Siftome Phase 3L

GSE221608

Transcriptome sequencing of normal intestinal mucosal tissues, paired primary CRC tissues and liver metastases lesions in participants of CRC

Recommended Scores and metadata are strong enough for direct review.
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
2022-12-22
Last update
2025-12-10
Organization
SUN YAT-SEN UNIVERSITY
Department
Not available
Public date
2025-11-26
Experiment types
Expression profiling by high throughput sequencing
Platforms
GPL20301 Illumina HiSeq 4000 (Homo sapiens)
Series type
Series
SubSeries
Not available
BioProject
PRJNA915076
Supplementary files
XLSX: GSE221608_processed_data.xlsx
Organism
Homo sapiens
Assay
bulk RNA-seq
Samples
52
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

Review before analysis
88% 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

3/15 pts

Unassigned or review-needed samples remain before analysis.

Blocking warnings

10/10 pts

No dataset warnings are present.

Metadata normalization

10/10 pts

Metadata quality is high enough to support downstream handoff.

Blockers

  • 18 samples are still unassigned.

Next Steps

  • Resolve unassigned or review-needed samples in the grouping table.

Analysis Preparation Checklist

4/6 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

Needs review

0 review-needed samples and 18 unassigned samples remain.

Resolve ambiguous and unassigned samples before finalizing the contrast.

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

Bioinformatician review required

Ask a bioinformatician to review grouping, count availability, exclusions, and design before DE.

  • Analysis readiness has blockers that must be resolved before DE.
  • One or more samples are unassigned and need manual grouping decisions.

Why This Is Ranked Here

Patient tissue tumor-vs-normal
Recommended Scores and metadata are strong enough for direct review.

Score Components

  • relevance 100% Disease or condition metadata normalized. Organism normalized. Assay type normalized. Tissue metadata normalized.
  • comparison suitability 100% Case and control sample groups detected: colorectal cancer vs normal tissue. 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. Colorectal, colon, rectal, or CRC disease context boosted for tumor-vs-normal tissue ranking.
  • metadata quality 100% 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 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 100% Weighted score: 30% relevance, 30% comparison suitability, 25% metadata quality, 15% data availability.

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 colorectal cancer 20 samples
  • Likely control group normal tissue 14 samples

Warnings

No ranking warnings are active.

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 colorectal cancer 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 0 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 Missing or unclear metadata: Treatment clarity: No unclear treatment split detected in the sample metadata. Derived from current-intent ranking reasons and warnings.

Applied Review Decisions

No active review decisions affect this ranking.

Ranking Facts

  • Recommendation Recommended Scores and metadata are strong enough for direct review.
  • Supporting fact Tumor vs unmatched normal · Tissue · suitability 100%. 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 Prioritized disease context: colorectal, colon, rectal, or CRC metadata detected. Contributed to match or upgrade evidence.
  • Supporting fact Processed data is available for downstream review. Contributed to match or upgrade 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.

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
GSE221608
Sample records
52 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
GSE221608
  • 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
GSE221608
  • 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
GSE221608
  • 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: GSE221608
dataset_title: Transcriptome sequencing of normal intestinal mucosal tissues, paired primary CRC tissues and liver metastases lesions in participants of CRC
organism: Homo sapiens
assay_type: bulk RNA-seq
processed_data_available: true
raw_data_available: true
submission_date: 2022-12-22
last_update_date: 2025-12-10
organization_name: SUN YAT-SEN UNIVERSITY
department: Not available
public_date: 2025-11-26
experiment_types: Expression profiling by high throughput sequencing
platforms: GPL20301 Illumina HiSeq 4000 (Homo sapiens)
sub_series: Not available
bioproject: PRJNA915076
supplementary_files: XLSX: GSE221608_processed_data.xlsx
series_type: Series

Why It Matched

  • Tumor vs unmatched normal · Tissue · suitability 100%.
  • Prioritized assay: bulk RNA-seq is the active assay expectation.
  • Prioritized disease context: colorectal, colon, rectal, or CRC metadata detected.
  • Processed data is available for downstream review.

Why It May Not Be Suitable

  • Missing or unclear metadata: Treatment clarity: No unclear treatment split detected in the sample metadata.

