Siftome Phase 3L

GSE228012

Potential driver genes involved in the initiation 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
2023-03-22
Last update
2025-04-10
Organization
Sun Yat-sen university cancer center
Department
Not available
Public date
2025-02-08
Experiment types
Expression profiling by high throughput sequencing
Platforms
GPL23227 BGISEQ-500 (Homo sapiens)
Series type
Series
SubSeries
Not available
BioProject
Not available
Supplementary files
TXT: GSE228012_all.gene.FPKM.mRNA_processed.txt.gz
Organism
Homo sapiens
Assay
bulk RNA-seq
Samples
33
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

  • 11 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 11 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% 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. 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 tumor sample 11 samples
  • Likely control group normal tissue 11 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 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 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
GSE228012
Sample records
33 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
GSE228012
  • 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
GSE228012
  • 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
GSE228012
  • 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: GSE228012
dataset_title: Potential driver genes involved in the initiation of CRC
organism: Homo sapiens
assay_type: bulk RNA-seq
processed_data_available: true
raw_data_available: true
submission_date: 2023-03-22
last_update_date: 2025-04-10
organization_name: Sun Yat-sen university cancer center
department: Not available
public_date: 2025-02-08
experiment_types: Expression profiling by high throughput sequencing
platforms: GPL23227 BGISEQ-500 (Homo sapiens)
sub_series: Not available
bioproject: Not available
supplementary_files: TXT: GSE228012_all.gene.FPKM.mRNA_processed.txt.gz
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

