Siftome Phase 3L

GSE266302

Cell of origin and expression profiles of pseudomyxoma peritonei derived from the appendix

Exploratory only Dataset can inform exploration but is not strong enough for primary analysis.
Sample grouping CSV Contrast CSV DESeq2 metadata CSV R handoff notes Handoff report Download instructions Open GEO dataset
Source
GEO
Search intent
Patient tissue tumor-vs-normal
Intent behavior
search-intent-behavior-v1
Submission date
2024-04-30
Last update
2025-04-30
Organization
National Cancer Center Research Institute
Department
Division of Rare Cancer Research
Public date
2025-04-30
Experiment types
Expression profiling by high throughput sequencing
Platforms
GPL17303 Ion Torrent Proton (Homo sapiens)
Series type
Series
SubSeries
Not available
BioProject
PRJNA1106532
Supplementary files
XLSX: GSE266302_all_bcmatrix_summary.xlsx; XLSX: GSE266302_all_rpmmatrix_summary.xlsx
Organism
Homo sapiens
Assay
bulk RNA-seq
Samples
20
Study design
Tumor vs unmatched normal
Specimen/source
Tissue
Scoring version
intent-aware-scoring-v15
Ranking batch
b69568dd1e4fe1b9ee2d880bf5495d748a7e4c5c11e4107f02528c3be0e76012
Ranking created
2026-06-05T20:20:27.088676Z
Warning version
intent-aware-warnings-v2

Current Intent Interpretation

Patient tissue tumor-vs-normal

Expectations

Organism
Homo sapiens
Assay
bulk RNA-seq
Specimen/source
patient tissue or biopsy
Controls
matched normal, adjacent normal, paired normal, healthy tissue control, or otherwise normal tissue control

Rules

Default filters
Human only; Bulk RNA-seq only; Tumor-normal only; Tissue or biopsy only; Hide biofluid/model systems
Warning rules
missing or unclear control group, unclear disease context, unclear tissue source, mixed sample types, model-system markers, secondary assay context, missing processed data, or small cohort size
Score caps
non-human datasets stay below the primary recommendation band, missing colorectal/colon/rectal/CRC context stays below the primary recommendation band, biofluid and model-system datasets cannot reach Recommended by default, microarray and secondary assays are capped unless explicitly enabled, or small cohorts are capped below high-confidence recommendations
Downgraded contexts
microarray unless explicitly enabled, biofluid-only datasets, cell-line datasets, organoid datasets, xenograft or PDX datasets, non-colorectal disease contexts, or treatment-only experiments

Study Classification

Tumor vs unmatched normal Tissue

Analysis Readiness

Ready after review
97% DE readiness

Contrast completeness

25/25 pts

Both case and control groups are present in the proposed grouping.

Minimum group size

20/20 pts

Each contrast group has at least 2 samples.

Processed data availability

20/20 pts

Processed data is marked available in the GEO index.

Sample decision clarity

15/15 pts

All samples are assigned to a case or control group.

Blocking warnings

7/10 pts

Warnings are present, but none are critical blockers.

Metadata normalization

10/10 pts

Metadata quality is high enough to support downstream handoff.

Blockers

No readiness blockers detected.

Next Steps

  • Review the sample grouping CSV and contrast CSV before running differential expression.
  • Confirm processed count files and sample identifiers match the exported metadata.

Analysis Preparation Checklist

5/6 ready

Group labels reviewed

Needs review

Siftome proposed case and control labels, but no reviewer confirmation is stored yet.

Open the sample grouping CSV and confirm group labels before analysis.

Minimum sample count met

Ready

Both groups meet the minimum of 2 samples.

Confirm whether the cohort is large enough for the intended statistical analysis.

Processed counts available

Ready

Processed data availability is marked true in the GEO index.

Verify that downloaded processed files contain usable count or expression identifiers.

Ambiguous samples handled

Ready

No review-needed or unassigned samples are present in the proposed grouping.

Still scan the grouping table for biology-specific ambiguity.

Exclusion decisions recorded

Ready

No hard-excluded samples were detected by the current rules.

Record any manual exclusions in the downstream analysis notes.

Source links preserved

Ready

The dataset and sample accessions can be linked back to GEO.

Keep GEO dataset and sample links with exported metadata.