Warnings

No warnings

Normalized Fields

56 fields
Field Value Source Origin Confidence Evidence Reason
assay_type bulk RNA-seq dataset GSE221608 Runtime Siftome inference GEO:dataset:GSE221608:3fe4fe6547c3938fba0b43be004f2e5ed8584384182b02a84612304dbaad59e2 high confidence bulk rna-seq dataset_accession: GSE221608 dataset_title: Transcriptome sequencing of normal intestinal mucosal tissues, paired primary CRC tissues and liver metastases lesions in participant... keyword match keyword match: bulk rna-seq
disease colorectal cancer dataset GSE221608 Runtime Siftome inference GEO:dataset:GSE221608:3fe4fe6547c3938fba0b43be004f2e5ed8584384182b02a84612304dbaad59e2 medium confidence crc dataset_accession: GSE221608 dataset_title: Transcriptome sequencing of normal intestinal mucosal tissues, paired primary CRC tissues and liver metastases lesions in participant... controlled vocabulary controlled vocabulary disease match: crc
disease colorectal cancer sample GSM6890233 Runtime Siftome inference GEO:sample:GSM6890233:fc0c650cbbd8e1a83ebe69ccf3ddfc44bb65e41b23ad89b70588791adaa1fe1a medium confidence crc sample_accession: GSM6890233 sample_title: Group A-1 source_name: CRC tissues characteristics: tissue: CRC tissues; donor: 1 Group A-1 controlled vocabulary controlled vocabulary disease match: crc
disease colorectal cancer sample GSM6890236 Runtime Siftome inference GEO:sample:GSM6890236:776a1681aa85bca40ccb41875ccd15be724c1b2a0b9ec0c8dc6afaba1cd916bf medium confidence crc sample_accession: GSM6890236 sample_title: Group A-2 source_name: CRC tissues characteristics: tissue: CRC tissues; donor: 2 Group A-2 controlled vocabulary controlled vocabulary disease match: crc
disease colorectal cancer sample GSM6890239 Runtime Siftome inference GEO:sample:GSM6890239:57a00723a8b47b16b2a5b9143dc9844f751710bf4ca55244225a752d65147cba medium confidence crc sample_accession: GSM6890239 sample_title: Group A-3 source_name: CRC tissues characteristics: tissue: CRC tissues; donor: 3 Group A-3 controlled vocabulary controlled vocabulary disease match: crc
disease colorectal cancer sample GSM6890242 Runtime Siftome inference GEO:sample:GSM6890242:64fddcbc1d5c56f3c79c2452eea36f0dc8352cff65593934efa8dfc7918e1577 medium confidence crc sample_accession: GSM6890242 sample_title: Group A-4 source_name: CRC tissues characteristics: tissue: CRC tissues; donor: 4 Group A-4 controlled vocabulary controlled vocabulary disease match: crc
disease colorectal cancer sample GSM6890244 Runtime Siftome inference GEO:sample:GSM6890244:31fedc9e059690c925e17c41c44bc8f800a7c6cd97b1b9a786b35bea8e9a38d1 medium confidence crc sample_accession: GSM6890244 sample_title: Group A-5 source_name: CRC tissues characteristics: tissue: CRC tissues; donor: 5 Group A-5 controlled vocabulary controlled vocabulary disease match: crc
disease colorectal cancer sample GSM6890247 Runtime Siftome inference GEO:sample:GSM6890247:80c7e089fe8d12b841d28d59e4bd35247e3fb685f6dc900af590551ac3bb71ad medium confidence crc sample_accession: GSM6890247 sample_title: Group A-6 source_name: CRC tissues characteristics: tissue: CRC tissues; donor: 6 Group A-6 controlled vocabulary controlled vocabulary disease match: crc
disease colorectal cancer sample GSM6890250 Runtime Siftome inference GEO:sample:GSM6890250:5fbd7c5fbe794f4bb727d8176944f5fc8471ca05febc4181a0ff24bf0006c589 medium confidence crc sample_accession: GSM6890250 sample_title: Group A-7 source_name: CRC tissues characteristics: tissue: CRC tissues; donor: 7 Group A-7 controlled vocabulary controlled vocabulary disease match: crc
disease colorectal cancer sample GSM6890253 Runtime Siftome inference GEO:sample:GSM6890253:aa5b739564869e850bb58ce6a0b48d3917f5ac746526b0f3b9707ed967cb3a91 medium confidence crc sample_accession: GSM6890253 sample_title: Group A-8 source_name: CRC tissues characteristics: tissue: CRC tissues; donor: 8 Group A-8 controlled vocabulary controlled vocabulary disease match: crc
disease colorectal cancer sample GSM6890256 Runtime Siftome inference GEO:sample:GSM6890256:7f5744c534d63f8dc48001ceaf59103c4bf0878dc108b6e5f544bf9f8cf2251d medium confidence crc sample_accession: GSM6890256 sample_title: Group A-9 source_name: CRC tissues characteristics: tissue: CRC tissues; donor: 9 Group A-9 controlled vocabulary controlled vocabulary disease match: crc
disease colorectal cancer sample GSM6890258 Runtime Siftome inference GEO:sample:GSM6890258:7336df38b8894e56afa4d70eae8e8b71c3a824753c488defb0d2980ebf7a3b03 medium confidence crc sample_accession: GSM6890258 sample_title: Group A-10 source_name: CRC tissues characteristics: tissue: CRC tissues; donor: 10 Group A-10 controlled vocabulary controlled vocabulary disease match: crc
disease colorectal cancer sample GSM6890261 Runtime Siftome inference GEO:sample:GSM6890261:7f84ef62def25fde08d0b16a40b5f06f48863df6595ee1b45612419d65f3b61a medium confidence crc sample_accession: GSM6890261 sample_title: Group A-11 source_name: CRC tissues characteristics: tissue: CRC tissues; donor: 11 Group A-11 controlled vocabulary controlled vocabulary disease match: crc
disease colorectal cancer sample GSM6890264 Runtime Siftome inference GEO:sample:GSM6890264:1d5b2cd266bcaace73b6b9bb55cb2c8cf4f32e8c1282a626db52c9d65b5ee71d medium confidence crc sample_accession: GSM6890264 sample_title: Group A-12 source_name: CRC tissues characteristics: tissue: CRC tissues; donor: 12 Group A-12 controlled vocabulary controlled vocabulary disease match: crc