58 fields
Field Value Source Origin Confidence Evidence Reason
assay_type bulk RNA-seq dataset GSE228012 Runtime Siftome inference GEO:dataset:GSE228012:f4cb72c32e3e79d1cdd5fdf43f60e87869aeecf3011811f74ca2ad4dde33fee0 high confidence bulk rna-seq dataset_accession: GSE228012 dataset_title: Potential driver genes involved in the initiation of CRC organism: Homo sapiens assay_type: bulk RNA-seq processed_data_available: tr... keyword match keyword match: bulk rna-seq
disease colorectal cancer dataset GSE228012 Runtime Siftome inference GEO:dataset:GSE228012:f4cb72c32e3e79d1cdd5fdf43f60e87869aeecf3011811f74ca2ad4dde33fee0 medium confidence crc dataset_accession: GSE228012 dataset_title: Potential driver genes involved in the initiation of CRC organism: Homo sapiens assay_type: bulk RNA-seq processed_data_available: tr... controlled vocabulary controlled vocabulary disease match: crc
organism Homo sapiens dataset GSE228012 Runtime Siftome inference GEO:dataset:GSE228012:f4cb72c32e3e79d1cdd5fdf43f60e87869aeecf3011811f74ca2ad4dde33fee0 high confidence homo sapiens dataset_accession: GSE228012 dataset_title: Potential driver genes involved in the initiation of CRC organism: Homo sapiens assay_type: bulk RNA-seq processed_data_available: tr... keyword match keyword match: homo sapiens
sample_type tumor sample sample GSM7112499 Runtime Siftome inference GEO:sample:GSM7112499:f618b3a18bdd637d592dc246935f94b61714b2957db2cab84be7d740bd49b6ba low confidence tumor sample_accession: GSM7112499 sample_title: X2798T source_name: colorectal tumor1 characteristics: tissue: colorectal tumor1 X2798T controlled vocabulary controlled vocabulary sample type match: tumor
sample_type normal tissue sample GSM7112501 Runtime Siftome inference GEO:sample:GSM7112501:c5125ea6a3d05867bd6b56dad9b56a9eb792fae6d07f6b5ecc93c25c56bacca9 low confidence normal sample_accession: GSM7112501 sample_title: X2536N source_name: normal colorectal tissue1 characteristics: tissue: normal colorectal tissue1 X2536N controlled vocabulary controlled vocabulary sample type match: normal
sample_type normal tissue sample GSM7112502 Runtime Siftome inference GEO:sample:GSM7112502:79120e47640811f9c33d763a0a2549b7cbb5ad777486dee223a9957ad9b2d4f8 low confidence normal sample_accession: GSM7112502 sample_title: X3376N source_name: normal colorectal tissue2 characteristics: tissue: normal colorectal tissue2 X3376N controlled vocabulary controlled vocabulary sample type match: normal
sample_type tumor sample sample GSM7112503 Runtime Siftome inference GEO:sample:GSM7112503:f96d43f53f9724247689350d17ad46ba1d359321084fa7615215af6fb11e0137 low confidence tumor sample_accession: GSM7112503 sample_title: X2476T source_name: colorectal tumor2 characteristics: tissue: colorectal tumor2 X2476T controlled vocabulary controlled vocabulary sample type match: tumor
sample_type normal tissue sample GSM7112504 Runtime Siftome inference GEO:sample:GSM7112504:91caebfdf511c7c0b945ed5914f041f815068458cbfca87a79fcbeac2616084d low confidence normal sample_accession: GSM7112504 sample_title: X2637N source_name: normal colorectal tissue3 characteristics: tissue: normal colorectal tissue3 X2637N controlled vocabulary controlled vocabulary sample type match: normal
sample_type normal tissue sample GSM7112506 Runtime Siftome inference GEO:sample:GSM7112506:2ce14acc253343ac41457f203c09b68a7bf058d9cc99b46915a8247a3cc0bfbb low confidence normal sample_accession: GSM7112506 sample_title: X2476N source_name: normal colorectal tissue4 characteristics: tissue: normal colorectal tissue4 X2476N controlled vocabulary controlled vocabulary sample type match: normal
sample_type tumor sample sample GSM7112507 Runtime Siftome inference GEO:sample:GSM7112507:e15544596967a87b6955f26979aa727b1c4d55751efdaaff5c6260fb994ddd5a low confidence tumor sample_accession: GSM7112507 sample_title: X2712T source_name: colorectal tumor3 characteristics: tissue: colorectal tumor3 X2712T controlled vocabulary controlled vocabulary sample type match: tumor
sample_type normal tissue sample GSM7112508 Runtime Siftome inference GEO:sample:GSM7112508:4f46ac0028ee64be00f081664999d858361af56117ab34c138b6193f69a3273d low confidence normal sample_accession: GSM7112508 sample_title: X2712N source_name: normal colorectal tissue5 characteristics: tissue: normal colorectal tissue5 X2712N controlled vocabulary controlled vocabulary sample type match: normal
