Siftome Phase 3L

GSE102101

Transcriptomics profiles of patient-matched normal kidney and ccRCC pairs

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
2017-07-31
Last update
2021-07-25
Organization
Genome Institute of Singapore
Department
Not available
Public date
2017-08-22
Experiment types
Expression profiling by high throughput sequencing
Platforms
GPL11154 Illumina HiSeq 2000 (Homo sapiens)
Series type
SubSeries
SubSeries
Not available
BioProject
PRJNA396588
Supplementary files
TAR: GSE102101_RAW.tar
Organism
Homo sapiens
Assay
bulk RNA-seq
Samples
20
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 10 samples
  • Likely control group normal tissue 10 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
GSE102101
Sample records
20 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
GSE102101
  • 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
GSE102101
  • 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
GSE102101
  • 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: GSE102101
dataset_title: Transcriptomics profiles of patient-matched normal kidney and ccRCC pairs
organism: Homo sapiens
assay_type: bulk RNA-seq
processed_data_available: true
raw_data_available: true
submission_date: 2017-07-31
last_update_date: 2021-07-25
organization_name: Genome Institute of Singapore
department: Not available
public_date: 2017-08-22
experiment_types: Expression profiling by high throughput sequencing
platforms: GPL11154 Illumina HiSeq 2000 (Homo sapiens)
sub_series: Not available
bioproject: PRJNA396588
supplementary_files: TAR: GSE102101_RAW.tar
series_type: SubSeries

