Siftome Phase 3L

GSE136630

RNA-seq access dataset for epigenomics landscape of colorectal cancer

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
2019-08-29
Last update
2021-06-02
Organization
Broad Institute of MIT and Harvard
Department
Epigenomics Program
Public date
2021-05-22
Experiment types
Expression profiling by high throughput sequencing
Platforms
GPL11154 Illumina HiSeq 2000 (Homo sapiens)
Series type
SubSeries
SubSeries
Not available
BioProject
PRJNA562898
Supplementary files
TXT: GSE136630_DEGs_CRCT-Normal_All.txt.gz; TAR: GSE136630_RAW.tar
Organism
Homo sapiens
Assay
bulk RNA-seq
Samples
12
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
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. 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 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 matched normal Study design remains rule-derived: Tumor vs matched normal.
  • Specimen/source Tissue Specimen/source remains rule-derived: Tissue.
  • Likely case group tumor sample 7 samples
  • Likely control group normal tissue 5 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 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 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.

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
GSE136630
Sample records
12 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
GSE136630
  • 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
GSE136630
  • 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
GSE136630
  • 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: GSE136630
dataset_title: RNA-seq access dataset for epigenomics landscape of colorectal cancer
organism: Homo sapiens
assay_type: bulk RNA-seq
processed_data_available: true
raw_data_available: true
submission_date: 2019-08-29
last_update_date: 2021-06-02
organization_name: Broad Institute of MIT and Harvard
department: Epigenomics Program
public_date: 2021-05-22
experiment_types: Expression profiling by high throughput sequencing
platforms: GPL11154 Illumina HiSeq 2000 (Homo sapiens)
sub_series: Not available
bioproject: PRJNA562898
supplementary_files: TXT: GSE136630_DEGs_CRCT-Normal_All.txt.gz; TAR: GSE136630_RAW.tar
series_type: SubSeries

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.

