Siftome Phase 3L

GSE144259

RNA-seq of CRC tissues

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
2020-01-26
Last update
2020-03-16
Organization
Fudan University
Department
Not available
Public date
2020-01-27
Experiment types
Expression profiling by high throughput sequencing
Platforms
GPL11154 Illumina HiSeq 2000 (Homo sapiens)
Series type
Series
SubSeries
Not available
BioProject
PRJNA603221
Supplementary files
TXT: GSE144259_all.fpkm.exp.txt.gz
Organism
Homo sapiens
Assay
bulk RNA-seq
Samples
9
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
100% 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

10/10 pts

No dataset warnings are present.

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 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. Matched 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 55% Weighted score: 30% relevance, 30% comparison suitability, 25% metadata quality, 15% data availability. Overall score capped because fewer than ten samples limit cohort confidence.

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 colorectal cancer 6 samples
  • Likely control group normal tissue 3 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 matched 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 Exploratory only Dataset can inform exploration but is not strong enough for primary analysis.
  • Supporting fact Tumor vs matched normal · Tissue · suitability 100%. 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 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.
  • Caution fact Overall score capped because fewer than ten samples limit cohort confidence. 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
GSE144259
Sample records
9 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
GSE144259
  • 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
GSE144259
  • 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
GSE144259
  • 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: GSE144259
dataset_title: RNA-seq of CRC tissues
organism: Homo sapiens
assay_type: bulk RNA-seq
processed_data_available: true
raw_data_available: true
submission_date: 2020-01-26
last_update_date: 2020-03-16
organization_name: Fudan University
department: Not available
public_date: 2020-01-27
experiment_types: Expression profiling by high throughput sequencing
platforms: GPL11154 Illumina HiSeq 2000 (Homo sapiens)
sub_series: Not available
bioproject: PRJNA603221
supplementary_files: TXT: GSE144259_all.fpkm.exp.txt.gz
series_type: Series

Why It Matched

  • Tumor vs matched normal · Tissue · suitability 100%.
  • Prioritized for patient tissue tumor-vs-normal triage.
  • 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.
  • Overall score capped because fewer than ten samples limit cohort confidence.