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

53 fields
Field Value Source Origin Confidence Evidence Reason
assay_type bulk RNA-seq dataset GSE102101 Runtime Siftome inference GEO:dataset:GSE102101:cc3200efcbdf3de9444cabf926562cb2208d318eb8d317092ae2385793af8641 high confidence bulk rna-seq dataset_accession: GSE102101 dataset_title: Transcriptomics profiles of patient-matched normal kidney and ccRCC pairs organism: Homo sapiens assay_type: bulk RNA-seq processed_d... keyword match keyword match: bulk rna-seq
disease colorectal cancer dataset GSE102101 Runtime Siftome inference GEO:dataset:GSE102101:cc3200efcbdf3de9444cabf926562cb2208d318eb8d317092ae2385793af8641 medium confidence crc dataset_accession: GSE102101 dataset_title: Transcriptomics profiles of patient-matched normal kidney and ccRCC pairs organism: Homo sapiens assay_type: bulk RNA-seq processed_d... controlled vocabulary controlled vocabulary disease match: crc
disease colorectal cancer sample GSM2723919 Runtime Siftome inference GEO:sample:GSM2723919:8adc6711e7a59001b93e28c21256a62f931ce4f90f64b4d1f66ee5746c384e7c medium confidence crc sample_accession: GSM2723919 sample_title: 12364284N normal kidney RNA-Seq source_name: adjacent normal kidney characteristics: individual: patient 12364284; disease state: ccRC... controlled vocabulary controlled vocabulary disease match: crc
disease colorectal cancer sample GSM2723920 Runtime Siftome inference GEO:sample:GSM2723920:974583b4283a142317be0039ddc263140560361b017530edcf875bcf7fae8289 medium confidence crc sample_accession: GSM2723920 sample_title: 12364284T ccRCC RNA-Seq source_name: ccRCC tumor characteristics: individual: patient 12364284; disease state: ccRCC; tissue: ccRCC tu... controlled vocabulary controlled vocabulary disease match: crc
disease colorectal cancer sample GSM2723921 Runtime Siftome inference GEO:sample:GSM2723921:a3dfe32a6a646f4284eb476b0231b7b469115a0f048db7689a52ae64227f9103 medium confidence crc sample_accession: GSM2723921 sample_title: 17621953N normal kidney RNA-Seq source_name: adjacent normal kidney characteristics: individual: patient 17621953; disease state: ccRC... controlled vocabulary controlled vocabulary disease match: crc
disease colorectal cancer sample GSM2723922 Runtime Siftome inference GEO:sample:GSM2723922:c1105921ce01bd94a602222e41c671166e96e8296d27ee69182729c47ac229a9 medium confidence crc sample_accession: GSM2723922 sample_title: 17621953T ccRCC RNA-Seq source_name: ccRCC tumor characteristics: individual: patient 17621953; disease state: ccRCC; tissue: ccRCC tu... controlled vocabulary controlled vocabulary disease match: crc
disease colorectal cancer sample GSM2723923 Runtime Siftome inference GEO:sample:GSM2723923:b9aebec09bc14a5e15c5d4601751d888ed292852d9f05f6b55e5f58b6acc9663 medium confidence crc sample_accession: GSM2723923 sample_title: 20431713N normal kidney RNA-seq source_name: adjacent normal kidney characteristics: individual: patient 20431713; disease state: ccRC... controlled vocabulary controlled vocabulary disease match: crc
disease colorectal cancer sample GSM2723924 Runtime Siftome inference GEO:sample:GSM2723924:5c3aa51528e6bb67e1ae06ed3f9c7d0ba5bb3c8d4841700b89dbe6631e29ac14 medium confidence crc sample_accession: GSM2723924 sample_title: 20431713T ccRCC RNA-seq source_name: ccRCC tumor characteristics: individual: patient 20431713; disease state: ccRCC; tissue: ccRCC tu... controlled vocabulary controlled vocabulary disease match: crc
disease colorectal cancer sample GSM2723925 Runtime Siftome inference GEO:sample:GSM2723925:6a6f3073ce4dfe3e437161b30a4d402e1290fc32299d7e0a043bdcffd01a60df medium confidence crc sample_accession: GSM2723925 sample_title: 40911432N normal kidney RNA-seq source_name: adjacent normal kidney characteristics: individual: patient 40911432; disease state: ccRC... controlled vocabulary controlled vocabulary disease match: crc
disease colorectal cancer sample GSM2723926 Runtime Siftome inference GEO:sample:GSM2723926:a306e952b07af3e715dc5b61a8ca22592d33892e30b577f26bcc4c4844f38384 medium confidence crc sample_accession: GSM2723926 sample_title: 40911432T ccRCC RNA-seq source_name: ccRCC tumor characteristics: individual: patient 40911432; disease state: ccRCC; tissue: ccRCC tu... controlled vocabulary controlled vocabulary disease match: crc
disease colorectal cancer sample GSM2723927 Runtime Siftome inference GEO:sample:GSM2723927:9a68aecf3a0fcc5180c1970faa7e3c9ef2c7b750f7173f5d36b0b5fc57ebe136 medium confidence crc sample_accession: GSM2723927 sample_title: 57398667N normal kidney RNA-seq source_name: adjacent normal kidney characteristics: individual: patient 57398667; disease state: ccRC... controlled vocabulary controlled vocabulary disease match: crc