Warnings

No warnings

Normalized Fields

45 fields
Field Value Source Origin Confidence Evidence Reason
assay_type bulk RNA-seq dataset GSE136630 Runtime Siftome inference GEO:dataset:GSE136630:40b96db597f28a3b2efaee9b81dd397da0848cc94555e0942ad7d68c7f336234 high confidence bulk rna-seq dataset_accession: GSE136630 dataset_title: RNA-seq access dataset for epigenomics landscape of colorectal cancer organism: Homo sapiens assay_type: bulk RNA-seq processed_data_... keyword match keyword match: bulk rna-seq
disease colorectal cancer dataset GSE136630 Runtime Siftome inference GEO:dataset:GSE136630:40b96db597f28a3b2efaee9b81dd397da0848cc94555e0942ad7d68c7f336234 high confidence colorectal cancer dataset_accession: GSE136630 dataset_title: RNA-seq access dataset for epigenomics landscape of colorectal cancer organism: Homo sapiens assay_type: bulk RNA-seq processed_data_... controlled vocabulary controlled vocabulary disease match: colorectal cancer
disease colorectal cancer sample GSM4053401 Runtime Siftome inference GEO:sample:GSM4053401:44e5bd02f99669874801346f61b1ac321beb0ed9ac2f9c234276934bceed1fd8 medium confidence coad sample_accession: GSM4053401 sample_title: COAD-T001 RNA-seq source_name: Tumor characteristics: tissue: Colorectal tumor; patient: COAD-001 COAD-T001 RNA-seq controlled vocabulary controlled vocabulary disease match: coad
disease colorectal cancer sample GSM4053402 Runtime Siftome inference GEO:sample:GSM4053402:68bf001ac09bdfb295c312801c6fa80df212b83187061b0d5e022fd7135fd7e1 medium confidence coad sample_accession: GSM4053402 sample_title: COAD-T004 RNA-seq source_name: Tumor characteristics: tissue: Colorectal tumor; patient: COAD-004 COAD-T004 RNA-seq controlled vocabulary controlled vocabulary disease match: coad
disease colorectal cancer sample GSM4053403 Runtime Siftome inference GEO:sample:GSM4053403:3080555d8eed302ef5f9d5b3936202f4f10dad227ddeb57ebfdda869fde8e81e medium confidence coad sample_accession: GSM4053403 sample_title: COAD-T012 RNA-seq source_name: Tumor characteristics: tissue: Colorectal tumor; patient: COAD-012 COAD-T012 RNA-seq controlled vocabulary controlled vocabulary disease match: coad
disease colorectal cancer sample GSM4053404 Runtime Siftome inference GEO:sample:GSM4053404:a1a6afc791f9e53c459e73e6432efb8c122d27a28fc7e59eefd4407a718abe99 medium confidence coad sample_accession: GSM4053404 sample_title: COAD-T014 RNA-seq source_name: Tumor characteristics: tissue: Colorectal tumor; patient: COAD-014 COAD-T014 RNA-seq controlled vocabulary controlled vocabulary disease match: coad
disease colorectal cancer sample GSM4053405 Runtime Siftome inference GEO:sample:GSM4053405:3732037b2caea051e17ec4e49baecc0f40fb7082e4fa5d99c94b216cc96122ac medium confidence coad sample_accession: GSM4053405 sample_title: COAD-T015 RNA-seq source_name: Tumor characteristics: tissue: Colorectal tumor; patient: COAD-015 COAD-T015 RNA-seq controlled vocabulary controlled vocabulary disease match: coad
disease colorectal cancer sample GSM4053406 Runtime Siftome inference GEO:sample:GSM4053406:ab279bb63087f1ae183fd5c9a3cde04d148dcc0ed1d6bfcc76726568f82a33ec medium confidence coad sample_accession: GSM4053406 sample_title: COAD-T016 RNA-seq source_name: Tumor characteristics: tissue: Colorectal tumor; patient: COAD-016 COAD-T016 RNA-seq controlled vocabulary controlled vocabulary disease match: coad
disease colorectal cancer sample GSM4053407 Runtime Siftome inference GEO:sample:GSM4053407:e87c797a529c807bb3edd22370da96ce67526710e4992288c559939cc3c41110 medium confidence coad sample_accession: GSM4053407 sample_title: COAD-T017 RNA-seq source_name: Tumor characteristics: tissue: Colorectal tumor; patient: COAD-017 COAD-T017 RNA-seq controlled vocabulary controlled vocabulary disease match: coad
disease colorectal cancer sample GSM4053408 Runtime Siftome inference GEO:sample:GSM4053408:83b599b7be4dd65c46ff4aa0a667f0e6735cde19fbd4255bd54de776b65733eb medium confidence coad sample_accession: GSM4053408 sample_title: COAD-N004 RNA-seq source_name: Adjacent Normal characteristics: tissue: Adjacent normal colon; patient: COAD-004 COAD-N004 RNA-seq controlled vocabulary controlled vocabulary disease match: coad
disease colorectal cancer sample GSM4053409 Runtime Siftome inference GEO:sample:GSM4053409:788fc7cccd64c14aa82b503464e88bdeb8c24971069d69db1227b03b4ecc0ce9 medium confidence coad sample_accession: GSM4053409 sample_title: COAD-N012 RNA-seq source_name: Adjacent Normal characteristics: tissue: Adjacent normal colon; patient: COAD-012 COAD-N012 RNA-seq controlled vocabulary controlled vocabulary disease match: coad
disease colorectal cancer sample GSM4053410 Runtime Siftome inference GEO:sample:GSM4053410:d4e6af26506c15e579d7eabe421e7d85ef9e251160dfefffd0e51c97a4bf2818 medium confidence coad sample_accession: GSM4053410 sample_title: COAD-N014 RNA-seq source_name: Adjacent Normal characteristics: tissue: Adjacent normal colon; patient: COAD-014 COAD-N014 RNA-seq controlled vocabulary controlled vocabulary disease match: coad