sample_type tumor sample sample GSM7112509 Runtime Siftome inference GEO:sample:GSM7112509:71332290a247e27177aaae7761f7fadc89d97f42e574c99b074e8703e1d4d402 low confidence tumor sample_accession: GSM7112509 sample_title: X2525T source_name: colorectal tumor4 characteristics: tissue: colorectal tumor4 X2525T controlled vocabulary controlled vocabulary sample type match: tumor
sample_type normal tissue sample GSM7112510 Runtime Siftome inference GEO:sample:GSM7112510:0fbe10d2d4c4f72f69bad63d3e22d69b32f5b9b98ffcf927db80f99f5f592d6f low confidence normal sample_accession: GSM7112510 sample_title: X2740N source_name: normal colorectal tissue6 characteristics: tissue: normal colorectal tissue6 X2740N controlled vocabulary controlled vocabulary sample type match: normal
sample_type tumor sample sample GSM7112512 Runtime Siftome inference GEO:sample:GSM7112512:d8a75500be88389bc75d68c74b155d38c06dbaa1ce4a576872c8f8ca8320f4ae low confidence tumor sample_accession: GSM7112512 sample_title: X2740T source_name: colorectal tumor5 characteristics: tissue: colorectal tumor5 X2740T controlled vocabulary controlled vocabulary sample type match: tumor
sample_type normal tissue sample GSM7112513 Runtime Siftome inference GEO:sample:GSM7112513:4339f8261dd43ffaaac29c7aa3bdc06d9c397b8985553fdc0a58a1911b33e350 low confidence normal sample_accession: GSM7112513 sample_title: X3N source_name: normal colorectal tissue7 characteristics: tissue: normal colorectal tissue7 X3N controlled vocabulary controlled vocabulary sample type match: normal
sample_type normal tissue sample GSM7112515 Runtime Siftome inference GEO:sample:GSM7112515:04be7fbfb64c76cc9b359c585d21578f1b638295682436cae665fa056f8882ee low confidence normal sample_accession: GSM7112515 sample_title: X2525N source_name: normal colorectal tissue8 characteristics: tissue: normal colorectal tissue8 X2525N controlled vocabulary controlled vocabulary sample type match: normal
sample_type normal tissue sample GSM7112517 Runtime Siftome inference GEO:sample:GSM7112517:56f5e79506ab459f44b366939c6e4d28cbe0412bc48679b3c20eb78db73c1fd7 low confidence normal sample_accession: GSM7112517 sample_title: X2798N source_name: normal colorectal tissue9 characteristics: tissue: normal colorectal tissue9 X2798N controlled vocabulary controlled vocabulary sample type match: normal
sample_type normal tissue sample GSM7112518 Runtime Siftome inference GEO:sample:GSM7112518:2a4e0cdfc959a9b824d9f43640dafbfc148a18f4a8f55238f8108c26832dc5d6 low confidence normal sample_accession: GSM7112518 sample_title: X7N source_name: normal colorectal tissue10 characteristics: tissue: normal colorectal tissue10 X7N controlled vocabulary controlled vocabulary sample type match: normal
sample_type tumor sample sample GSM7112519 Runtime Siftome inference GEO:sample:GSM7112519:2fc05dc82ec481a342bd33ce1d800c2b5c0e7f4e632835fd225a9a36b7220342 low confidence tumor sample_accession: GSM7112519 sample_title: X2637T source_name: colorectal tumor6 characteristics: tissue: colorectal tumor6 X2637T controlled vocabulary controlled vocabulary sample type match: tumor
sample_type tumor sample sample GSM7112522 Runtime Siftome inference GEO:sample:GSM7112522:f2a3e8cee7fa12654263fed3239d017cafd2fc8ba5b5faebbf684352ee7e8846 low confidence tumor sample_accession: GSM7112522 sample_title: X2800T source_name: colorectal tumor7 characteristics: tissue: colorectal tumor7 X2800T controlled vocabulary controlled vocabulary sample type match: tumor
sample_type tumor sample sample GSM7112523 Runtime Siftome inference GEO:sample:GSM7112523:b59ea5d5296564140245f829799f92d932c62c4b7421dce1c431c163f132855c low confidence tumor sample_accession: GSM7112523 sample_title: X2536T source_name: colorectal tumor8 characteristics: tissue: colorectal tumor8 X2536T controlled vocabulary controlled vocabulary sample type match: tumor
sample_type tumor sample sample GSM7112524 Runtime Siftome inference GEO:sample:GSM7112524:ea6b713336668fa4f453d68747f97201ab488f3561d60cacf976b5b4c39238b2 low confidence tumor sample_accession: GSM7112524 sample_title: X3T source_name: colorectal tumor9 characteristics: tissue: colorectal tumor9 X3T controlled vocabulary controlled vocabulary sample type match: tumor
sample_type tumor sample sample GSM7112526 Runtime Siftome inference GEO:sample:GSM7112526:74d16d1760a1498995e604b0de12325624fafb9ec8b60673f81ab3063bcb8df4 low confidence tumor sample_accession: GSM7112526 sample_title: X3376T source_name: colorectal tumor10 characteristics: tissue: colorectal tumor10 X3376T controlled vocabulary controlled vocabulary sample type match: tumor