disease colorectal cancer sample GSM2723928 Runtime Siftome inference GEO:sample:GSM2723928:1c74b889c2f583d1ffb825c9c3f8c02cd0b283a2cbdc21055f1c234302421db3 medium confidence crc sample_accession: GSM2723928 sample_title: 57398667T ccRCC RNA-seq source_name: ccRCC tumor characteristics: individual: patient 57398667; disease state: ccRCC; tissue: ccRCC tu... controlled vocabulary controlled vocabulary disease match: crc
disease colorectal cancer sample GSM2723929 Runtime Siftome inference GEO:sample:GSM2723929:0065e39355e44081466528e5c21f88e40708af8aa62f0ea47100e807f684bfab medium confidence crc sample_accession: GSM2723929 sample_title: 70528835N normal kidney RNA-seq source_name: adjacent normal kidney characteristics: individual: patient 70528835; disease state: ccRC... controlled vocabulary controlled vocabulary disease match: crc
disease colorectal cancer sample GSM2723930 Runtime Siftome inference GEO:sample:GSM2723930:4dfd456e88a1ae8653c0003c6f3f24704e999bff108637cf239bd301a9ba8252 medium confidence crc sample_accession: GSM2723930 sample_title: 70528835T ccRCC RNA-seq source_name: ccRCC tumor characteristics: individual: patient 70528835; disease state: ccRCC; tissue: ccRCC tu... controlled vocabulary controlled vocabulary disease match: crc
disease colorectal cancer sample GSM2723931 Runtime Siftome inference GEO:sample:GSM2723931:e394588f1c8582ba249ec7dd72a3caf8f075d0e0163a8fd01e99e44cab942297 medium confidence crc sample_accession: GSM2723931 sample_title: 74575859N normal kidney RNA-seq source_name: adjacent normal kidney characteristics: individual: patient 74575859; disease state: ccRC... controlled vocabulary controlled vocabulary disease match: crc
disease colorectal cancer sample GSM2723932 Runtime Siftome inference GEO:sample:GSM2723932:3f11886ba6ce6271894904f622cb0d9a809278e64b3bd80a43147de21fd84a2c medium confidence crc sample_accession: GSM2723932 sample_title: 74575859T ccRCC RNA-seq source_name: ccRCC tumor characteristics: individual: patient 74575859; disease state: ccRCC; tissue: ccRCC tu... controlled vocabulary controlled vocabulary disease match: crc
disease colorectal cancer sample GSM2723933 Runtime Siftome inference GEO:sample:GSM2723933:7b6c78de0a52764250687215e8bdfcb9e7a1baad2fb93b3513bca572aab54535 medium confidence crc sample_accession: GSM2723933 sample_title: 75416923N normal kidney RNA-seq source_name: adjacent normal kidney characteristics: individual: patient 75416923; disease state: ccRC... controlled vocabulary controlled vocabulary disease match: crc
disease colorectal cancer sample GSM2723934 Runtime Siftome inference GEO:sample:GSM2723934:1605106827ffd5cb398e964b2aaa24d0397cb8bc7bdf9735dd2a9fc5d149f7b1 medium confidence crc sample_accession: GSM2723934 sample_title: 75416923T ccRCC RNA-seq source_name: ccRCC tumor characteristics: individual: patient 75416923; disease state: ccRCC; tissue: ccRCC tu... controlled vocabulary controlled vocabulary disease match: crc
disease colorectal cancer sample GSM2723935 Runtime Siftome inference GEO:sample:GSM2723935:309bf1896003c996d1accdf81252cd374a646c89df796c4bf8e6a4c47380554b medium confidence crc sample_accession: GSM2723935 sample_title: 77972083N normal kidney RNA-seq source_name: adjacent normal kidney characteristics: individual: patient 77972083; disease state: ccRC... controlled vocabulary controlled vocabulary disease match: crc
disease colorectal cancer sample GSM2723936 Runtime Siftome inference GEO:sample:GSM2723936:b23959f0af78c6d692e87ba1130f826cee153e0f84b5b6cf75aa35f201db96f3 medium confidence crc sample_accession: GSM2723936 sample_title: 77972083T ccRCC RNA-seq source_name: ccRCC tumor characteristics: individual: patient 77972083; disease state: ccRCC; tissue: ccRCC tu... controlled vocabulary controlled vocabulary disease match: crc
disease colorectal cancer sample GSM2723937 Runtime Siftome inference GEO:sample:GSM2723937:68a48979e61ebc8fb6166ebd264ba16a8d4ed188d3ce27235387faec4c4f6c0b medium confidence crc sample_accession: GSM2723937 sample_title: 86049102N normal kidney RNA-seq source_name: adjacent normal kidney characteristics: individual: patient 86049102; disease state: ccRC... controlled vocabulary controlled vocabulary disease match: crc
disease colorectal cancer sample GSM2723938 Runtime Siftome inference GEO:sample:GSM2723938:3b03c45ff196ecb031c666f26e2411b3007e6cdafef9c41619ae85bfbc09bdfb medium confidence crc sample_accession: GSM2723938 sample_title: 86049102T ccRCC RNA-seq source_name: ccRCC tumor characteristics: individual: patient 86049102; disease state: ccRCC; tissue: ccRCC tu... controlled vocabulary controlled vocabulary disease match: crc