Warnings

No warnings

Normalized Fields

36 fields
Field Value Source Origin Confidence Evidence Reason
assay_type bulk RNA-seq dataset GSE144259 Runtime Siftome inference GEO:dataset:GSE144259:ea140d6ee606dd81e5e95c531d47e9b6af22fdf0ae22d2b668899afe9abe9172 high confidence bulk rna-seq dataset_accession: GSE144259 dataset_title: RNA-seq of CRC tissues organism: Homo sapiens assay_type: bulk RNA-seq processed_data_available: true raw_data_available: true submis... keyword match keyword match: bulk rna-seq
disease colorectal cancer dataset GSE144259 Runtime Siftome inference GEO:dataset:GSE144259:ea140d6ee606dd81e5e95c531d47e9b6af22fdf0ae22d2b668899afe9abe9172 medium confidence crc dataset_accession: GSE144259 dataset_title: RNA-seq of CRC tissues organism: Homo sapiens assay_type: bulk RNA-seq processed_data_available: true raw_data_available: true submis... controlled vocabulary controlled vocabulary disease match: crc
disease colorectal cancer sample GSM4284531 Runtime Siftome inference GEO:sample:GSM4284531:f164caa2d600e50b0f9af5bcf2162ef34de99cf921b1330e13b951f3ca301830 medium confidence crc sample_accession: GSM4284531 sample_title: CRC1N source_name: Matched normal colon characteristics: tissue: Matched normal colon tissue CRC1N controlled vocabulary controlled vocabulary disease match: crc
disease colorectal cancer sample GSM4284532 Runtime Siftome inference GEO:sample:GSM4284532:fd0b454e06af9bd6f5c77ccdf753ec7ad71b5ce194fc5ed4b68e7a0edbe865c7 high confidence colon cancer sample_accession: GSM4284532 sample_title: CRC1T source_name: Primary colon cancer characteristics: tissue: Primary colon cancer tissue CRC1T controlled vocabulary controlled vocabulary disease match: colon cancer
disease colorectal cancer sample GSM4284533 Runtime Siftome inference GEO:sample:GSM4284533:1cdd1c975eea7d0688a1cdd3105a5ce174524a3387fc7392f32165554099ef58 high confidence colon cancer sample_accession: GSM4284533 sample_title: CRC1M source_name: Liver metastasis colon cancer characteristics: tissue: Liver metastasis colon cancer tissue CRC1M controlled vocabulary controlled vocabulary disease match: colon cancer
disease colorectal cancer sample GSM4284534 Runtime Siftome inference GEO:sample:GSM4284534:5ccfaa669424255ccd27b92f2fef087163eafb04ab1b7ec6f85c31aacbfef32d medium confidence crc sample_accession: GSM4284534 sample_title: CRC2N source_name: Matched normal colon characteristics: tissue: Matched normal colon tissue CRC2N controlled vocabulary controlled vocabulary disease match: crc
disease colorectal cancer sample GSM4284535 Runtime Siftome inference GEO:sample:GSM4284535:f03d2520ed0e29d30f2a33d9c860fb65517d9e31d58f7d66db88115b3b33f4bc high confidence colon cancer sample_accession: GSM4284535 sample_title: CRC2T source_name: Primary colon cancer characteristics: tissue: Primary colon cancer tissue CRC2T controlled vocabulary controlled vocabulary disease match: colon cancer
disease colorectal cancer sample GSM4284536 Runtime Siftome inference GEO:sample:GSM4284536:554e82802028e9038b2cfedb803aa828e1ae59fca5c3dd7a1f187ff9ed448a79 high confidence colon cancer sample_accession: GSM4284536 sample_title: CRC2M source_name: Liver metastasis colon cancer characteristics: tissue: Liver metastasis colon cancer tissue CRC2M controlled vocabulary controlled vocabulary disease match: colon cancer
disease colorectal cancer sample GSM4284537 Runtime Siftome inference GEO:sample:GSM4284537:34d82b12c9c2d6b48e92e3696e99ea4f26a227ef511b200315cc4eed7edf6f62 medium confidence crc sample_accession: GSM4284537 sample_title: CRC3N source_name: Matched normal colon characteristics: tissue: Matched normal colon tissue CRC3N controlled vocabulary controlled vocabulary disease match: crc
disease colorectal cancer sample GSM4284538 Runtime Siftome inference GEO:sample:GSM4284538:cb2cb588ffec563c8cfadaad72c65833a66fbf93ec5256f47173a3872b5ef0ed high confidence colon cancer sample_accession: GSM4284538 sample_title: CRC3T source_name: Primary colon cancer characteristics: tissue: Primary colon cancer tissue CRC3T controlled vocabulary controlled vocabulary disease match: colon cancer
disease colorectal cancer sample GSM4284539 Runtime Siftome inference GEO:sample:GSM4284539:2aa2de84348b4dc79df894dd5263d0efc9aef0ae6ea56e1ac5c2d51e851845be high confidence colon cancer sample_accession: GSM4284539 sample_title: CRC3M source_name: Liver metastasis colon cancer characteristics: tissue: Liver metastasis colon cancer tissue CRC3M controlled vocabulary controlled vocabulary disease match: colon cancer
normal_tissue_type adjacent normal sample GSM4284531 Runtime Siftome inference GEO:sample:GSM4284531:f164caa2d600e50b0f9af5bcf2162ef34de99cf921b1330e13b951f3ca301830 high confidence matched normal sample_accession: GSM4284531 sample_title: CRC1N source_name: Matched normal colon characteristics: tissue: Matched normal colon tissue CRC1N controlled vocabulary controlled vocabulary normal tissue type match: matched normal