sample_type normal tissue sample GSM7112529 Runtime Siftome inference GEO:sample:GSM7112529:bda0b7e6cf0618b5e95352f2870199f3462eb1d773b3fa8d0b2049271b212171 low confidence normal sample_accession: GSM7112529 sample_title: X2800N source_name: normal colorectal tissue11 characteristics: tissue: normal colorectal tissue11 X2800N controlled vocabulary controlled vocabulary sample type match: normal
sample_type tumor sample sample GSM7112531 Runtime Siftome inference GEO:sample:GSM7112531:cee602b8c20d6806aba18b6d417317ec6a7aef67a8b67e8c0e329df47291d54a low confidence tumor sample_accession: GSM7112531 sample_title: X7T source_name: colorectal tumor11 characteristics: tissue: colorectal tumor11 X7T controlled vocabulary controlled vocabulary sample type match: tumor
tissue colon sample GSM7112499 Runtime Siftome inference GEO:sample:GSM7112499:f618b3a18bdd637d592dc246935f94b61714b2957db2cab84be7d740bd49b6ba medium confidence colorectal sample_accession: GSM7112499 sample_title: X2798T source_name: colorectal tumor1 characteristics: tissue: colorectal tumor1 X2798T controlled vocabulary controlled vocabulary tissue match: colorectal
tissue colon sample GSM7112500 Runtime Siftome inference GEO:sample:GSM7112500:ab79dff2c8b28989ebae6fb5e3280b72a8336159a48c2e0137bfd5a1def1cb2f medium confidence colorectal sample_accession: GSM7112500 sample_title: X3pre source_name: colorectal adenoma1 characteristics: tissue: colorectal adenoma1 X3pre controlled vocabulary controlled vocabulary tissue match: colorectal
tissue colon sample GSM7112501 Runtime Siftome inference GEO:sample:GSM7112501:c5125ea6a3d05867bd6b56dad9b56a9eb792fae6d07f6b5ecc93c25c56bacca9 medium confidence colorectal sample_accession: GSM7112501 sample_title: X2536N source_name: normal colorectal tissue1 characteristics: tissue: normal colorectal tissue1 X2536N controlled vocabulary controlled vocabulary tissue match: colorectal
tissue colon sample GSM7112502 Runtime Siftome inference GEO:sample:GSM7112502:79120e47640811f9c33d763a0a2549b7cbb5ad777486dee223a9957ad9b2d4f8 medium confidence colorectal sample_accession: GSM7112502 sample_title: X3376N source_name: normal colorectal tissue2 characteristics: tissue: normal colorectal tissue2 X3376N controlled vocabulary controlled vocabulary tissue match: colorectal
tissue colon sample GSM7112503 Runtime Siftome inference GEO:sample:GSM7112503:f96d43f53f9724247689350d17ad46ba1d359321084fa7615215af6fb11e0137 medium confidence colorectal sample_accession: GSM7112503 sample_title: X2476T source_name: colorectal tumor2 characteristics: tissue: colorectal tumor2 X2476T controlled vocabulary controlled vocabulary tissue match: colorectal
tissue colon sample GSM7112504 Runtime Siftome inference GEO:sample:GSM7112504:91caebfdf511c7c0b945ed5914f041f815068458cbfca87a79fcbeac2616084d medium confidence colorectal sample_accession: GSM7112504 sample_title: X2637N source_name: normal colorectal tissue3 characteristics: tissue: normal colorectal tissue3 X2637N controlled vocabulary controlled vocabulary tissue match: colorectal
tissue colon sample GSM7112505 Runtime Siftome inference GEO:sample:GSM7112505:476f2112f076884823adea46c36abbcb859e4342024d4b8a5daaf2e6366ec7c6 medium confidence colorectal sample_accession: GSM7112505 sample_title: X11pre source_name: colorectal adenoma2 characteristics: tissue: colorectal adenoma2 X11pre controlled vocabulary controlled vocabulary tissue match: colorectal
tissue colon sample GSM7112506 Runtime Siftome inference GEO:sample:GSM7112506:2ce14acc253343ac41457f203c09b68a7bf058d9cc99b46915a8247a3cc0bfbb medium confidence colorectal sample_accession: GSM7112506 sample_title: X2476N source_name: normal colorectal tissue4 characteristics: tissue: normal colorectal tissue4 X2476N controlled vocabulary controlled vocabulary tissue match: colorectal
tissue colon sample GSM7112507 Runtime Siftome inference GEO:sample:GSM7112507:e15544596967a87b6955f26979aa727b1c4d55751efdaaff5c6260fb994ddd5a medium confidence colorectal sample_accession: GSM7112507 sample_title: X2712T source_name: colorectal tumor3 characteristics: tissue: colorectal tumor3 X2712T controlled vocabulary controlled vocabulary tissue match: colorectal