normal_tissue_type adjacent normal sample GSM2723919 Runtime Siftome inference GEO:sample:GSM2723919:8adc6711e7a59001b93e28c21256a62f931ce4f90f64b4d1f66ee5746c384e7c high confidence adjacent normal sample_accession: GSM2723919 sample_title: 12364284N normal kidney RNA-Seq source_name: adjacent normal kidney characteristics: individual: patient 12364284; disease state: ccRC... controlled vocabulary controlled vocabulary normal tissue type match: adjacent normal
normal_tissue_type adjacent normal sample GSM2723921 Runtime Siftome inference GEO:sample:GSM2723921:a3dfe32a6a646f4284eb476b0231b7b469115a0f048db7689a52ae64227f9103 high confidence adjacent normal sample_accession: GSM2723921 sample_title: 17621953N normal kidney RNA-Seq source_name: adjacent normal kidney characteristics: individual: patient 17621953; disease state: ccRC... controlled vocabulary controlled vocabulary normal tissue type match: adjacent normal
normal_tissue_type adjacent normal sample GSM2723923 Runtime Siftome inference GEO:sample:GSM2723923:b9aebec09bc14a5e15c5d4601751d888ed292852d9f05f6b55e5f58b6acc9663 high confidence adjacent normal sample_accession: GSM2723923 sample_title: 20431713N normal kidney RNA-seq source_name: adjacent normal kidney characteristics: individual: patient 20431713; disease state: ccRC... controlled vocabulary controlled vocabulary normal tissue type match: adjacent normal
normal_tissue_type adjacent normal sample GSM2723925 Runtime Siftome inference GEO:sample:GSM2723925:6a6f3073ce4dfe3e437161b30a4d402e1290fc32299d7e0a043bdcffd01a60df high confidence adjacent normal sample_accession: GSM2723925 sample_title: 40911432N normal kidney RNA-seq source_name: adjacent normal kidney characteristics: individual: patient 40911432; disease state: ccRC... controlled vocabulary controlled vocabulary normal tissue type match: adjacent normal
normal_tissue_type adjacent normal sample GSM2723927 Runtime Siftome inference GEO:sample:GSM2723927:9a68aecf3a0fcc5180c1970faa7e3c9ef2c7b750f7173f5d36b0b5fc57ebe136 high confidence adjacent normal sample_accession: GSM2723927 sample_title: 57398667N normal kidney RNA-seq source_name: adjacent normal kidney characteristics: individual: patient 57398667; disease state: ccRC... controlled vocabulary controlled vocabulary normal tissue type match: adjacent normal
normal_tissue_type adjacent normal sample GSM2723929 Runtime Siftome inference GEO:sample:GSM2723929:0065e39355e44081466528e5c21f88e40708af8aa62f0ea47100e807f684bfab high confidence adjacent normal sample_accession: GSM2723929 sample_title: 70528835N normal kidney RNA-seq source_name: adjacent normal kidney characteristics: individual: patient 70528835; disease state: ccRC... controlled vocabulary controlled vocabulary normal tissue type match: adjacent normal
normal_tissue_type adjacent normal sample GSM2723931 Runtime Siftome inference GEO:sample:GSM2723931:e394588f1c8582ba249ec7dd72a3caf8f075d0e0163a8fd01e99e44cab942297 high confidence adjacent normal sample_accession: GSM2723931 sample_title: 74575859N normal kidney RNA-seq source_name: adjacent normal kidney characteristics: individual: patient 74575859; disease state: ccRC... controlled vocabulary controlled vocabulary normal tissue type match: adjacent normal
normal_tissue_type adjacent normal sample GSM2723933 Runtime Siftome inference GEO:sample:GSM2723933:7b6c78de0a52764250687215e8bdfcb9e7a1baad2fb93b3513bca572aab54535 high confidence adjacent normal sample_accession: GSM2723933 sample_title: 75416923N normal kidney RNA-seq source_name: adjacent normal kidney characteristics: individual: patient 75416923; disease state: ccRC... controlled vocabulary controlled vocabulary normal tissue type match: adjacent normal
normal_tissue_type adjacent normal sample GSM2723935 Runtime Siftome inference GEO:sample:GSM2723935:309bf1896003c996d1accdf81252cd374a646c89df796c4bf8e6a4c47380554b high confidence adjacent normal sample_accession: GSM2723935 sample_title: 77972083N normal kidney RNA-seq source_name: adjacent normal kidney characteristics: individual: patient 77972083; disease state: ccRC... controlled vocabulary controlled vocabulary normal tissue type match: adjacent normal
normal_tissue_type adjacent normal sample GSM2723937 Runtime Siftome inference GEO:sample:GSM2723937:68a48979e61ebc8fb6166ebd264ba16a8d4ed188d3ce27235387faec4c4f6c0b high confidence adjacent normal sample_accession: GSM2723937 sample_title: 86049102N normal kidney RNA-seq source_name: adjacent normal kidney characteristics: individual: patient 86049102; disease state: ccRC... controlled vocabulary controlled vocabulary normal tissue type match: adjacent normal