disease colorectal cancer sample GSM6890267 Runtime Siftome inference GEO:sample:GSM6890267:b1f2d1f0713f781b555694a756ff46fec4f4cebef76f28cee152d8d6321c17de medium confidence crc sample_accession: GSM6890267 sample_title: Group A-13 source_name: CRC tissues characteristics: tissue: CRC tissues; donor: 13 Group A-13 controlled vocabulary controlled vocabulary disease match: crc
disease colorectal cancer sample GSM6890268 Runtime Siftome inference GEO:sample:GSM6890268:c4ae50bf6fcbea7f448376b913191159338b40424dee0720ba6d2460d36b5a7e medium confidence crc sample_accession: GSM6890268 sample_title: Group A-14 source_name: CRC tissues characteristics: tissue: CRC tissues; donor: 14 Group A-14 controlled vocabulary controlled vocabulary disease match: crc
disease colorectal cancer sample GSM6890270 Runtime Siftome inference GEO:sample:GSM6890270:6c8e3dcd9c5888cf3d58dc68ca9bb7ef66ecf34bad91a5b99f8c24ddc9b58cfd medium confidence crc sample_accession: GSM6890270 sample_title: Group A-15 source_name: CRC tissues characteristics: tissue: CRC tissues; donor: 15 Group A-15 controlled vocabulary controlled vocabulary disease match: crc
disease colorectal cancer sample GSM6890273 Runtime Siftome inference GEO:sample:GSM6890273:c78919064cd335495100e4ad899f1b5627eee9b1e685a6bf25864207b7c6251c medium confidence crc sample_accession: GSM6890273 sample_title: Group A-16 source_name: CRC tissues characteristics: tissue: CRC tissues; donor: 16 Group A-16 controlled vocabulary controlled vocabulary disease match: crc
disease colorectal cancer sample GSM6890275 Runtime Siftome inference GEO:sample:GSM6890275:abf8c4ba2477177f99328e4fe9a1fba3691cf5d57964b795771af4996d0c3477 medium confidence crc sample_accession: GSM6890275 sample_title: Group A-17 source_name: CRC tissues characteristics: tissue: CRC tissues; donor: 17 Group A-17 controlled vocabulary controlled vocabulary disease match: crc
disease colorectal cancer sample GSM6890277 Runtime Siftome inference GEO:sample:GSM6890277:404abd5f4c883ba8ad5be004a44f9a25fa95c4959d4eb6197d3bea4de278ec7b medium confidence crc sample_accession: GSM6890277 sample_title: Group A-18 source_name: CRC tissues characteristics: tissue: CRC tissues; donor: 18 Group A-18 controlled vocabulary controlled vocabulary disease match: crc
disease colorectal cancer sample GSM6890280 Runtime Siftome inference GEO:sample:GSM6890280:efbdf41424277ab25e34d1096fd1dc6e24d32e36d9364d472a9d45d76b74a846 medium confidence crc sample_accession: GSM6890280 sample_title: Group A-19 source_name: CRC tissues characteristics: tissue: CRC tissues; donor: 19 Group A-19 controlled vocabulary controlled vocabulary disease match: crc
disease colorectal cancer sample GSM6890282 Runtime Siftome inference GEO:sample:GSM6890282:b1dddd319937348a60c2c89cfa20a5b127ac8a695639cc5f608d544d48219d41 medium confidence crc sample_accession: GSM6890282 sample_title: Group A-20 source_name: CRC tissues characteristics: tissue: CRC tissues; donor: 20 Group A-20 controlled vocabulary controlled vocabulary disease match: crc
organism Homo sapiens dataset GSE221608 Runtime Siftome inference GEO:dataset:GSE221608:3fe4fe6547c3938fba0b43be004f2e5ed8584384182b02a84612304dbaad59e2 high confidence homo sapiens dataset_accession: GSE221608 dataset_title: Transcriptome sequencing of normal intestinal mucosal tissues, paired primary CRC tissues and liver metastases lesions in participant... keyword match keyword match: homo sapiens
sample_type normal tissue sample GSM6890235 Runtime Siftome inference GEO:sample:GSM6890235:4dc6a52d35c8d303269b51a8db80c3ffee5b5132a68a70ee4393571e7801ac1f low confidence normal sample_accession: GSM6890235 sample_title: Group C-1 source_name: normal intestinal mucosal tissues characteristics: tissue: normal intestinal mucosal tissues; donor: 1 Group C-1 controlled vocabulary controlled vocabulary sample type match: normal
sample_type normal tissue sample GSM6890238 Runtime Siftome inference GEO:sample:GSM6890238:6b43d086b7c85620deded97102890537bddee486cecc898fd1c951ec999accb2 low confidence normal sample_accession: GSM6890238 sample_title: Group C-2 source_name: normal intestinal mucosal tissues characteristics: tissue: normal intestinal mucosal tissues; donor: 2 Group C-2 controlled vocabulary controlled vocabulary sample type match: normal
sample_type normal tissue sample GSM6890241 Runtime Siftome inference GEO:sample:GSM6890241:dc1d4287c7bcb3a99b3dc22a602ad7c4d84467b639adc36cb4cd3ac46a93273d low confidence normal sample_accession: GSM6890241 sample_title: Group C-3 source_name: normal intestinal mucosal tissues characteristics: tissue: normal intestinal mucosal tissues; donor: 3 Group C-3 controlled vocabulary controlled vocabulary sample type match: normal
sample_type normal tissue sample GSM6890246 Runtime Siftome inference GEO:sample:GSM6890246:7fd32c684ae875f9e68a82824eb381b18ac43f02041d45a6e84e5fad1559ee86 low confidence normal sample_accession: GSM6890246 sample_title: Group C-5 source_name: normal intestinal mucosal tissues characteristics: tissue: normal intestinal mucosal tissues; donor: 5 Group C-5 controlled vocabulary controlled vocabulary sample type match: normal
sample_type normal tissue sample GSM6890249 Runtime Siftome inference GEO:sample:GSM6890249:1544ad16868995c051c58301fe545fbc3643b395929cdb0b8af6f33de5694146 low confidence normal sample_accession: GSM6890249 sample_title: Group C-6 source_name: normal intestinal mucosal tissues characteristics: tissue: normal intestinal mucosal tissues; donor: 6 Group C-6 controlled vocabulary controlled vocabulary sample type match: normal