tissue colon sample GSM7112508 Runtime Siftome inference GEO:sample:GSM7112508:4f46ac0028ee64be00f081664999d858361af56117ab34c138b6193f69a3273d medium confidence colorectal sample_accession: GSM7112508 sample_title: X2712N source_name: normal colorectal tissue5 characteristics: tissue: normal colorectal tissue5 X2712N controlled vocabulary controlled vocabulary tissue match: colorectal
tissue colon sample GSM7112509 Runtime Siftome inference GEO:sample:GSM7112509:71332290a247e27177aaae7761f7fadc89d97f42e574c99b074e8703e1d4d402 medium confidence colorectal sample_accession: GSM7112509 sample_title: X2525T source_name: colorectal tumor4 characteristics: tissue: colorectal tumor4 X2525T controlled vocabulary controlled vocabulary tissue match: colorectal
tissue colon sample GSM7112510 Runtime Siftome inference GEO:sample:GSM7112510:0fbe10d2d4c4f72f69bad63d3e22d69b32f5b9b98ffcf927db80f99f5f592d6f medium confidence colorectal sample_accession: GSM7112510 sample_title: X2740N source_name: normal colorectal tissue6 characteristics: tissue: normal colorectal tissue6 X2740N controlled vocabulary controlled vocabulary tissue match: colorectal
tissue colon sample GSM7112511 Runtime Siftome inference GEO:sample:GSM7112511:71a1919a58128bb8df1ac32207364eb081cdc706bcda7b23de0c4937a09bcc0a medium confidence colorectal sample_accession: GSM7112511 sample_title: X9pre source_name: colorectal adenoma3 characteristics: tissue: colorectal adenoma3 X9pre controlled vocabulary controlled vocabulary tissue match: colorectal
tissue colon sample GSM7112512 Runtime Siftome inference GEO:sample:GSM7112512:d8a75500be88389bc75d68c74b155d38c06dbaa1ce4a576872c8f8ca8320f4ae medium confidence colorectal sample_accession: GSM7112512 sample_title: X2740T source_name: colorectal tumor5 characteristics: tissue: colorectal tumor5 X2740T controlled vocabulary controlled vocabulary tissue match: colorectal
tissue colon sample GSM7112513 Runtime Siftome inference GEO:sample:GSM7112513:4339f8261dd43ffaaac29c7aa3bdc06d9c397b8985553fdc0a58a1911b33e350 medium confidence colorectal sample_accession: GSM7112513 sample_title: X3N source_name: normal colorectal tissue7 characteristics: tissue: normal colorectal tissue7 X3N controlled vocabulary controlled vocabulary tissue match: colorectal
tissue colon sample GSM7112514 Runtime Siftome inference GEO:sample:GSM7112514:259f7f26c7c3cf172ff0c2f1e0a6fb54966c5ccbd44909d68f6c80a069693bfb medium confidence colorectal sample_accession: GSM7112514 sample_title: X1pre source_name: colorectal adenoma4 characteristics: tissue: colorectal adenoma4 X1pre controlled vocabulary controlled vocabulary tissue match: colorectal
tissue colon sample GSM7112515 Runtime Siftome inference GEO:sample:GSM7112515:04be7fbfb64c76cc9b359c585d21578f1b638295682436cae665fa056f8882ee medium confidence colorectal sample_accession: GSM7112515 sample_title: X2525N source_name: normal colorectal tissue8 characteristics: tissue: normal colorectal tissue8 X2525N controlled vocabulary controlled vocabulary tissue match: colorectal
tissue colon sample GSM7112516 Runtime Siftome inference GEO:sample:GSM7112516:f2e6257b3d39aa763ecfd0925f04c4e276b6784073478c410b78578b69e5ee22 medium confidence colorectal sample_accession: GSM7112516 sample_title: X2pre source_name: colorectal adenoma5 characteristics: tissue: colorectal adenoma5 X2pre controlled vocabulary controlled vocabulary tissue match: colorectal
tissue colon sample GSM7112517 Runtime Siftome inference GEO:sample:GSM7112517:56f5e79506ab459f44b366939c6e4d28cbe0412bc48679b3c20eb78db73c1fd7 medium confidence colorectal sample_accession: GSM7112517 sample_title: X2798N source_name: normal colorectal tissue9 characteristics: tissue: normal colorectal tissue9 X2798N controlled vocabulary controlled vocabulary tissue match: colorectal
tissue colon sample GSM7112518 Runtime Siftome inference GEO:sample:GSM7112518:2a4e0cdfc959a9b824d9f43640dafbfc148a18f4a8f55238f8108c26832dc5d6 medium confidence colorectal sample_accession: GSM7112518 sample_title: X7N source_name: normal colorectal tissue10 characteristics: tissue: normal colorectal tissue10 X7N controlled vocabulary controlled vocabulary tissue match: colorectal
tissue colon sample GSM7112519 Runtime Siftome inference GEO:sample:GSM7112519:2fc05dc82ec481a342bd33ce1d800c2b5c0e7f4e632835fd225a9a36b7220342 medium confidence colorectal sample_accession: GSM7112519 sample_title: X2637T source_name: colorectal tumor6 characteristics: tissue: colorectal tumor6 X2637T controlled vocabulary controlled vocabulary tissue match: colorectal