organism Homo sapiens dataset GSE102101 Runtime Siftome inference GEO:dataset:GSE102101:cc3200efcbdf3de9444cabf926562cb2208d318eb8d317092ae2385793af8641 high confidence homo sapiens dataset_accession: GSE102101 dataset_title: Transcriptomics profiles of patient-matched normal kidney and ccRCC pairs organism: Homo sapiens assay_type: bulk RNA-seq processed_d... keyword match keyword match: homo sapiens
sample_type normal tissue sample GSM2723919 Runtime Siftome inference GEO:sample:GSM2723919:8adc6711e7a59001b93e28c21256a62f931ce4f90f64b4d1f66ee5746c384e7c high confidence adjacent normal sample_accession: GSM2723919 sample_title: 12364284N normal kidney RNA-Seq source_name: adjacent normal kidney characteristics: individual: patient 12364284; disease state: ccRC... controlled vocabulary controlled vocabulary sample type match: adjacent normal
sample_type tumor sample sample GSM2723920 Runtime Siftome inference GEO:sample:GSM2723920:974583b4283a142317be0039ddc263140560361b017530edcf875bcf7fae8289 low confidence tumor sample_accession: GSM2723920 sample_title: 12364284T ccRCC RNA-Seq source_name: ccRCC tumor characteristics: individual: patient 12364284; disease state: ccRCC; tissue: ccRCC tu... controlled vocabulary controlled vocabulary sample type match: tumor
sample_type normal tissue sample GSM2723921 Runtime Siftome inference GEO:sample:GSM2723921:a3dfe32a6a646f4284eb476b0231b7b469115a0f048db7689a52ae64227f9103 high confidence adjacent normal sample_accession: GSM2723921 sample_title: 17621953N normal kidney RNA-Seq source_name: adjacent normal kidney characteristics: individual: patient 17621953; disease state: ccRC... controlled vocabulary controlled vocabulary sample type match: adjacent normal
sample_type tumor sample sample GSM2723922 Runtime Siftome inference GEO:sample:GSM2723922:c1105921ce01bd94a602222e41c671166e96e8296d27ee69182729c47ac229a9 low confidence tumor sample_accession: GSM2723922 sample_title: 17621953T ccRCC RNA-Seq source_name: ccRCC tumor characteristics: individual: patient 17621953; disease state: ccRCC; tissue: ccRCC tu... controlled vocabulary controlled vocabulary sample type match: tumor
sample_type normal tissue sample GSM2723923 Runtime Siftome inference GEO:sample:GSM2723923:b9aebec09bc14a5e15c5d4601751d888ed292852d9f05f6b55e5f58b6acc9663 high confidence adjacent normal sample_accession: GSM2723923 sample_title: 20431713N normal kidney RNA-seq source_name: adjacent normal kidney characteristics: individual: patient 20431713; disease state: ccRC... controlled vocabulary controlled vocabulary sample type match: adjacent normal
sample_type tumor sample sample GSM2723924 Runtime Siftome inference GEO:sample:GSM2723924:5c3aa51528e6bb67e1ae06ed3f9c7d0ba5bb3c8d4841700b89dbe6631e29ac14 low confidence tumor sample_accession: GSM2723924 sample_title: 20431713T ccRCC RNA-seq source_name: ccRCC tumor characteristics: individual: patient 20431713; disease state: ccRCC; tissue: ccRCC tu... controlled vocabulary controlled vocabulary sample type match: tumor
sample_type normal tissue sample GSM2723925 Runtime Siftome inference GEO:sample:GSM2723925:6a6f3073ce4dfe3e437161b30a4d402e1290fc32299d7e0a043bdcffd01a60df high confidence adjacent normal sample_accession: GSM2723925 sample_title: 40911432N normal kidney RNA-seq source_name: adjacent normal kidney characteristics: individual: patient 40911432; disease state: ccRC... controlled vocabulary controlled vocabulary sample type match: adjacent normal
sample_type tumor sample sample GSM2723926 Runtime Siftome inference GEO:sample:GSM2723926:a306e952b07af3e715dc5b61a8ca22592d33892e30b577f26bcc4c4844f38384 low confidence tumor sample_accession: GSM2723926 sample_title: 40911432T ccRCC RNA-seq source_name: ccRCC tumor characteristics: individual: patient 40911432; disease state: ccRCC; tissue: ccRCC tu... controlled vocabulary controlled vocabulary sample type match: tumor
sample_type normal tissue sample GSM2723927 Runtime Siftome inference GEO:sample:GSM2723927:9a68aecf3a0fcc5180c1970faa7e3c9ef2c7b750f7173f5d36b0b5fc57ebe136 high confidence adjacent normal sample_accession: GSM2723927 sample_title: 57398667N normal kidney RNA-seq source_name: adjacent normal kidney characteristics: individual: patient 57398667; disease state: ccRC... controlled vocabulary controlled vocabulary sample type match: adjacent normal