normal_tissue_type adjacent normal sample GSM4284534 Runtime Siftome inference GEO:sample:GSM4284534:5ccfaa669424255ccd27b92f2fef087163eafb04ab1b7ec6f85c31aacbfef32d high confidence matched normal sample_accession: GSM4284534 sample_title: CRC2N source_name: Matched normal colon characteristics: tissue: Matched normal colon tissue CRC2N controlled vocabulary controlled vocabulary normal tissue type match: matched normal
normal_tissue_type adjacent normal sample GSM4284537 Runtime Siftome inference GEO:sample:GSM4284537:34d82b12c9c2d6b48e92e3696e99ea4f26a227ef511b200315cc4eed7edf6f62 high confidence matched normal sample_accession: GSM4284537 sample_title: CRC3N source_name: Matched normal colon characteristics: tissue: Matched normal colon tissue CRC3N controlled vocabulary controlled vocabulary normal tissue type match: matched normal
organism Homo sapiens dataset GSE144259 Runtime Siftome inference GEO:dataset:GSE144259:ea140d6ee606dd81e5e95c531d47e9b6af22fdf0ae22d2b668899afe9abe9172 high confidence homo sapiens dataset_accession: GSE144259 dataset_title: RNA-seq of CRC tissues organism: Homo sapiens assay_type: bulk RNA-seq processed_data_available: true raw_data_available: true submis... keyword match keyword match: homo sapiens
sample_type normal tissue sample GSM4284531 Runtime Siftome inference GEO:sample:GSM4284531:f164caa2d600e50b0f9af5bcf2162ef34de99cf921b1330e13b951f3ca301830 low confidence normal sample_accession: GSM4284531 sample_title: CRC1N source_name: Matched normal colon characteristics: tissue: Matched normal colon tissue CRC1N controlled vocabulary controlled vocabulary sample type match: normal
sample_type tumor sample sample GSM4284533 Runtime Siftome inference GEO:sample:GSM4284533:1cdd1c975eea7d0688a1cdd3105a5ce174524a3387fc7392f32165554099ef58 medium confidence metastasis sample_accession: GSM4284533 sample_title: CRC1M source_name: Liver metastasis colon cancer characteristics: tissue: Liver metastasis colon cancer tissue CRC1M controlled vocabulary controlled vocabulary sample type match: metastasis
sample_type normal tissue sample GSM4284534 Runtime Siftome inference GEO:sample:GSM4284534:5ccfaa669424255ccd27b92f2fef087163eafb04ab1b7ec6f85c31aacbfef32d low confidence normal sample_accession: GSM4284534 sample_title: CRC2N source_name: Matched normal colon characteristics: tissue: Matched normal colon tissue CRC2N controlled vocabulary controlled vocabulary sample type match: normal
sample_type tumor sample sample GSM4284536 Runtime Siftome inference GEO:sample:GSM4284536:554e82802028e9038b2cfedb803aa828e1ae59fca5c3dd7a1f187ff9ed448a79 medium confidence metastasis sample_accession: GSM4284536 sample_title: CRC2M source_name: Liver metastasis colon cancer characteristics: tissue: Liver metastasis colon cancer tissue CRC2M controlled vocabulary controlled vocabulary sample type match: metastasis
sample_type normal tissue sample GSM4284537 Runtime Siftome inference GEO:sample:GSM4284537:34d82b12c9c2d6b48e92e3696e99ea4f26a227ef511b200315cc4eed7edf6f62 low confidence normal sample_accession: GSM4284537 sample_title: CRC3N source_name: Matched normal colon characteristics: tissue: Matched normal colon tissue CRC3N controlled vocabulary controlled vocabulary sample type match: normal
sample_type tumor sample sample GSM4284539 Runtime Siftome inference GEO:sample:GSM4284539:2aa2de84348b4dc79df894dd5263d0efc9aef0ae6ea56e1ac5c2d51e851845be medium confidence metastasis sample_accession: GSM4284539 sample_title: CRC3M source_name: Liver metastasis colon cancer characteristics: tissue: Liver metastasis colon cancer tissue CRC3M controlled vocabulary controlled vocabulary sample type match: metastasis
tissue colon sample GSM4284531 Runtime Siftome inference GEO:sample:GSM4284531:f164caa2d600e50b0f9af5bcf2162ef34de99cf921b1330e13b951f3ca301830 low confidence colon sample_accession: GSM4284531 sample_title: CRC1N source_name: Matched normal colon characteristics: tissue: Matched normal colon tissue CRC1N controlled vocabulary controlled vocabulary tissue match: colon
tissue colon sample GSM4284532 Runtime Siftome inference GEO:sample:GSM4284532:fd0b454e06af9bd6f5c77ccdf753ec7ad71b5ce194fc5ed4b68e7a0edbe865c7 low confidence colon sample_accession: GSM4284532 sample_title: CRC1T source_name: Primary colon cancer characteristics: tissue: Primary colon cancer tissue CRC1T controlled vocabulary controlled vocabulary tissue match: colon
tissue colon sample GSM4284533 Runtime Siftome inference GEO:sample:GSM4284533:1cdd1c975eea7d0688a1cdd3105a5ce174524a3387fc7392f32165554099ef58 low confidence colon sample_accession: GSM4284533 sample_title: CRC1M source_name: Liver metastasis colon cancer characteristics: tissue: Liver metastasis colon cancer tissue CRC1M controlled vocabulary controlled vocabulary tissue match: colon