Bioinformatician Review

Standard analyst review

Proceed only after the analyst confirms grouping, exclusions, and source files.

No expert-review triggers were detected by Siftome.

Why This Is Ranked Here

Patient tissue tumor-vs-normal
Exploratory only Dataset can inform exploration but is not strong enough for primary analysis.

Score Components

  • relevance 60% Organism normalized. Assay type normalized. Tissue metadata normalized.
  • comparison suitability 5% Tumor and normal sample groups detected. No excluded sample type flags detected. Tumor/normal design boosted for colorectal tumor-vs-normal tissue triage. Patient tissue or biopsy specimens boosted for tissue comparison triage. Missing colorectal disease context downgraded for tumor-vs-normal tissue ranking.
  • metadata quality 85% Sample source clarity: All samples have source metadata and clear GSE/GSM accessions. Group clarity: Rule-based grouping found both case and control samples. Disease clarity: Disease or condition metadata was not normalized. Tissue clarity: Tissue metadata normalized. Treatment clarity: No unclear treatment split detected in the sample metadata. Replicate clarity: No pooled sample or technical replicate flags detected. Data availability clarity: Dataset-level processed or raw data availability is explicit.
  • data availability 100% Processed data available. Raw data available.
  • overall 45% 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 colorectal/CRC disease context is not explicit.

Derived Classifications

  • Organism Homo sapiens Organism remains rule-derived: Homo sapiens.
  • Assay bulk RNA-seq Assay remains rule-derived: bulk RNA-seq.
  • Study design Tumor vs unmatched normal Study design remains rule-derived: Tumor vs unmatched normal.
  • Specimen/source Tissue Specimen/source remains rule-derived: Tissue.
  • Likely case group tumor sample 10 samples
  • Likely control group normal tissue 10 samples

Warnings

  • DISEASE_LABEL_UNCLEAR warning Disease or condition label could not be normalized.

Intent Interpretation

  • Active intent Patient tissue tumor-vs-normal Ranks human colorectal tissue or biopsy cohorts where tumor samples can be compared with normal controls.
  • Organism expectation Homo sapiens Dataset organism is interpreted as Homo sapiens.
  • Assay expectation bulk RNA-seq Dataset assay is interpreted as bulk RNA-seq.
  • Specimen assumption patient tissue or biopsy Derived specimen/source is Tissue.
  • Control-group assumption matched normal, adjacent normal, paired normal, healthy tissue control, or otherwise normal tissue control Derived study design is Tumor vs unmatched normal; likely groups are tumor sample vs normal tissue.
  • Score caps Applied when matching conditions are present non-human datasets stay below the primary recommendation band, missing colorectal/colon/rectal/CRC context stays below the primary recommendation band, biofluid and model-system datasets cannot reach Recommended by default, microarray and secondary assays are capped unless explicitly enabled, or small cohorts are capped below high-confidence recommendations
  • Warning rules 1 active warning missing or unclear control group, unclear disease context, unclear tissue source, mixed sample types, model-system markers, secondary assay context, missing processed data, or small cohort size
  • Downgrade or exclusion reason Downgraded disease context: 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 Exploratory only Dataset can inform exploration but is not strong enough for primary analysis.
  • Supporting fact Tumor vs unmatched normal · Tissue · suitability 5%. 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 Disease or condition label could not be normalized. Contributed to downgrade or manual-review evidence.
  • Caution fact Missing colorectal disease context downgraded for tumor-vs-normal tissue ranking. Contributed to downgrade or manual-review evidence.
  • Caution fact Missing or unclear metadata: Missing colorectal disease context downgraded for tumor-vs-normal tissue ranking. Contributed to downgrade or manual-review evidence.
  • Caution fact Missing or unclear metadata: Disease clarity: Disease or condition metadata was not normalized. Contributed to downgrade or manual-review evidence.
  • Caution fact Missing or unclear metadata: Treatment clarity: No unclear treatment split detected in the sample metadata. Contributed to downgrade or manual-review evidence.
  • Caution fact Overall score capped because comparison suitability is weak for the selected search intent. Contributed to downgrade or manual-review evidence.
  • Caution fact Overall score capped because colorectal/CRC disease context is not explicit. 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
GSE266302
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
GSE266302
  • 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
GSE266302
  • 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
GSE266302
  • 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: GSE266302
dataset_title: Cell of origin and expression profiles of pseudomyxoma peritonei derived from the appendix
organism: Homo sapiens
assay_type: bulk RNA-seq
processed_data_available: true
raw_data_available: true
submission_date: 2024-04-30
last_update_date: 2025-04-30
organization_name: National Cancer Center Research Institute
department: Division of Rare Cancer Research
public_date: 2025-04-30
experiment_types: Expression profiling by high throughput sequencing
platforms: GPL17303 Ion Torrent Proton (Homo sapiens)
sub_series: Not available
bioproject: PRJNA1106532
supplementary_files: XLSX: GSE266302_all_bcmatrix_summary.xlsx; XLSX: GSE266302_all_rpmmatrix_summary.xlsx
series_type: Series