sample_type normal tissue sample GSM6890252 Runtime Siftome inference GEO:sample:GSM6890252:cf17f7f0860e5ac38aa5e6ca4e3145fd45f8c772a3b60ecb0c501a5c6fa9e2d6 low confidence normal sample_accession: GSM6890252 sample_title: Group C-7 source_name: normal intestinal mucosal tissues characteristics: tissue: normal intestinal mucosal tissues; donor: 7 Group C-7 controlled vocabulary controlled vocabulary sample type match: normal
sample_type normal tissue sample GSM6890255 Runtime Siftome inference GEO:sample:GSM6890255:0653f025494f52cb291de6dcb0250b00472ca46dfdb07ef66f97d6d1303d07f3 low confidence normal sample_accession: GSM6890255 sample_title: Group C-8 source_name: normal intestinal mucosal tissues characteristics: tissue: normal intestinal mucosal tissues; donor: 8 Group C-8 controlled vocabulary controlled vocabulary sample type match: normal
sample_type normal tissue sample GSM6890260 Runtime Siftome inference GEO:sample:GSM6890260:17e29db05024bb5eb00aa97f1eeba0029e815c729cc0e9d00f3e398866e1959c low confidence normal sample_accession: GSM6890260 sample_title: Group C-10 source_name: normal intestinal mucosal tissues characteristics: tissue: normal intestinal mucosal tissues; donor: 10 Group ... controlled vocabulary controlled vocabulary sample type match: normal
sample_type normal tissue sample GSM6890263 Runtime Siftome inference GEO:sample:GSM6890263:cd76fa0a15c9205c0dea87b7600674455544e2ccece560e17a192cd4822bba83 low confidence normal sample_accession: GSM6890263 sample_title: Group C-11 source_name: normal intestinal mucosal tissues characteristics: tissue: normal intestinal mucosal tissues; donor: 11 Group ... controlled vocabulary controlled vocabulary sample type match: normal
sample_type normal tissue sample GSM6890266 Runtime Siftome inference GEO:sample:GSM6890266:4a304f1a1116504d5a6bb97163b5e4006a72bc02f93d395da99f88e3df92b3ca low confidence normal sample_accession: GSM6890266 sample_title: Group C-12 source_name: normal intestinal mucosal tissues characteristics: tissue: normal intestinal mucosal tissues; donor: 12 Group ... controlled vocabulary controlled vocabulary sample type match: normal
sample_type normal tissue sample GSM6890269 Runtime Siftome inference GEO:sample:GSM6890269:a8ef3defaaabfd912e0cb8968ab66d3c7c47826d9a6ca900e848d7b8efd411bd low confidence normal sample_accession: GSM6890269 sample_title: Group C-14 source_name: normal intestinal mucosal tissues characteristics: tissue: normal intestinal mucosal tissues; donor: 14 Group ... controlled vocabulary controlled vocabulary sample type match: normal
sample_type normal tissue sample GSM6890272 Runtime Siftome inference GEO:sample:GSM6890272:572a9333ad29367e2e8ae41afc4fa85acbf2c01becf8cb113e9847f5469a711e low confidence normal sample_accession: GSM6890272 sample_title: Group C-15 source_name: normal intestinal mucosal tissues characteristics: tissue: normal intestinal mucosal tissues; donor: 15 Group ... controlled vocabulary controlled vocabulary sample type match: normal
sample_type normal tissue sample GSM6890279 Runtime Siftome inference GEO:sample:GSM6890279:2de1ef0697950d9c0f0a43b9f84f3a8a7754800aaee0a83ffcbd464ba2fb2b80 low confidence normal sample_accession: GSM6890279 sample_title: Group C-18 source_name: normal intestinal mucosal tissues characteristics: tissue: normal intestinal mucosal tissues; donor: 18 Group ... controlled vocabulary controlled vocabulary sample type match: normal
sample_type normal tissue sample GSM6890284 Runtime Siftome inference GEO:sample:GSM6890284:d54c0068210f875e269f036acb10dc6e2df07f5726f425c09ca9304890eba53d low confidence normal sample_accession: GSM6890284 sample_title: Group C-20 source_name: normal intestinal mucosal tissues characteristics: tissue: normal intestinal mucosal tissues; donor: 20 Group ... controlled vocabulary controlled vocabulary sample type match: normal
tissue liver dataset GSE221608 Runtime Siftome inference GEO:dataset:GSE221608:3fe4fe6547c3938fba0b43be004f2e5ed8584384182b02a84612304dbaad59e2 low confidence liver dataset_accession: GSE221608 dataset_title: Transcriptome sequencing of normal intestinal mucosal tissues, paired primary CRC tissues and liver metastases lesions in participant... controlled vocabulary controlled vocabulary tissue match: liver
tissue liver sample GSM6890234 Runtime Siftome inference GEO:sample:GSM6890234:53079b224cbd6d7051384733fbd9783fc945c937b07f1bf2941f1a4896f93119 low confidence liver sample_accession: GSM6890234 sample_title: Group B-1 source_name: liver metastases characteristics: tissue: liver metastases; donor: 1 Group B-1 controlled vocabulary controlled vocabulary tissue match: liver
tissue liver sample GSM6890237 Runtime Siftome inference GEO:sample:GSM6890237:ed54b57fc60ad5ae7f7fc6cb4c9f61effdd8567425194975635889e80bcf199b low confidence liver sample_accession: GSM6890237 sample_title: Group B-2 source_name: liver metastases characteristics: tissue: liver metastases; donor: 2 Group B-2 controlled vocabulary controlled vocabulary tissue match: liver
tissue liver sample GSM6890240 Runtime Siftome inference GEO:sample:GSM6890240:f8df32e592c14c92992029effcabab7b156e93ccac7df31f241046572c514bd7 low confidence liver sample_accession: GSM6890240 sample_title: Group B-3 source_name: liver metastases characteristics: tissue: liver metastases; donor: 3 Group B-3 controlled vocabulary controlled vocabulary tissue match: liver
