSM8003779 sample_title: human sample 9s source_name: kidney characteristics: tissue: kidney; tumor stage: normal human sample 9s controlled vocabulary controlled vocabulary sample type match: tumor
sample_type normal tissue sample GSM8003780 Runtime Siftome inference GEO:sample:GSM8003780:9fac513f3c1e61f2cfe6a593b8464b3b8a2523b9f8640f595c602b17ea94d12a low confidence normal sample_accession: GSM8003780 sample_title: human sample 10s source_name: kidney characteristics: tissue: kidney; tumor stage: normal human sample 10s controlled vocabulary controlled vocabulary sample type match: normal
sample_type tumor sample sample GSM8003780 Runtime Siftome inference GEO:sample:GSM8003780:9fac513f3c1e61f2cfe6a593b8464b3b8a2523b9f8640f595c602b17ea94d12a low confidence tumor sample_accession: GSM8003780 sample_title: human sample 10s source_name: kidney characteristics: tissue: kidney; tumor stage: normal human sample 10s controlled vocabulary controlled vocabulary sample type match: tumor
sample_type normal tissue sample GSM8003781 Runtime Siftome inference GEO:sample:GSM8003781:2b85533ed136037621cf91d064386a3ce1f26ebd2fdbf3d9ba40fa7e0fe46520 low confidence normal sample_accession: GSM8003781 sample_title: human sample 12s source_name: kidney characteristics: tissue: kidney; tumor stage: normal human sample 12s controlled vocabulary controlled vocabulary sample type match: normal
sample_type tumor sample sample GSM8003781 Runtime Siftome inference GEO:sample:GSM8003781:2b85533ed136037621cf91d064386a3ce1f26ebd2fdbf3d9ba40fa7e0fe46520 low confidence tumor sample_accession: GSM8003781 sample_title: human sample 12s source_name: kidney characteristics: tissue: kidney; tumor stage: normal human sample 12s controlled vocabulary controlled vocabulary sample type match: tumor

Sample Group Preview

Possible case samples

Samples currently treated as the comparison case group.

9
  • GSM8003764 human sample 1, stage 2 tumor sample Case marker detected. kidney tissue: kidney; tumor stage: tumor stage 2; disease: clear cell renal cell carcinoma
  • GSM8003765 human sample 2, stage 1 tumor sample Case marker detected. kidney tissue: kidney; tumor stage: tumor stage 1; disease: clear cell renal cell carcinoma
  • GSM8003766 human sample 3, stage 3 tumor sample Case marker detected. kidney tissue: kidney; tumor stage: tumor stage 3; disease: clear cell renal cell carcinoma
  • GSM8003767 human sample 4, stage 1 tumor sample Case marker detected. kidney tissue: kidney; tumor stage: tumor stage 1; disease: clear cell renal cell carcinoma
  • GSM8003768 human sample 5, stage 1 tumor sample Case marker detected. kidney tissue: kidney; tumor stage: tumor stage 1; disease: clear cell renal cell carcinoma
  • GSM8003769 human sample 8, stage 3 tumor sample Case marker detected. kidney tissue: kidney; tumor stage: tumor stage 3; disease: clear cell renal cell carcinoma
  • GSM8003770 human sample 9, stage 4 tumor sample Case marker detected. kidney tissue: kidney; tumor stage: tumor stage 4; disease: clear cell renal cell carcinoma
  • GSM8003771 human sample 10, stage 2 tumor sample Case marker detected. kidney tissue: kidney; tumor stage: tumor stage 2; disease: clear cell renal cell carcinoma
  • GSM8003772 human sample 12, stage 4 tumor sample Case marker detected. kidney tissue: kidney; tumor stage: tumor stage 4; disease: clear cell renal cell carcinoma

Possible control samples

Samples currently treated as controls or baseline.

9
  • GSM8003773 human sample 1s normal tissue Control marker detected. kidney tissue: kidney; tumor stage: normal
  • GSM8003774 human sample 2s normal tissue Control marker detected. kidney tissue: kidney; tumor stage: normal
  • GSM8003775 human sample 3s normal tissue Control marker detected. kidney tissue: kidney; tumor stage: normal
  • GSM8003776 human sample 4s normal tissue Control marker detected. kidney tissue: kidney; tumor stage: normal
  • GSM8003777 human sample 5s normal tissue Control marker detected. kidney tissue: kidney; tumor stage: normal
  • GSM8003778 human sample 8s normal tissue Control marker detected. kidney tissue: kidney; tumor stage: normal
  • GSM8003779 human sample 9s normal tissue Control marker detected. kidney tissue: kidney; tumor stage: normal
  • GSM8003780 human sample 10s normal tissue Control marker detected. kidney tissue: kidney; tumor stage: normal
  • GSM8003781 human sample 12s normal tissue Control marker detected. kidney tissue: kidney; tumor stage: 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

70 pts
Clarity
70%
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 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

tumor sample

9 samples
  • GSM8003764 human sample 1, stage 2 kidney tissue: kidney; tumor stage: tumor stage 2; disease: clear cell renal cell carcinoma
  • GSM8003765 human sample 2, stage 1 kidney tissue: kidney; tumor stage: tumor stage 1; disease: clear cell renal cell carcinoma
  • GSM8003766 human sample 3, stage 3 kidney tissue: kidney; tumor stage: tumor stage 3; disease: clear cell renal cell carcinoma
  • GSM8003767 human sample 4, stage 1 kidney tissue: kidney; tumor stage: tumor stage 1; disease: clear cell renal cell carcinoma
  • GSM8003768 human sample 5, stage 1 kidney tissue: kidney; tumor stage: tumor stage 1; disease: clear cell renal cell carcinoma
  • GSM8003769 human sample 8, stage 3 kidney tissue: kidney; tumor stage: tumor stage 3; disease: clear cell renal cell carcinoma
  • GSM8003770 human sample 9, stage 4 kidney tissue: kidney; tumor stage: tumor stage 4; disease: clear cell renal cell carcinoma
  • GSM8003771 human sample 10, stage 2 kidney tissue: kidney; tumor stage: tumor stage 2; disease: clear cell renal cell carcinoma
  • GSM8003772 human sample 12, stage 4 kidney tissue: kidney; tumor stage: tumor stage 4; disease: clear cell renal cell carcinoma

normal tissue

9 samples
  • GSM8003773 human sample 1s kidney tissue: kidney; tumor stage: normal
  • GSM8003774 human sample 2s kidney tissue: kidney; tumor stage: normal
  • GSM8003775 human sample 3s kidney tissue: kidney; tumor stage: normal
  • GSM8003776 human sample 4s kidney tissue: kidney; tumor stage: normal
  • GSM8003777 human sample 5s kidney tissue: kidney; tumor stage: normal
  • GSM8003778 human sample 8s kidney tissue: kidney; tumor stage: normal
  • GSM8003779 human sample 9s kidney tissue: kidney; tumor stage: normal
  • GSM8003780 human sample 10s kidney tissue: kidney; tumor stage: normal
  • GSM8003781 human sample 12s kidney tissue: kidney; tumor stage: normal

Score Breakdown

50%

relevance

  • Organism normalized.
  • Assay type 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.
70%

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 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

18 samples

Review Audit Trail

0 decisions

No review decisions have been stored for this dataset.