Why It Matched

  • Tumor vs unmatched normal · Tissue · suitability 5%.
  • 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

  • Disease or condition label could not be normalized.
  • Missing colorectal disease context downgraded for tumor-vs-normal tissue ranking.
  • Missing or unclear metadata: Missing colorectal disease context downgraded for tumor-vs-normal tissue ranking.
  • Missing or unclear metadata: Disease clarity: Disease or condition metadata was not normalized.
  • Missing or unclear metadata: Treatment clarity: No unclear treatment split detected in the sample metadata.
  • Overall score capped because comparison suitability is weak for the selected search intent.
  • Overall score capped because colorectal/CRC disease context is not explicit.
  • Downgraded disease context: colorectal/GI relevance is unclear.
  • Missing or unclear metadata: Downgraded disease context: colorectal/GI relevance is unclear.
  • Comparison suitability score is below the Phase 1 recommended threshold.

Warnings

  • warning DISEASE_LABEL_UNCLEAR Disease or condition label could not be normalized.

Normalized Fields

32 fields
Field Value Source Origin Confidence Evidence Reason
assay_type bulk RNA-seq dataset GSE266302 Runtime Siftome inference GEO:dataset:GSE266302:623eae64efd050524e00d9e449096f1ff2c66c161ebb44b4ee0617506bd51c51 high confidence bulk rna-seq dataset_accession: GSE266302 dataset_title: Cell of origin and expression profiles of pseudomyxoma peritonei derived from the appendix organism: Homo sapiens assay_type: bulk RN... keyword match keyword match: bulk rna-seq
organism Homo sapiens dataset GSE266302 Runtime Siftome inference GEO:dataset:GSE266302:623eae64efd050524e00d9e449096f1ff2c66c161ebb44b4ee0617506bd51c51 high confidence homo sapiens dataset_accession: GSE266302 dataset_title: Cell of origin and expression profiles of pseudomyxoma peritonei derived from the appendix organism: Homo sapiens assay_type: bulk RN... keyword match keyword match: homo sapiens
sample_type tumor sample sample GSM8244625 Runtime Siftome inference GEO:sample:GSM8244625:f81ef50df500ddb1c94059beeb20ea5f6c4e753b6aef84ba844705980d753d02 low confidence tumor sample_accession: GSM8244625 sample_title: PT id1 tumor tissue source_name: PMP tumor characteristics: tissue: PMP tumor PT id1 tumor tissue controlled vocabulary controlled vocabulary sample type match: tumor
sample_type normal tissue sample GSM8244626 Runtime Siftome inference GEO:sample:GSM8244626:1a57797c02bb23db7bce591c66db986e7c0c2e8d022f49bb1b7b3ebbbe702949 low confidence normal sample_accession: GSM8244626 sample_title: PT id1 normal tissue source_name: normal colon characteristics: tissue: normal colon PT id1 normal tissue controlled vocabulary controlled vocabulary sample type match: normal
sample_type tumor sample sample GSM8244627 Runtime Siftome inference GEO:sample:GSM8244627:13a5a1d0da706186cd015bc7a831335a360bcffe3ecdaa63627c7d5f10abf731 low confidence tumor sample_accession: GSM8244627 sample_title: PT id2 tumor tissue source_name: PMP tumor characteristics: tissue: PMP tumor PT id2 tumor tissue controlled vocabulary controlled vocabulary sample type match: tumor
sample_type normal tissue sample GSM8244628 Runtime Siftome inference GEO:sample:GSM8244628:fa02aa3526a72e91a80919e07b3b8d8606236d0f504aa171a978d4dd77325e8a low confidence normal sample_accession: GSM8244628 sample_title: PT id2 normal tissue source_name: normal colon characteristics: tissue: normal colon PT id2 normal tissue controlled vocabulary controlled vocabulary sample type match: normal
sample_type tumor sample sample GSM8244629 Runtime Siftome inference GEO:sample:GSM8244629:a80c0bada87832c3dbf00d96e812c227979f0f7afd1d0875bc8ca83cfd058945 low confidence tumor sample_accession: GSM8244629 sample_title: PT id3 tumor tissue source_name: PMP tumor characteristics: tissue: PMP tumor PT id3 tumor tissue controlled vocabulary controlled vocabulary sample type match: tumor
sample_type normal tissue sample GSM8244630 Runtime Siftome inference GEO:sample:GSM8244630:98bd28e99e43348e88f120b9b4c267a76f4f40aede3c929eb36d927a2e70bca2 low confidence normal sample_accession: GSM8244630 sample_title: PT id3 normal tissue source_name: normal colon characteristics: tissue: normal colon PT id3 normal tissue controlled vocabulary controlled vocabulary sample type match: normal