tissue liver sample GSM6890243 Runtime Siftome inference GEO:sample:GSM6890243:46518adb5335db431b67825a9a1ccab7266a3c64710bdccd93a93e19b819ad1f low confidence liver sample_accession: GSM6890243 sample_title: Group B-4 source_name: liver metastases characteristics: tissue: liver metastases; donor: 4 Group B-4 controlled vocabulary controlled vocabulary tissue match: liver
tissue liver sample GSM6890245 Runtime Siftome inference GEO:sample:GSM6890245:a9c7f6ef8b4f8f6076bef11383b0fbfa8a3c85dab30034b7fe5088aecf672994 low confidence liver sample_accession: GSM6890245 sample_title: Group B-5 source_name: liver metastases characteristics: tissue: liver metastases; donor: 5 Group B-5 controlled vocabulary controlled vocabulary tissue match: liver
tissue liver sample GSM6890248 Runtime Siftome inference GEO:sample:GSM6890248:78c6648c83855e3eff299abe306223a16bbd04193d27e6ec075157b32b3899c1 low confidence liver sample_accession: GSM6890248 sample_title: Group B-6 source_name: liver metastases characteristics: tissue: liver metastases; donor: 6 Group B-6 controlled vocabulary controlled vocabulary tissue match: liver
tissue liver sample GSM6890251 Runtime Siftome inference GEO:sample:GSM6890251:cc751c3355ce0244b367d5049c8ab14ddfdd6e425f70bda7800d39a440f1091c low confidence liver sample_accession: GSM6890251 sample_title: Group B-7 source_name: liver metastases characteristics: tissue: liver metastases; donor: 7 Group B-7 controlled vocabulary controlled vocabulary tissue match: liver
tissue liver sample GSM6890254 Runtime Siftome inference GEO:sample:GSM6890254:cff6b62efe1885d6f48132bbdc1758a96e5b2aea53b4a3510dc9557553547c87 low confidence liver sample_accession: GSM6890254 sample_title: Group B-8 source_name: liver metastases characteristics: tissue: liver metastases; donor: 8 Group B-8 controlled vocabulary controlled vocabulary tissue match: liver
tissue liver sample GSM6890257 Runtime Siftome inference GEO:sample:GSM6890257:a6146af752a18e0df15a86fa469953d8d8137a3f42c68dded176d5905019dba8 low confidence liver sample_accession: GSM6890257 sample_title: Group B-9 source_name: liver metastases characteristics: tissue: liver metastases; donor: 9 Group B-9 controlled vocabulary controlled vocabulary tissue match: liver
tissue liver sample GSM6890259 Runtime Siftome inference GEO:sample:GSM6890259:4a58cdfb1dfa2a09feee940d39654bd7e427879306974d92c440aad4bffd584a low confidence liver sample_accession: GSM6890259 sample_title: Group B-10 source_name: liver metastases characteristics: tissue: liver metastases; donor: 10 Group B-10 controlled vocabulary controlled vocabulary tissue match: liver
tissue liver sample GSM6890262 Runtime Siftome inference GEO:sample:GSM6890262:35acd4290d63552fd4640849c1f7b3b06c3379786c7773ad7863e0caab75abfa low confidence liver sample_accession: GSM6890262 sample_title: Group B-11 source_name: liver metastases characteristics: tissue: liver metastases; donor: 11 Group B-11 controlled vocabulary controlled vocabulary tissue match: liver
tissue liver sample GSM6890265 Runtime Siftome inference GEO:sample:GSM6890265:986c0248548ff4757eb75981d906162342bb3c35c1cb89b856066bd99dfd54bd low confidence liver sample_accession: GSM6890265 sample_title: Group B-12 source_name: liver metastases characteristics: tissue: liver metastases; donor: 12 Group B-12 controlled vocabulary controlled vocabulary tissue match: liver
tissue liver sample GSM6890271 Runtime Siftome inference GEO:sample:GSM6890271:543cb144b996106ebc2bb40a147075a83b7a80587fcda812553014ae477fa3c0 low confidence liver sample_accession: GSM6890271 sample_title: Group B-15 source_name: liver metastases characteristics: tissue: liver metastases; donor: 15 Group B-15 controlled vocabulary controlled vocabulary tissue match: liver
tissue liver sample GSM6890274 Runtime Siftome inference GEO:sample:GSM6890274:51c26a60e0917700c0c5c047028cc8d79b10578cae3a06137c7850cb17c31de0 low confidence liver sample_accession: GSM6890274 sample_title: Group B-16 source_name: liver metastases characteristics: tissue: liver metastases; donor: 16 Group B-16 controlled vocabulary controlled vocabulary tissue match: liver
tissue liver sample GSM6890276 Runtime Siftome inference GEO:sample:GSM6890276:fe0dd41c71501b3a532725c75a6a90608ccbe935ee68de9eae94ce98a5eba1ce low confidence liver sample_accession: GSM6890276 sample_title: Group B-17 source_name: liver metastases characteristics: tissue: liver metastases; donor: 17 Group B-17 controlled vocabulary controlled vocabulary tissue match: liver
tissue liver sample GSM6890278 Runtime Siftome inference GEO:sample:GSM6890278:c541045d1c2deb8aa6a8dcebbdef814f4f67cffb9458d98b6d558eca75d70f82 low confidence liver sample_accession: GSM6890278 sample_title: Group B-18 source_name: liver metastases characteristics: tissue: liver metastases; donor: 18 Group B-18 controlled vocabulary controlled vocabulary tissue match: liver
tissue liver sample GSM6890281 Runtime Siftome inference GEO:sample:GSM6890281:20c0c1708c560aa5a7a2c78aa3158c116a61b84add87b79f7bcd57bd73f98bc1 low confidence liver sample_accession: GSM6890281 sample_title: Group B-19 source_name: liver metastases characteristics: tissue: liver metastases; donor: 19 Group B-19 controlled vocabulary controlled vocabulary tissue match: liver
tissue liver sample GSM6890283 Runtime Siftome inference GEO:sample:GSM6890283:03ac2bacd16520ec15d20bf3a4ca0a19380eca465dafe4560705b49a8c7b0df1 low confidence liver sample_accession: GSM6890283 sample_title: Group B-20 source_name: liver metastases characteristics: tissue: liver metastases; donor: 20 Group B-20 controlled vocabulary controlled vocabulary tissue match: liver