tissue colon sample GSM7112520 Runtime Siftome inference GEO:sample:GSM7112520:3198473b9d2b26506f0f2a913c201740b1372a090931dd9a62a70f051c3fcee6 medium confidence colorectal sample_accession: GSM7112520 sample_title: X6pre source_name: colorectal adenoma6 characteristics: tissue: colorectal adenoma6 X6pre controlled vocabulary controlled vocabulary tissue match: colorectal
tissue colon sample GSM7112521 Runtime Siftome inference GEO:sample:GSM7112521:ad6ef9ae4d5aac8b489a7458b4bda34e71a098dd44edc1b12226e64d6903c60a medium confidence colorectal sample_accession: GSM7112521 sample_title: X10pre source_name: colorectal adenoma7 characteristics: tissue: colorectal adenoma7 X10pre controlled vocabulary controlled vocabulary tissue match: colorectal
tissue colon sample GSM7112522 Runtime Siftome inference GEO:sample:GSM7112522:f2a3e8cee7fa12654263fed3239d017cafd2fc8ba5b5faebbf684352ee7e8846 medium confidence colorectal sample_accession: GSM7112522 sample_title: X2800T source_name: colorectal tumor7 characteristics: tissue: colorectal tumor7 X2800T controlled vocabulary controlled vocabulary tissue match: colorectal
tissue colon sample GSM7112523 Runtime Siftome inference GEO:sample:GSM7112523:b59ea5d5296564140245f829799f92d932c62c4b7421dce1c431c163f132855c medium confidence colorectal sample_accession: GSM7112523 sample_title: X2536T source_name: colorectal tumor8 characteristics: tissue: colorectal tumor8 X2536T controlled vocabulary controlled vocabulary tissue match: colorectal
tissue colon sample GSM7112524 Runtime Siftome inference GEO:sample:GSM7112524:ea6b713336668fa4f453d68747f97201ab488f3561d60cacf976b5b4c39238b2 medium confidence colorectal sample_accession: GSM7112524 sample_title: X3T source_name: colorectal tumor9 characteristics: tissue: colorectal tumor9 X3T controlled vocabulary controlled vocabulary tissue match: colorectal
tissue colon sample GSM7112525 Runtime Siftome inference GEO:sample:GSM7112525:ba126448bc83ce08fa2d2e42fa9de0b793717588b6cf116b9aa85fbb54738a2a medium confidence colorectal sample_accession: GSM7112525 sample_title: X4pre source_name: colorectal adenoma8 characteristics: tissue: colorectal adenoma8 X4pre controlled vocabulary controlled vocabulary tissue match: colorectal
tissue colon sample GSM7112526 Runtime Siftome inference GEO:sample:GSM7112526:74d16d1760a1498995e604b0de12325624fafb9ec8b60673f81ab3063bcb8df4 medium confidence colorectal sample_accession: GSM7112526 sample_title: X3376T source_name: colorectal tumor10 characteristics: tissue: colorectal tumor10 X3376T controlled vocabulary controlled vocabulary tissue match: colorectal
tissue colon sample GSM7112527 Runtime Siftome inference GEO:sample:GSM7112527:99563fa838e89b70f6aa8a06bad1047658502c85145f939dfc51ea8cc17ce848 medium confidence colorectal sample_accession: GSM7112527 sample_title: X8pre source_name: colorectal adenoma9 characteristics: tissue: colorectal adenoma9 X8pre controlled vocabulary controlled vocabulary tissue match: colorectal
tissue colon sample GSM7112528 Runtime Siftome inference GEO:sample:GSM7112528:f277d91575e52f6253affcc1eaba65ac76c37c5fd296ef3a211f1544664bb3ee medium confidence colorectal sample_accession: GSM7112528 sample_title: X5pre source_name: colorectal adenoma10 characteristics: tissue: colorectal adenoma10 X5pre controlled vocabulary controlled vocabulary tissue match: colorectal
tissue colon sample GSM7112529 Runtime Siftome inference GEO:sample:GSM7112529:bda0b7e6cf0618b5e95352f2870199f3462eb1d773b3fa8d0b2049271b212171 medium confidence colorectal sample_accession: GSM7112529 sample_title: X2800N source_name: normal colorectal tissue11 characteristics: tissue: normal colorectal tissue11 X2800N controlled vocabulary controlled vocabulary tissue match: colorectal
tissue colon sample GSM7112530 Runtime Siftome inference GEO:sample:GSM7112530:d97f501413b84a990479b7604240b8af890f8d7084cd0085f204db2ad31fc3a1 medium confidence colorectal sample_accession: GSM7112530 sample_title: X7pre source_name: colorectal adenoma11 characteristics: tissue: colorectal adenoma11 X7pre controlled vocabulary controlled vocabulary tissue match: colorectal
tissue colon sample GSM7112531 Runtime Siftome inference GEO:sample:GSM7112531:cee602b8c20d6806aba18b6d417317ec6a7aef67a8b67e8c0e329df47291d54a medium confidence colorectal sample_accession: GSM7112531 sample_title: X7T source_name: colorectal tumor11 characteristics: tissue: colorectal tumor11 X7T controlled vocabulary controlled vocabulary tissue match: colorectal