sample_type tumor sample sample GSM2723928 Runtime Siftome inference GEO:sample:GSM2723928:1c74b889c2f583d1ffb825c9c3f8c02cd0b283a2cbdc21055f1c234302421db3 low confidence tumor sample_accession: GSM2723928 sample_title: 57398667T ccRCC RNA-seq source_name: ccRCC tumor characteristics: individual: patient 57398667; disease state: ccRCC; tissue: ccRCC tu... controlled vocabulary controlled vocabulary sample type match: tumor
sample_type normal tissue sample GSM2723929 Runtime Siftome inference GEO:sample:GSM2723929:0065e39355e44081466528e5c21f88e40708af8aa62f0ea47100e807f684bfab high confidence adjacent normal sample_accession: GSM2723929 sample_title: 70528835N normal kidney RNA-seq source_name: adjacent normal kidney characteristics: individual: patient 70528835; disease state: ccRC... controlled vocabulary controlled vocabulary sample type match: adjacent normal
sample_type tumor sample sample GSM2723930 Runtime Siftome inference GEO:sample:GSM2723930:4dfd456e88a1ae8653c0003c6f3f24704e999bff108637cf239bd301a9ba8252 low confidence tumor sample_accession: GSM2723930 sample_title: 70528835T ccRCC RNA-seq source_name: ccRCC tumor characteristics: individual: patient 70528835; disease state: ccRCC; tissue: ccRCC tu... controlled vocabulary controlled vocabulary sample type match: tumor
sample_type normal tissue sample GSM2723931 Runtime Siftome inference GEO:sample:GSM2723931:e394588f1c8582ba249ec7dd72a3caf8f075d0e0163a8fd01e99e44cab942297 high confidence adjacent normal sample_accession: GSM2723931 sample_title: 74575859N normal kidney RNA-seq source_name: adjacent normal kidney characteristics: individual: patient 74575859; disease state: ccRC... controlled vocabulary controlled vocabulary sample type match: adjacent normal
sample_type tumor sample sample GSM2723932 Runtime Siftome inference GEO:sample:GSM2723932:3f11886ba6ce6271894904f622cb0d9a809278e64b3bd80a43147de21fd84a2c low confidence tumor sample_accession: GSM2723932 sample_title: 74575859T ccRCC RNA-seq source_name: ccRCC tumor characteristics: individual: patient 74575859; disease state: ccRCC; tissue: ccRCC tu... controlled vocabulary controlled vocabulary sample type match: tumor
sample_type normal tissue sample GSM2723933 Runtime Siftome inference GEO:sample:GSM2723933:7b6c78de0a52764250687215e8bdfcb9e7a1baad2fb93b3513bca572aab54535 high confidence adjacent normal sample_accession: GSM2723933 sample_title: 75416923N normal kidney RNA-seq source_name: adjacent normal kidney characteristics: individual: patient 75416923; disease state: ccRC... controlled vocabulary controlled vocabulary sample type match: adjacent normal
sample_type tumor sample sample GSM2723934 Runtime Siftome inference GEO:sample:GSM2723934:1605106827ffd5cb398e964b2aaa24d0397cb8bc7bdf9735dd2a9fc5d149f7b1 low confidence tumor sample_accession: GSM2723934 sample_title: 75416923T ccRCC RNA-seq source_name: ccRCC tumor characteristics: individual: patient 75416923; disease state: ccRCC; tissue: ccRCC tu... controlled vocabulary controlled vocabulary sample type match: tumor
sample_type normal tissue sample GSM2723935 Runtime Siftome inference GEO:sample:GSM2723935:309bf1896003c996d1accdf81252cd374a646c89df796c4bf8e6a4c47380554b high confidence adjacent normal sample_accession: GSM2723935 sample_title: 77972083N normal kidney RNA-seq source_name: adjacent normal kidney characteristics: individual: patient 77972083; disease state: ccRC... controlled vocabulary controlled vocabulary sample type match: adjacent normal
sample_type tumor sample sample GSM2723936 Runtime Siftome inference GEO:sample:GSM2723936:b23959f0af78c6d692e87ba1130f826cee153e0f84b5b6cf75aa35f201db96f3 low confidence tumor sample_accession: GSM2723936 sample_title: 77972083T ccRCC RNA-seq source_name: ccRCC tumor characteristics: individual: patient 77972083; disease state: ccRCC; tissue: ccRCC tu... controlled vocabulary controlled vocabulary sample type match: tumor
sample_type normal tissue sample GSM2723937 Runtime Siftome inference GEO:sample:GSM2723937:68a48979e61ebc8fb6166ebd264ba16a8d4ed188d3ce27235387faec4c4f6c0b high confidence adjacent normal sample_accession: GSM2723937 sample_title: 86049102N normal kidney RNA-seq source_name: adjacent normal kidney characteristics: individual: patient 86049102; disease state: ccRC... controlled vocabulary controlled vocabulary sample type match: adjacent normal
sample_type tumor sample sample GSM2723938 Runtime Siftome inference GEO:sample:GSM2723938:3b03c45ff196ecb031c666f26e2411b3007e6cdafef9c41619ae85bfbc09bdfb low confidence tumor sample_accession: GSM2723938 sample_title: 86049102T ccRCC RNA-seq source_name: ccRCC tumor characteristics: individual: patient 86049102; disease state: ccRCC; tissue: ccRCC tu... controlled vocabulary controlled vocabulary sample type match: tumor