Sample Group Preview

Possible case samples

Samples currently treated as the comparison case group.

20
  • GSM6890233 Group A-1 colorectal cancer Case marker detected. CRC tissues tissue: CRC tissues; donor: 1
  • GSM6890236 Group A-2 colorectal cancer Case marker detected. CRC tissues tissue: CRC tissues; donor: 2
  • GSM6890239 Group A-3 colorectal cancer Case marker detected. CRC tissues tissue: CRC tissues; donor: 3
  • GSM6890242 Group A-4 colorectal cancer Case marker detected. CRC tissues tissue: CRC tissues; donor: 4
  • GSM6890244 Group A-5 colorectal cancer Case marker detected. CRC tissues tissue: CRC tissues; donor: 5
  • GSM6890247 Group A-6 colorectal cancer Case marker detected. CRC tissues tissue: CRC tissues; donor: 6
  • GSM6890250 Group A-7 colorectal cancer Case marker detected. CRC tissues tissue: CRC tissues; donor: 7
  • GSM6890253 Group A-8 colorectal cancer Case marker detected. CRC tissues tissue: CRC tissues; donor: 8
  • GSM6890256 Group A-9 colorectal cancer Case marker detected. CRC tissues tissue: CRC tissues; donor: 9
  • GSM6890258 Group A-10 colorectal cancer Case marker detected. CRC tissues tissue: CRC tissues; donor: 10
  • GSM6890261 Group A-11 colorectal cancer Case marker detected. CRC tissues tissue: CRC tissues; donor: 11
  • GSM6890264 Group A-12 colorectal cancer Case marker detected. CRC tissues tissue: CRC tissues; donor: 12
  • GSM6890267 Group A-13 colorectal cancer Case marker detected. CRC tissues tissue: CRC tissues; donor: 13
  • GSM6890268 Group A-14 colorectal cancer Case marker detected. CRC tissues tissue: CRC tissues; donor: 14
  • GSM6890270 Group A-15 colorectal cancer Case marker detected. CRC tissues tissue: CRC tissues; donor: 15
  • GSM6890273 Group A-16 colorectal cancer Case marker detected. CRC tissues tissue: CRC tissues; donor: 16
  • GSM6890275 Group A-17 colorectal cancer Case marker detected. CRC tissues tissue: CRC tissues; donor: 17
  • GSM6890277 Group A-18 colorectal cancer Case marker detected. CRC tissues tissue: CRC tissues; donor: 18
  • GSM6890280 Group A-19 colorectal cancer Case marker detected. CRC tissues tissue: CRC tissues; donor: 19
  • GSM6890282 Group A-20 colorectal cancer Case marker detected. CRC tissues tissue: CRC tissues; donor: 20

Possible control samples

Samples currently treated as controls or baseline.