sample_type tumor sample sample GSM8244631 Runtime Siftome inference GEO:sample:GSM8244631:0342a50cb24c32831b7045c2557e3c4d3725c9a861d52ca49dada5f0fd311336 low confidence tumor sample_accession: GSM8244631 sample_title: PT id4 tumor tissue source_name: PMP tumor characteristics: tissue: PMP tumor PT id4 tumor tissue controlled vocabulary controlled vocabulary sample type match: tumor
sample_type normal tissue sample GSM8244632 Runtime Siftome inference GEO:sample:GSM8244632:3923dd1aa1ca90e040104385b27b89f76e4e91d9ca5b5984cb708b528fc5c95c low confidence normal sample_accession: GSM8244632 sample_title: PT id4 normal tissue source_name: normal colon characteristics: tissue: normal colon PT id4 normal tissue controlled vocabulary controlled vocabulary sample type match: normal
sample_type tumor sample sample GSM8244633 Runtime Siftome inference GEO:sample:GSM8244633:db9730487a469e902483398770d047343f643912d21b52c513c807d3478a06e0 low confidence tumor sample_accession: GSM8244633 sample_title: PT id5 tumor tissue source_name: PMP tumor characteristics: tissue: PMP tumor PT id5 tumor tissue controlled vocabulary controlled vocabulary sample type match: tumor
sample_type normal tissue sample GSM8244634 Runtime Siftome inference GEO:sample:GSM8244634:932a5ebd0dc3742f8ee1351b409c9e985c8ef3aa23883ce09eec996e62e83a35 low confidence normal sample_accession: GSM8244634 sample_title: PT id5 normal tissue source_name: normal colon characteristics: tissue: normal colon PT id5 normal tissue controlled vocabulary controlled vocabulary sample type match: normal
sample_type tumor sample sample GSM8244635 Runtime Siftome inference GEO:sample:GSM8244635:56c5bae3ff7660f4431b71ba0d37d33204dfe5b48b86d3198439b44e50f4e9e3 low confidence tumor sample_accession: GSM8244635 sample_title: PT id6 tumor tissue source_name: PMP tumor characteristics: tissue: PMP tumor PT id6 tumor tissue controlled vocabulary controlled vocabulary sample type match: tumor
sample_type normal tissue sample GSM8244636 Runtime Siftome inference GEO:sample:GSM8244636:e737e013bbef9945ca4b5270e1fc2f84a8499be90376e1d2559fa3ed66fbc92c low confidence normal sample_accession: GSM8244636 sample_title: PT id6 normal tissue source_name: normal colon characteristics: tissue: normal colon PT id6 normal tissue controlled vocabulary controlled vocabulary sample type match: normal
sample_type tumor sample sample GSM8244637 Runtime Siftome inference GEO:sample:GSM8244637:573d70c2594e1623622bb72bc2051dba8192ddb0308cbaac2fc29678cb94821e low confidence tumor sample_accession: GSM8244637 sample_title: PT id7 tumor tissue source_name: PMP tumor characteristics: tissue: PMP tumor PT id7 tumor tissue controlled vocabulary controlled vocabulary sample type match: tumor
sample_type normal tissue sample GSM8244638 Runtime Siftome inference GEO:sample:GSM8244638:4aafdeffc4ae1753680a12ec9db8dff71d95bb6963d2fb03d98aa39e9830ece5 low confidence normal sample_accession: GSM8244638 sample_title: PT id7 normal tissue source_name: normal colon characteristics: tissue: normal colon PT id7 normal tissue controlled vocabulary controlled vocabulary sample type match: normal
sample_type tumor sample sample GSM8244639 Runtime Siftome inference GEO:sample:GSM8244639:0da7374b3341eff24d50d7c5bb731cff665a139b55eb7a977e62d64193ce6d35 low confidence tumor sample_accession: GSM8244639 sample_title: PT id8 tumor tissue source_name: PMP tumor characteristics: tissue: PMP tumor PT id8 tumor tissue controlled vocabulary controlled vocabulary sample type match: tumor
sample_type normal tissue sample GSM8244640 Runtime Siftome inference GEO:sample:GSM8244640:8421d7a6d910b11bc42f2fcd17fd2005ec9706d604a1dafa722a8acdce11f263 low confidence normal sample_accession: GSM8244640 sample_title: PT id8 normal tissue source_name: normal colon characteristics: tissue: normal colon PT id8 normal tissue controlled vocabulary controlled vocabulary sample type match: normal
sample_type tumor sample sample GSM8244641 Runtime Siftome inference GEO:sample:GSM8244641:0418718888f2acc9f8ea48be5e9c74dc60fae7cb58d3904501a59888002a9df2 low confidence tumor sample_accession: GSM8244641 sample_title: PT id9 tumor tissue source_name: PMP tumor characteristics: tissue: PMP tumor PT id9 tumor tissue controlled vocabulary controlled vocabulary sample type match: tumor
sample_type normal tissue sample GSM8244642 Runtime Siftome inference GEO:sample:GSM8244642:e5beebb87de9838335e094994860507e9f44087cbf68d360d39684706ef2a7d9 low confidence normal sample_accession: GSM8244642 sample_title: PT id9 normal tissue source_name: normal colon characteristics: tissue: normal colon PT id9 normal tissue controlled vocabulary controlled vocabulary sample type match: normal