Sample Group Preview

Possible case samples

Samples currently treated as the comparison case group.

11
  • GSM7112499 X2798T tumor sample Case marker detected. colorectal tumor1 tissue: colorectal tumor1
  • GSM7112503 X2476T tumor sample Case marker detected. colorectal tumor2 tissue: colorectal tumor2
  • GSM7112507 X2712T tumor sample Case marker detected. colorectal tumor3 tissue: colorectal tumor3
  • GSM7112509 X2525T tumor sample Case marker detected. colorectal tumor4 tissue: colorectal tumor4
  • GSM7112512 X2740T tumor sample Case marker detected. colorectal tumor5 tissue: colorectal tumor5
  • GSM7112519 X2637T tumor sample Case marker detected. colorectal tumor6 tissue: colorectal tumor6
  • GSM7112522 X2800T tumor sample Case marker detected. colorectal tumor7 tissue: colorectal tumor7
  • GSM7112523 X2536T tumor sample Case marker detected. colorectal tumor8 tissue: colorectal tumor8
  • GSM7112524 X3T tumor sample Case marker detected. colorectal tumor9 tissue: colorectal tumor9
  • GSM7112526 X3376T tumor sample Case marker detected. colorectal tumor10 tissue: colorectal tumor10
  • GSM7112531 X7T tumor sample Case marker detected. colorectal tumor11 tissue: colorectal tumor11

Possible control samples

Samples currently treated as controls or baseline.

11
  • GSM7112501 X2536N normal tissue Control marker detected. normal colorectal tissue1 tissue: normal colorectal tissue1
  • GSM7112502 X3376N normal tissue Control marker detected. normal colorectal tissue2 tissue: normal colorectal tissue2
  • GSM7112504 X2637N normal tissue Control marker detected. normal colorectal tissue3 tissue: normal colorectal tissue3
  • GSM7112506 X2476N normal tissue Control marker detected. normal colorectal tissue4 tissue: normal colorectal tissue4
  • GSM7112508 X2712N normal tissue Control marker detected. normal colorectal tissue5 tissue: normal colorectal tissue5
  • GSM7112510 X2740N normal tissue Control marker detected. normal colorectal tissue6 tissue: normal colorectal tissue6
  • GSM7112513 X3N normal tissue Control marker detected. normal colorectal tissue7 tissue: normal colorectal tissue7
  • GSM7112515 X2525N normal tissue Control marker detected. normal colorectal tissue8 tissue: normal colorectal tissue8
  • GSM7112517 X2798N normal tissue Control marker detected. normal colorectal tissue9 tissue: normal colorectal tissue9
  • GSM7112518 X7N normal tissue Control marker detected. normal colorectal tissue10 tissue: normal colorectal tissue10
  • GSM7112529 X2800N normal tissue Control marker detected. normal colorectal tissue11 tissue: normal colorectal tissue11

Unassigned samples

Samples with no explicit case or control marker.