tissue liver sample GSM4284533 Runtime Siftome inference GEO:sample:GSM4284533:1cdd1c975eea7d0688a1cdd3105a5ce174524a3387fc7392f32165554099ef58 low confidence liver sample_accession: GSM4284533 sample_title: CRC1M source_name: Liver metastasis colon cancer characteristics: tissue: Liver metastasis colon cancer tissue CRC1M controlled vocabulary controlled vocabulary tissue match: liver
tissue colon sample GSM4284534 Runtime Siftome inference GEO:sample:GSM4284534:5ccfaa669424255ccd27b92f2fef087163eafb04ab1b7ec6f85c31aacbfef32d low confidence colon sample_accession: GSM4284534 sample_title: CRC2N source_name: Matched normal colon characteristics: tissue: Matched normal colon tissue CRC2N controlled vocabulary controlled vocabulary tissue match: colon
tissue colon sample GSM4284535 Runtime Siftome inference GEO:sample:GSM4284535:f03d2520ed0e29d30f2a33d9c860fb65517d9e31d58f7d66db88115b3b33f4bc low confidence colon sample_accession: GSM4284535 sample_title: CRC2T source_name: Primary colon cancer characteristics: tissue: Primary colon cancer tissue CRC2T controlled vocabulary controlled vocabulary tissue match: colon
tissue colon sample GSM4284536 Runtime Siftome inference GEO:sample:GSM4284536:554e82802028e9038b2cfedb803aa828e1ae59fca5c3dd7a1f187ff9ed448a79 low confidence colon sample_accession: GSM4284536 sample_title: CRC2M source_name: Liver metastasis colon cancer characteristics: tissue: Liver metastasis colon cancer tissue CRC2M controlled vocabulary controlled vocabulary tissue match: colon
tissue liver sample GSM4284536 Runtime Siftome inference GEO:sample:GSM4284536:554e82802028e9038b2cfedb803aa828e1ae59fca5c3dd7a1f187ff9ed448a79 low confidence liver sample_accession: GSM4284536 sample_title: CRC2M source_name: Liver metastasis colon cancer characteristics: tissue: Liver metastasis colon cancer tissue CRC2M controlled vocabulary controlled vocabulary tissue match: liver
tissue colon sample GSM4284537 Runtime Siftome inference GEO:sample:GSM4284537:34d82b12c9c2d6b48e92e3696e99ea4f26a227ef511b200315cc4eed7edf6f62 low confidence colon sample_accession: GSM4284537 sample_title: CRC3N source_name: Matched normal colon characteristics: tissue: Matched normal colon tissue CRC3N controlled vocabulary controlled vocabulary tissue match: colon
tissue colon sample GSM4284538 Runtime Siftome inference GEO:sample:GSM4284538:cb2cb588ffec563c8cfadaad72c65833a66fbf93ec5256f47173a3872b5ef0ed low confidence colon sample_accession: GSM4284538 sample_title: CRC3T source_name: Primary colon cancer characteristics: tissue: Primary colon cancer tissue CRC3T controlled vocabulary controlled vocabulary tissue match: colon
tissue colon sample GSM4284539 Runtime Siftome inference GEO:sample:GSM4284539:2aa2de84348b4dc79df894dd5263d0efc9aef0ae6ea56e1ac5c2d51e851845be low confidence colon sample_accession: GSM4284539 sample_title: CRC3M source_name: Liver metastasis colon cancer characteristics: tissue: Liver metastasis colon cancer tissue CRC3M controlled vocabulary controlled vocabulary tissue match: colon
tissue liver sample GSM4284539 Runtime Siftome inference GEO:sample:GSM4284539:2aa2de84348b4dc79df894dd5263d0efc9aef0ae6ea56e1ac5c2d51e851845be low confidence liver sample_accession: GSM4284539 sample_title: CRC3M source_name: Liver metastasis colon cancer characteristics: tissue: Liver metastasis colon cancer tissue CRC3M controlled vocabulary controlled vocabulary tissue match: liver
tumor_type metastatic tumor sample GSM4284533 Runtime Siftome inference GEO:sample:GSM4284533:1cdd1c975eea7d0688a1cdd3105a5ce174524a3387fc7392f32165554099ef58 medium confidence metastasis sample_accession: GSM4284533 sample_title: CRC1M source_name: Liver metastasis colon cancer characteristics: tissue: Liver metastasis colon cancer tissue CRC1M controlled vocabulary controlled vocabulary tumor type match: metastasis
tumor_type metastatic tumor sample GSM4284536 Runtime Siftome inference GEO:sample:GSM4284536:554e82802028e9038b2cfedb803aa828e1ae59fca5c3dd7a1f187ff9ed448a79 medium confidence metastasis sample_accession: GSM4284536 sample_title: CRC2M source_name: Liver metastasis colon cancer characteristics: tissue: Liver metastasis colon cancer tissue CRC2M controlled vocabulary controlled vocabulary tumor type match: metastasis
tumor_type metastatic tumor sample GSM4284539 Runtime Siftome inference GEO:sample:GSM4284539:2aa2de84348b4dc79df894dd5263d0efc9aef0ae6ea56e1ac5c2d51e851845be medium confidence metastasis sample_accession: GSM4284539 sample_title: CRC3M source_name: Liver metastasis colon cancer characteristics: tissue: Liver metastasis colon cancer tissue CRC3M controlled vocabulary controlled vocabulary tumor type match: metastasis