14
  • GSM6890235 Group C-1 normal tissue Control marker detected. normal intestinal mucosal tissues tissue: normal intestinal mucosal tissues; donor: 1
  • GSM6890238 Group C-2 normal tissue Control marker detected. normal intestinal mucosal tissues tissue: normal intestinal mucosal tissues; donor: 2
  • GSM6890241 Group C-3 normal tissue Control marker detected. normal intestinal mucosal tissues tissue: normal intestinal mucosal tissues; donor: 3
  • GSM6890246 Group C-5 normal tissue Control marker detected. normal intestinal mucosal tissues tissue: normal intestinal mucosal tissues; donor: 5
  • GSM6890249 Group C-6 normal tissue Control marker detected. normal intestinal mucosal tissues tissue: normal intestinal mucosal tissues; donor: 6
  • GSM6890252 Group C-7 normal tissue Control marker detected. normal intestinal mucosal tissues tissue: normal intestinal mucosal tissues; donor: 7
  • GSM6890255 Group C-8 normal tissue Control marker detected. normal intestinal mucosal tissues tissue: normal intestinal mucosal tissues; donor: 8
  • GSM6890260 Group C-10 normal tissue Control marker detected. normal intestinal mucosal tissues tissue: normal intestinal mucosal tissues; donor: 10
  • GSM6890263 Group C-11 normal tissue Control marker detected. normal intestinal mucosal tissues tissue: normal intestinal mucosal tissues; donor: 11
  • GSM6890266 Group C-12 normal tissue Control marker detected. normal intestinal mucosal tissues tissue: normal intestinal mucosal tissues; donor: 12
  • GSM6890269 Group C-14 normal tissue Control marker detected. normal intestinal mucosal tissues tissue: normal intestinal mucosal tissues; donor: 14
  • GSM6890272 Group C-15 normal tissue Control marker detected. normal intestinal mucosal tissues tissue: normal intestinal mucosal tissues; donor: 15
  • GSM6890279 Group C-18 normal tissue Control marker detected. normal intestinal mucosal tissues tissue: normal intestinal mucosal tissues; donor: 18
  • GSM6890284 Group C-20 normal tissue Control marker detected. normal intestinal mucosal tissues tissue: normal intestinal mucosal tissues; donor: 20

Unassigned samples

Samples with no explicit case or control marker.

18
  • GSM6890234 Group B-1 unassigned No explicit case or control marker detected. liver metastases tissue: liver metastases; donor: 1
  • GSM6890237 Group B-2 unassigned No explicit case or control marker detected. liver metastases tissue: liver metastases; donor: 2
  • GSM6890240 Group B-3 unassigned No explicit case or control marker detected. liver metastases tissue: liver metastases; donor: 3
  • GSM6890243 Group B-4 unassigned No explicit case or control marker detected. liver metastases tissue: liver metastases; donor: 4
  • GSM6890245 Group B-5 unassigned No explicit case or control marker detected. liver metastases tissue: liver metastases; donor: 5
  • GSM6890248 Group B-6 unassigned No explicit case or control marker detected. liver metastases tissue: liver metastases; donor: 6
  • GSM6890251 Group B-7 unassigned No explicit case or control marker detected. liver metastases tissue: liver metastases; donor: 7
  • GSM6890254 Group B-8 unassigned No explicit case or control marker detected. liver metastases tissue: liver metastases; donor: 8
  • GSM6890257 Group B-9 unassigned No explicit case or control marker detected. liver metastases tissue: liver metastases; donor: 9
  • GSM6890259 Group B-10 unassigned No explicit case or control marker detected. liver metastases tissue: liver metastases; donor: 10
  • GSM6890262 Group B-11 unassigned No explicit case or control marker detected. liver metastases tissue: liver metastases; donor: 11
  • GSM6890265 Group B-12 unassigned No explicit case or control marker detected. liver metastases tissue: liver metastases; donor: 12
  • GSM6890271 Group B-15 unassigned No explicit case or control marker detected. liver metastases tissue: liver metastases; donor: 15
  • GSM6890274 Group B-16 unassigned No explicit case or control marker detected. liver metastases tissue: liver metastases; donor: 16
  • GSM6890276 Group B-17 unassigned No explicit case or control marker detected. liver metastases tissue: liver metastases; donor: 17
  • GSM6890278 Group B-18 unassigned No explicit case or control marker detected. liver metastases tissue: liver metastases; donor: 18
  • GSM6890281 Group B-19 unassigned No explicit case or control marker detected. liver metastases tissue: liver metastases; donor: 19
  • GSM6890283 Group B-20 unassigned No explicit case or control marker detected. liver metastases tissue: liver metastases; donor: 20