Sample Group Preview

Possible case samples

Samples currently treated as the comparison case group.

10
  • GSM2723920 12364284T ccRCC RNA-Seq tumor sample Case marker detected. ccRCC tumor individual: patient 12364284; disease state: ccRCC; tissue: ccRCC tumor
  • GSM2723922 17621953T ccRCC RNA-Seq tumor sample Case marker detected. ccRCC tumor individual: patient 17621953; disease state: ccRCC; tissue: ccRCC tumor
  • GSM2723924 20431713T ccRCC RNA-seq tumor sample Case marker detected. ccRCC tumor individual: patient 20431713; disease state: ccRCC; tissue: ccRCC tumor
  • GSM2723926 40911432T ccRCC RNA-seq tumor sample Case marker detected. ccRCC tumor individual: patient 40911432; disease state: ccRCC; tissue: ccRCC tumor
  • GSM2723928 57398667T ccRCC RNA-seq tumor sample Case marker detected. ccRCC tumor individual: patient 57398667; disease state: ccRCC; tissue: ccRCC tumor
  • GSM2723930 70528835T ccRCC RNA-seq tumor sample Case marker detected. ccRCC tumor individual: patient 70528835; disease state: ccRCC; tissue: ccRCC tumor
  • GSM2723932 74575859T ccRCC RNA-seq tumor sample Case marker detected. ccRCC tumor individual: patient 74575859; disease state: ccRCC; tissue: ccRCC tumor
  • GSM2723934 75416923T ccRCC RNA-seq tumor sample Case marker detected. ccRCC tumor individual: patient 75416923; disease state: ccRCC; tissue: ccRCC tumor
  • GSM2723936 77972083T ccRCC RNA-seq tumor sample Case marker detected. ccRCC tumor individual: patient 77972083; disease state: ccRCC; tissue: ccRCC tumor
  • GSM2723938 86049102T ccRCC RNA-seq tumor sample Case marker detected. ccRCC tumor individual: patient 86049102; disease state: ccRCC; tissue: ccRCC tumor

Possible control samples

Samples currently treated as controls or baseline.

10
  • GSM2723919 12364284N normal kidney RNA-Seq normal tissue Control marker detected. adjacent normal kidney individual: patient 12364284; disease state: ccRCC; tissue: adjacent normal kidney
  • GSM2723921 17621953N normal kidney RNA-Seq normal tissue Control marker detected. adjacent normal kidney individual: patient 17621953; disease state: ccRCC; tissue: adjacent normal kidney
  • GSM2723923 20431713N normal kidney RNA-seq normal tissue Control marker detected. adjacent normal kidney individual: patient 20431713; disease state: ccRCC; tissue: adjacent normal kidney
  • GSM2723925 40911432N normal kidney RNA-seq normal tissue Control marker detected. adjacent normal kidney individual: patient 40911432; disease state: ccRCC; tissue: adjacent normal kidney
  • GSM2723927 57398667N normal kidney RNA-seq normal tissue Control marker detected. adjacent normal kidney individual: patient 57398667; disease state: ccRCC; tissue: adjacent normal kidney
  • GSM2723929 70528835N normal kidney RNA-seq normal tissue Control marker detected. adjacent normal kidney individual: patient 70528835; disease state: ccRCC; tissue: adjacent normal kidney
  • GSM2723931 74575859N normal kidney RNA-seq normal tissue Control marker detected. adjacent normal kidney individual: patient 74575859; disease state: ccRCC; tissue: adjacent normal kidney
  • GSM2723933 75416923N normal kidney RNA-seq normal tissue Control marker detected. adjacent normal kidney individual: patient 75416923; disease state: ccRCC; tissue: adjacent normal kidney
  • GSM2723935 77972083N normal kidney RNA-seq normal tissue Control marker detected. adjacent normal kidney individual: patient 77972083; disease state: ccRCC; tissue: adjacent normal kidney
  • GSM2723937 86049102N normal kidney RNA-seq normal tissue Control marker detected. adjacent normal kidney individual: patient 86049102; disease state: ccRCC; tissue: adjacent normal kidney