sample_type tumor sample sample GSM8244643 Runtime Siftome inference GEO:sample:GSM8244643:962c9540dd4a49bf022cfc8b7c914b94a8c4fe4b07472683848f254a19d7e87a low confidence tumor sample_accession: GSM8244643 sample_title: PT id10 tumor tissue source_name: PMP tumor characteristics: tissue: PMP tumor PT id10 tumor tissue controlled vocabulary controlled vocabulary sample type match: tumor
sample_type normal tissue sample GSM8244644 Runtime Siftome inference GEO:sample:GSM8244644:e84d0472cf3c1ee124b25653ae04410f4817780de8bf3c67f6cff9b42bd2255f low confidence normal sample_accession: GSM8244644 sample_title: PT id10 normal tissue source_name: normal colon characteristics: tissue: normal colon PT id10 normal tissue controlled vocabulary controlled vocabulary sample type match: normal
tissue colon sample GSM8244626 Runtime Siftome inference GEO:sample:GSM8244626:1a57797c02bb23db7bce591c66db986e7c0c2e8d022f49bb1b7b3ebbbe702949 low confidence colon sample_accession: GSM8244626 sample_title: PT id1 normal tissue source_name: normal colon characteristics: tissue: normal colon PT id1 normal tissue controlled vocabulary controlled vocabulary tissue match: colon
tissue colon sample GSM8244628 Runtime Siftome inference GEO:sample:GSM8244628:fa02aa3526a72e91a80919e07b3b8d8606236d0f504aa171a978d4dd77325e8a low confidence colon sample_accession: GSM8244628 sample_title: PT id2 normal tissue source_name: normal colon characteristics: tissue: normal colon PT id2 normal tissue controlled vocabulary controlled vocabulary tissue match: colon
tissue colon sample GSM8244630 Runtime Siftome inference GEO:sample:GSM8244630:98bd28e99e43348e88f120b9b4c267a76f4f40aede3c929eb36d927a2e70bca2 low confidence colon sample_accession: GSM8244630 sample_title: PT id3 normal tissue source_name: normal colon characteristics: tissue: normal colon PT id3 normal tissue controlled vocabulary controlled vocabulary tissue match: colon
tissue colon sample GSM8244632 Runtime Siftome inference GEO:sample:GSM8244632:3923dd1aa1ca90e040104385b27b89f76e4e91d9ca5b5984cb708b528fc5c95c low confidence colon sample_accession: GSM8244632 sample_title: PT id4 normal tissue source_name: normal colon characteristics: tissue: normal colon PT id4 normal tissue controlled vocabulary controlled vocabulary tissue match: colon
tissue colon sample GSM8244634 Runtime Siftome inference GEO:sample:GSM8244634:932a5ebd0dc3742f8ee1351b409c9e985c8ef3aa23883ce09eec996e62e83a35 low confidence colon sample_accession: GSM8244634 sample_title: PT id5 normal tissue source_name: normal colon characteristics: tissue: normal colon PT id5 normal tissue controlled vocabulary controlled vocabulary tissue match: colon
tissue colon sample GSM8244636 Runtime Siftome inference GEO:sample:GSM8244636:e737e013bbef9945ca4b5270e1fc2f84a8499be90376e1d2559fa3ed66fbc92c low confidence colon sample_accession: GSM8244636 sample_title: PT id6 normal tissue source_name: normal colon characteristics: tissue: normal colon PT id6 normal tissue controlled vocabulary controlled vocabulary tissue match: colon
tissue colon sample GSM8244638 Runtime Siftome inference GEO:sample:GSM8244638:4aafdeffc4ae1753680a12ec9db8dff71d95bb6963d2fb03d98aa39e9830ece5 low confidence colon sample_accession: GSM8244638 sample_title: PT id7 normal tissue source_name: normal colon characteristics: tissue: normal colon PT id7 normal tissue controlled vocabulary controlled vocabulary tissue match: colon
tissue colon sample GSM8244640 Runtime Siftome inference GEO:sample:GSM8244640:8421d7a6d910b11bc42f2fcd17fd2005ec9706d604a1dafa722a8acdce11f263 low confidence colon sample_accession: GSM8244640 sample_title: PT id8 normal tissue source_name: normal colon characteristics: tissue: normal colon PT id8 normal tissue controlled vocabulary controlled vocabulary tissue match: colon
tissue colon sample GSM8244642 Runtime Siftome inference GEO:sample:GSM8244642:e5beebb87de9838335e094994860507e9f44087cbf68d360d39684706ef2a7d9 low confidence colon sample_accession: GSM8244642 sample_title: PT id9 normal tissue source_name: normal colon characteristics: tissue: normal colon PT id9 normal tissue controlled vocabulary controlled vocabulary tissue match: colon
tissue colon sample GSM8244644 Runtime Siftome inference GEO:sample:GSM8244644:e84d0472cf3c1ee124b25653ae04410f4817780de8bf3c67f6cff9b42bd2255f low confidence colon sample_accession: GSM8244644 sample_title: PT id10 normal tissue source_name: normal colon characteristics: tissue: normal colon PT id10 normal tissue controlled vocabulary controlled vocabulary tissue match: colon