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

100 pts
Clarity
100%
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 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

colorectal cancer

20 samples
  • GSM6890233 Group A-1 CRC tissues tissue: CRC tissues; donor: 1
  • GSM6890236 Group A-2 CRC tissues tissue: CRC tissues; donor: 2
  • GSM6890239 Group A-3 CRC tissues tissue: CRC tissues; donor: 3
  • GSM6890242 Group A-4 CRC tissues tissue: CRC tissues; donor: 4
  • GSM6890244 Group A-5 CRC tissues tissue: CRC tissues; donor: 5
  • GSM6890247 Group A-6 CRC tissues tissue: CRC tissues; donor: 6
  • GSM6890250 Group A-7 CRC tissues tissue: CRC tissues; donor: 7
  • GSM6890253 Group A-8 CRC tissues tissue: CRC tissues; donor: 8
  • GSM6890256 Group A-9 CRC tissues tissue: CRC tissues; donor: 9
  • GSM6890258 Group A-10 CRC tissues tissue: CRC tissues; donor: 10
  • GSM6890261 Group A-11 CRC tissues tissue: CRC tissues; donor: 11
  • GSM6890264 Group A-12 CRC tissues tissue: CRC tissues; donor: 12
  • GSM6890267 Group A-13 CRC tissues tissue: CRC tissues; donor: 13
  • GSM6890268 Group A-14 CRC tissues tissue: CRC tissues; donor: 14
  • GSM6890270 Group A-15 CRC tissues tissue: CRC tissues; donor: 15
  • GSM6890273 Group A-16 CRC tissues tissue: CRC tissues; donor: 16
  • GSM6890275 Group A-17 CRC tissues tissue: CRC tissues; donor: 17
  • GSM6890277 Group A-18 CRC tissues tissue: CRC tissues; donor: 18
  • GSM6890280 Group A-19 CRC tissues tissue: CRC tissues; donor: 19
  • GSM6890282 Group A-20 CRC tissues tissue: CRC tissues; donor: 20

unassigned

18 samples
  • GSM6890234 Group B-1 liver metastases tissue: liver metastases; donor: 1
  • GSM6890237 Group B-2 liver metastases tissue: liver metastases; donor: 2
  • GSM6890240 Group B-3 liver metastases tissue: liver metastases; donor: 3
  • GSM6890243 Group B-4 liver metastases tissue: liver metastases; donor: 4
  • GSM6890245 Group B-5 liver metastases tissue: liver metastases; donor: 5
  • GSM6890248 Group B-6 liver metastases tissue: liver metastases; donor: 6
  • GSM6890251 Group B-7 liver metastases tissue: liver metastases; donor: 7
  • GSM6890254 Group B-8 liver metastases tissue: liver metastases; donor: 8
  • GSM6890257 Group B-9 liver metastases tissue: liver metastases; donor: 9
  • GSM6890259 Group B-10 liver metastases tissue: liver metastases; donor: 10
  • GSM6890262 Group B-11 liver metastases tissue: liver metastases; donor: 11
  • GSM6890265 Group B-12 liver metastases tissue: liver metastases; donor: 12
  • GSM6890271 Group B-15 liver metastases tissue: liver metastases; donor: 15
  • GSM6890274 Group B-16 liver metastases tissue: liver metastases; donor: 16
  • GSM6890276 Group B-17 liver metastases tissue: liver metastases; donor: 17
  • GSM6890278 Group B-18 liver metastases tissue: liver metastases; donor: 18
  • GSM6890281 Group B-19 liver metastases tissue: liver metastases; donor: 19
  • GSM6890283 Group B-20 liver metastases tissue: liver metastases; donor: 20

normal tissue

14 samples
  • GSM6890235 Group C-1 normal intestinal mucosal tissues tissue: normal intestinal mucosal tissues; donor: 1
  • GSM6890238 Group C-2 normal intestinal mucosal tissues tissue: normal intestinal mucosal tissues; donor: 2
  • GSM6890241 Group C-3 normal intestinal mucosal tissues tissue: normal intestinal mucosal tissues; donor: 3
  • GSM6890246 Group C-5 normal intestinal mucosal tissues tissue: normal intestinal mucosal tissues; donor: 5
  • GSM6890249 Group C-6 normal intestinal mucosal tissues tissue: normal intestinal mucosal tissues; donor: 6
  • GSM6890252 Group C-7 normal intestinal mucosal tissues tissue: normal intestinal mucosal tissues; donor: 7
  • GSM6890255 Group C-8 normal intestinal mucosal tissues tissue: normal intestinal mucosal tissues; donor: 8
  • GSM6890260 Group C-10 normal intestinal mucosal tissues tissue: normal intestinal mucosal tissues; donor: 10
  • GSM6890263 Group C-11 normal intestinal mucosal tissues tissue: normal intestinal mucosal tissues; donor: 11
  • GSM6890266 Group C-12 normal intestinal mucosal tissues tissue: normal intestinal mucosal tissues; donor: 12
  • GSM6890269 Group C-14 normal intestinal mucosal tissues tissue: normal intestinal mucosal tissues; donor: 14
  • GSM6890272 Group C-15 normal intestinal mucosal tissues tissue: normal intestinal mucosal tissues; donor: 15
  • GSM6890279 Group C-18 normal intestinal mucosal tissues tissue: normal intestinal mucosal tissues; donor: 18
  • GSM6890284 Group C-20 normal intestinal mucosal tissues tissue: normal intestinal mucosal tissues; donor: 20

Score Breakdown

100%

relevance

  • Disease or condition metadata normalized.
  • Organism normalized.
  • Assay type normalized.
  • Tissue metadata normalized.
100%

comparison suitability

  • Case and control sample groups detected: colorectal cancer vs normal tissue.
  • 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.
  • Colorectal, colon, rectal, or CRC disease context boosted for tumor-vs-normal tissue ranking.
100%

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 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.
100%

overall

  • Weighted score: 30% relevance, 30% comparison suitability, 25% metadata quality, 15% data availability.

Sample Links

52 samples

Review Audit Trail

0 decisions

No review decisions have been stored for this dataset.