Sample Group Preview

Possible case samples

Samples currently treated as the comparison case group.

6
  • GSM4284532 CRC1T colorectal cancer Case marker detected. Primary colon cancer tissue: Primary colon cancer tissue
  • GSM4284533 CRC1M tumor sample Case marker detected. Liver metastasis colon cancer tissue: Liver metastasis colon cancer tissue
  • GSM4284535 CRC2T colorectal cancer Case marker detected. Primary colon cancer tissue: Primary colon cancer tissue
  • GSM4284536 CRC2M tumor sample Case marker detected. Liver metastasis colon cancer tissue: Liver metastasis colon cancer tissue
  • GSM4284538 CRC3T colorectal cancer Case marker detected. Primary colon cancer tissue: Primary colon cancer tissue
  • GSM4284539 CRC3M tumor sample Case marker detected. Liver metastasis colon cancer tissue: Liver metastasis colon cancer tissue

Possible control samples

Samples currently treated as controls or baseline.

3
  • GSM4284531 CRC1N normal tissue Control marker detected. Matched normal colon tissue: Matched normal colon tissue
  • GSM4284534 CRC2N normal tissue Control marker detected. Matched normal colon tissue: Matched normal colon tissue
  • GSM4284537 CRC3N normal tissue Control marker detected. Matched normal colon tissue: Matched normal colon tissue

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

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

normal tissue

3 samples
  • GSM4284531 CRC1N Matched normal colon tissue: Matched normal colon tissue
  • GSM4284534 CRC2N Matched normal colon tissue: Matched normal colon tissue
  • GSM4284537 CRC3N Matched normal colon tissue: Matched normal colon tissue

colorectal cancer

3 samples
  • GSM4284532 CRC1T Primary colon cancer tissue: Primary colon cancer tissue
  • GSM4284535 CRC2T Primary colon cancer tissue: Primary colon cancer tissue
  • GSM4284538 CRC3T Primary colon cancer tissue: Primary colon cancer tissue

tumor sample

3 samples
  • GSM4284533 CRC1M Liver metastasis colon cancer tissue: Liver metastasis colon cancer tissue
  • GSM4284536 CRC2M Liver metastasis colon cancer tissue: Liver metastasis colon cancer tissue
  • GSM4284539 CRC3M Liver metastasis colon cancer tissue: Liver metastasis colon cancer tissue

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.
  • Matched 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.
55%

overall

  • Weighted score: 30% relevance, 30% comparison suitability, 25% metadata quality, 15% data availability.
  • Overall score capped because fewer than ten samples limit cohort confidence.

Sample Links

9 samples

Review Audit Trail

0 decisions

No review decisions have been stored for this dataset.