Sample Group Preview

Possible case samples

Samples currently treated as the comparison case group.

10
  • GSM8244625 PT id1 tumor tissue tumor sample Case marker detected. PMP tumor tissue: PMP tumor
  • GSM8244627 PT id2 tumor tissue tumor sample Case marker detected. PMP tumor tissue: PMP tumor
  • GSM8244629 PT id3 tumor tissue tumor sample Case marker detected. PMP tumor tissue: PMP tumor
  • GSM8244631 PT id4 tumor tissue tumor sample Case marker detected. PMP tumor tissue: PMP tumor
  • GSM8244633 PT id5 tumor tissue tumor sample Case marker detected. PMP tumor tissue: PMP tumor
  • GSM8244635 PT id6 tumor tissue tumor sample Case marker detected. PMP tumor tissue: PMP tumor
  • GSM8244637 PT id7 tumor tissue tumor sample Case marker detected. PMP tumor tissue: PMP tumor
  • GSM8244639 PT id8 tumor tissue tumor sample Case marker detected. PMP tumor tissue: PMP tumor
  • GSM8244641 PT id9 tumor tissue tumor sample Case marker detected. PMP tumor tissue: PMP tumor
  • GSM8244643 PT id10 tumor tissue tumor sample Case marker detected. PMP tumor tissue: PMP tumor

Possible control samples

Samples currently treated as controls or baseline.