11
  • GSM7112500 X3pre unassigned No explicit case or control marker detected. colorectal adenoma1 tissue: colorectal adenoma1
  • GSM7112505 X11pre unassigned No explicit case or control marker detected. colorectal adenoma2 tissue: colorectal adenoma2
  • GSM7112511 X9pre unassigned No explicit case or control marker detected. colorectal adenoma3 tissue: colorectal adenoma3
  • GSM7112514 X1pre unassigned No explicit case or control marker detected. colorectal adenoma4 tissue: colorectal adenoma4
  • GSM7112516 X2pre unassigned No explicit case or control marker detected. colorectal adenoma5 tissue: colorectal adenoma5
  • GSM7112520 X6pre unassigned No explicit case or control marker detected. colorectal adenoma6 tissue: colorectal adenoma6
  • GSM7112521 X10pre unassigned No explicit case or control marker detected. colorectal adenoma7 tissue: colorectal adenoma7
  • GSM7112525 X4pre unassigned No explicit case or control marker detected. colorectal adenoma8 tissue: colorectal adenoma8
  • GSM7112527 X8pre unassigned No explicit case or control marker detected. colorectal adenoma9 tissue: colorectal adenoma9
  • GSM7112528 X5pre unassigned No explicit case or control marker detected. colorectal adenoma10 tissue: colorectal adenoma10
  • GSM7112530 X7pre unassigned No explicit case or control marker detected. colorectal adenoma11 tissue: colorectal adenoma11

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

tumor sample

11 samples
  • GSM7112499 X2798T colorectal tumor1 tissue: colorectal tumor1
  • GSM7112503 X2476T colorectal tumor2 tissue: colorectal tumor2
  • GSM7112507 X2712T colorectal tumor3 tissue: colorectal tumor3
  • GSM7112509 X2525T colorectal tumor4 tissue: colorectal tumor4
  • GSM7112512 X2740T colorectal tumor5 tissue: colorectal tumor5
  • GSM7112519 X2637T colorectal tumor6 tissue: colorectal tumor6
  • GSM7112522 X2800T colorectal tumor7 tissue: colorectal tumor7
  • GSM7112523 X2536T colorectal tumor8 tissue: colorectal tumor8
  • GSM7112524 X3T colorectal tumor9 tissue: colorectal tumor9
  • GSM7112526 X3376T colorectal tumor10 tissue: colorectal tumor10
  • GSM7112531 X7T colorectal tumor11 tissue: colorectal tumor11

unassigned

11 samples
  • GSM7112500 X3pre colorectal adenoma1 tissue: colorectal adenoma1
  • GSM7112505 X11pre colorectal adenoma2 tissue: colorectal adenoma2
  • GSM7112511 X9pre colorectal adenoma3 tissue: colorectal adenoma3
  • GSM7112514 X1pre colorectal adenoma4 tissue: colorectal adenoma4
  • GSM7112516 X2pre colorectal adenoma5 tissue: colorectal adenoma5
  • GSM7112520 X6pre colorectal adenoma6 tissue: colorectal adenoma6
  • GSM7112521 X10pre colorectal adenoma7 tissue: colorectal adenoma7
  • GSM7112525 X4pre colorectal adenoma8 tissue: colorectal adenoma8
  • GSM7112527 X8pre colorectal adenoma9 tissue: colorectal adenoma9
  • GSM7112528 X5pre colorectal adenoma10 tissue: colorectal adenoma10
  • GSM7112530 X7pre colorectal adenoma11 tissue: colorectal adenoma11

normal tissue

11 samples
  • GSM7112501 X2536N normal colorectal tissue1 tissue: normal colorectal tissue1
  • GSM7112502 X3376N normal colorectal tissue2 tissue: normal colorectal tissue2
  • GSM7112504 X2637N normal colorectal tissue3 tissue: normal colorectal tissue3
  • GSM7112506 X2476N normal colorectal tissue4 tissue: normal colorectal tissue4
  • GSM7112508 X2712N normal colorectal tissue5 tissue: normal colorectal tissue5
  • GSM7112510 X2740N normal colorectal tissue6 tissue: normal colorectal tissue6
  • GSM7112513 X3N normal colorectal tissue7 tissue: normal colorectal tissue7
  • GSM7112515 X2525N normal colorectal tissue8 tissue: normal colorectal tissue8
  • GSM7112517 X2798N normal colorectal tissue9 tissue: normal colorectal tissue9
  • GSM7112518 X7N normal colorectal tissue10 tissue: normal colorectal tissue10
  • GSM7112529 X2800N normal colorectal tissue11 tissue: normal colorectal tissue11

Score Breakdown

100%

relevance

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

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.
  • 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

33 samples

Review Audit Trail

0 decisions

No review decisions have been stored for this dataset.