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

10 samples
  • GSM2723919 12364284N normal kidney RNA-Seq adjacent normal kidney individual: patient 12364284; disease state: ccRCC; tissue: adjacent normal kidney
  • GSM2723921 17621953N normal kidney RNA-Seq adjacent normal kidney individual: patient 17621953; disease state: ccRCC; tissue: adjacent normal kidney
  • GSM2723923 20431713N normal kidney RNA-seq adjacent normal kidney individual: patient 20431713; disease state: ccRCC; tissue: adjacent normal kidney
  • GSM2723925 40911432N normal kidney RNA-seq adjacent normal kidney individual: patient 40911432; disease state: ccRCC; tissue: adjacent normal kidney
  • GSM2723927 57398667N normal kidney RNA-seq adjacent normal kidney individual: patient 57398667; disease state: ccRCC; tissue: adjacent normal kidney
  • GSM2723929 70528835N normal kidney RNA-seq adjacent normal kidney individual: patient 70528835; disease state: ccRCC; tissue: adjacent normal kidney
  • GSM2723931 74575859N normal kidney RNA-seq adjacent normal kidney individual: patient 74575859; disease state: ccRCC; tissue: adjacent normal kidney
  • GSM2723933 75416923N normal kidney RNA-seq adjacent normal kidney individual: patient 75416923; disease state: ccRCC; tissue: adjacent normal kidney
  • GSM2723935 77972083N normal kidney RNA-seq adjacent normal kidney individual: patient 77972083; disease state: ccRCC; tissue: adjacent normal kidney
  • GSM2723937 86049102N normal kidney RNA-seq adjacent normal kidney individual: patient 86049102; disease state: ccRCC; tissue: adjacent normal kidney

tumor sample

10 samples
  • GSM2723920 12364284T ccRCC RNA-Seq ccRCC tumor individual: patient 12364284; disease state: ccRCC; tissue: ccRCC tumor
  • GSM2723922 17621953T ccRCC RNA-Seq ccRCC tumor individual: patient 17621953; disease state: ccRCC; tissue: ccRCC tumor
  • GSM2723924 20431713T ccRCC RNA-seq ccRCC tumor individual: patient 20431713; disease state: ccRCC; tissue: ccRCC tumor
  • GSM2723926 40911432T ccRCC RNA-seq ccRCC tumor individual: patient 40911432; disease state: ccRCC; tissue: ccRCC tumor
  • GSM2723928 57398667T ccRCC RNA-seq ccRCC tumor individual: patient 57398667; disease state: ccRCC; tissue: ccRCC tumor
  • GSM2723930 70528835T ccRCC RNA-seq ccRCC tumor individual: patient 70528835; disease state: ccRCC; tissue: ccRCC tumor
  • GSM2723932 74575859T ccRCC RNA-seq ccRCC tumor individual: patient 74575859; disease state: ccRCC; tissue: ccRCC tumor
  • GSM2723934 75416923T ccRCC RNA-seq ccRCC tumor individual: patient 75416923; disease state: ccRCC; tissue: ccRCC tumor
  • GSM2723936 77972083T ccRCC RNA-seq ccRCC tumor individual: patient 77972083; disease state: ccRCC; tissue: ccRCC tumor
  • GSM2723938 86049102T ccRCC RNA-seq ccRCC tumor individual: patient 86049102; disease state: ccRCC; tissue: ccRCC 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

20 samples

Review Audit Trail

0 decisions

No review decisions have been stored for this dataset.