10
  • GSM8244626 PT id1 normal tissue normal tissue Control marker detected. normal colon tissue: normal colon
  • GSM8244628 PT id2 normal tissue normal tissue Control marker detected. normal colon tissue: normal colon
  • GSM8244630 PT id3 normal tissue normal tissue Control marker detected. normal colon tissue: normal colon
  • GSM8244632 PT id4 normal tissue normal tissue Control marker detected. normal colon tissue: normal colon
  • GSM8244634 PT id5 normal tissue normal tissue Control marker detected. normal colon tissue: normal colon
  • GSM8244636 PT id6 normal tissue normal tissue Control marker detected. normal colon tissue: normal colon
  • GSM8244638 PT id7 normal tissue normal tissue Control marker detected. normal colon tissue: normal colon
  • GSM8244640 PT id8 normal tissue normal tissue Control marker detected. normal colon tissue: normal colon
  • GSM8244642 PT id9 normal tissue normal tissue Control marker detected. normal colon tissue: normal colon
  • GSM8244644 PT id10 normal tissue normal tissue Control marker detected. normal colon tissue: normal colon

Unassigned samples

Samples with no explicit case or control marker.

0

No samples

Excluded samples

Samples excluded from grouping by hard exclusion rules.

0

No samples

Ambiguous samples

Samples that need manual review before trusting grouping.

0

No samples

Metadata Quality Components

Persisted metadata quality

85 pts
Clarity
85%
Weight
100 pts

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

Detected Sample Groups

tumor sample

10 samples
  • GSM8244625 PT id1 tumor tissue PMP tumor tissue: PMP tumor
  • GSM8244627 PT id2 tumor tissue PMP tumor tissue: PMP tumor
  • GSM8244629 PT id3 tumor tissue PMP tumor tissue: PMP tumor
  • GSM8244631 PT id4 tumor tissue PMP tumor tissue: PMP tumor
  • GSM8244633 PT id5 tumor tissue PMP tumor tissue: PMP tumor
  • GSM8244635 PT id6 tumor tissue PMP tumor tissue: PMP tumor
  • GSM8244637 PT id7 tumor tissue PMP tumor tissue: PMP tumor
  • GSM8244639 PT id8 tumor tissue PMP tumor tissue: PMP tumor
  • GSM8244641 PT id9 tumor tissue PMP tumor tissue: PMP tumor
  • GSM8244643 PT id10 tumor tissue PMP tumor tissue: PMP tumor

normal tissue

10 samples
  • GSM8244626 PT id1 normal tissue normal colon tissue: normal colon
  • GSM8244628 PT id2 normal tissue normal colon tissue: normal colon
  • GSM8244630 PT id3 normal tissue normal colon tissue: normal colon
  • GSM8244632 PT id4 normal tissue normal colon tissue: normal colon
  • GSM8244634 PT id5 normal tissue normal colon tissue: normal colon
  • GSM8244636 PT id6 normal tissue normal colon tissue: normal colon
  • GSM8244638 PT id7 normal tissue normal colon tissue: normal colon
  • GSM8244640 PT id8 normal tissue normal colon tissue: normal colon
  • GSM8244642 PT id9 normal tissue normal colon tissue: normal colon
  • GSM8244644 PT id10 normal tissue normal colon tissue: normal colon

Score Breakdown

60%

relevance

  • Organism normalized.
  • Assay type normalized.
  • Tissue metadata normalized.
5%

comparison suitability

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

metadata quality

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

data availability

  • Processed data available.
  • Raw data available.
45%

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 colorectal/CRC disease context is not explicit.

Sample Links

20 samples

Review Audit Trail

0 decisions

No review decisions have been stored for this dataset.