disease colorectal cancer sample GSM4053411 Runtime Siftome inference GEO:sample:GSM4053411:11a25b4fcbaff42b865687871a372013df9735553c2ab4c00569a27eb9afae21 medium confidence coad sample_accession: GSM4053411 sample_title: COAD-N016 RNA-seq source_name: Adjacent Normal characteristics: tissue: Adjacent normal colon; patient: COAD-016 COAD-N016 RNA-seq controlled vocabulary controlled vocabulary disease match: coad
disease colorectal cancer sample GSM4053412 Runtime Siftome inference GEO:sample:GSM4053412:2c3eb103afffcdf8940a4cc5c6b094d7c8d678d7ac6f61ac0cd26d7f5974c4ab medium confidence coad sample_accession: GSM4053412 sample_title: COAD-N017 RNA-seq source_name: Adjacent Normal characteristics: tissue: Adjacent normal colon; patient: COAD-017 COAD-N017 RNA-seq controlled vocabulary controlled vocabulary disease match: coad
normal_tissue_type adjacent normal sample GSM4053408 Runtime Siftome inference GEO:sample:GSM4053408:83b599b7be4dd65c46ff4aa0a667f0e6735cde19fbd4255bd54de776b65733eb high confidence adjacent normal sample_accession: GSM4053408 sample_title: COAD-N004 RNA-seq source_name: Adjacent Normal characteristics: tissue: Adjacent normal colon; patient: COAD-004 COAD-N004 RNA-seq controlled vocabulary controlled vocabulary normal tissue type match: adjacent normal
normal_tissue_type adjacent normal sample GSM4053409 Runtime Siftome inference GEO:sample:GSM4053409:788fc7cccd64c14aa82b503464e88bdeb8c24971069d69db1227b03b4ecc0ce9 high confidence adjacent normal sample_accession: GSM4053409 sample_title: COAD-N012 RNA-seq source_name: Adjacent Normal characteristics: tissue: Adjacent normal colon; patient: COAD-012 COAD-N012 RNA-seq controlled vocabulary controlled vocabulary normal tissue type match: adjacent normal
normal_tissue_type adjacent normal sample GSM4053410 Runtime Siftome inference GEO:sample:GSM4053410:d4e6af26506c15e579d7eabe421e7d85ef9e251160dfefffd0e51c97a4bf2818 high confidence adjacent normal sample_accession: GSM4053410 sample_title: COAD-N014 RNA-seq source_name: Adjacent Normal characteristics: tissue: Adjacent normal colon; patient: COAD-014 COAD-N014 RNA-seq controlled vocabulary controlled vocabulary normal tissue type match: adjacent normal
normal_tissue_type adjacent normal sample GSM4053411 Runtime Siftome inference GEO:sample:GSM4053411:11a25b4fcbaff42b865687871a372013df9735553c2ab4c00569a27eb9afae21 high confidence adjacent normal sample_accession: GSM4053411 sample_title: COAD-N016 RNA-seq source_name: Adjacent Normal characteristics: tissue: Adjacent normal colon; patient: COAD-016 COAD-N016 RNA-seq controlled vocabulary controlled vocabulary normal tissue type match: adjacent normal
normal_tissue_type adjacent normal sample GSM4053412 Runtime Siftome inference GEO:sample:GSM4053412:2c3eb103afffcdf8940a4cc5c6b094d7c8d678d7ac6f61ac0cd26d7f5974c4ab high confidence adjacent normal sample_accession: GSM4053412 sample_title: COAD-N017 RNA-seq source_name: Adjacent Normal characteristics: tissue: Adjacent normal colon; patient: COAD-017 COAD-N017 RNA-seq controlled vocabulary controlled vocabulary normal tissue type match: adjacent normal
organism Homo sapiens dataset GSE136630 Runtime Siftome inference GEO:dataset:GSE136630:40b96db597f28a3b2efaee9b81dd397da0848cc94555e0942ad7d68c7f336234 high confidence homo sapiens dataset_accession: GSE136630 dataset_title: RNA-seq access dataset for epigenomics landscape of colorectal cancer organism: Homo sapiens assay_type: bulk RNA-seq processed_data_... keyword match keyword match: homo sapiens
sample_type tumor sample sample GSM4053401 Runtime Siftome inference GEO:sample:GSM4053401:44e5bd02f99669874801346f61b1ac321beb0ed9ac2f9c234276934bceed1fd8 low confidence tumor sample_accession: GSM4053401 sample_title: COAD-T001 RNA-seq source_name: Tumor characteristics: tissue: Colorectal tumor; patient: COAD-001 COAD-T001 RNA-seq controlled vocabulary controlled vocabulary sample type match: tumor
sample_type tumor sample sample GSM4053402 Runtime Siftome inference GEO:sample:GSM4053402:68bf001ac09bdfb295c312801c6fa80df212b83187061b0d5e022fd7135fd7e1 low confidence tumor sample_accession: GSM4053402 sample_title: COAD-T004 RNA-seq source_name: Tumor characteristics: tissue: Colorectal tumor; patient: COAD-004 COAD-T004 RNA-seq controlled vocabulary controlled vocabulary sample type match: tumor
sample_type tumor sample sample GSM4053403 Runtime Siftome inference GEO:sample:GSM4053403:3080555d8eed302ef5f9d5b3936202f4f10dad227ddeb57ebfdda869fde8e81e low confidence tumor sample_accession: GSM4053403 sample_title: COAD-T012 RNA-seq source_name: Tumor characteristics: tissue: Colorectal tumor; patient: COAD-012 COAD-T012 RNA-seq controlled vocabulary controlled vocabulary sample type match: tumor
sample_type tumor sample sample GSM4053404 Runtime Siftome inference GEO:sample:GSM4053404:a1a6afc791f9e53c459e73e6432efb8c122d27a28fc7e59eefd4407a718abe99 low confidence tumor sample_accession: GSM4053404 sample_title: COAD-T014 RNA-seq source_name: Tumor characteristics: tissue: Colorectal tumor; patient: COAD-014 COAD-T014 RNA-seq controlled vocabulary controlled vocabulary sample type match: tumor
sample_type tumor sample sample GSM4053405 Runtime Siftome inference GEO:sample:GSM4053405:3732037b2caea051e17ec4e49baecc0f40fb7082e4fa5d99c94b216cc96122ac low confidence tumor sample_accession: GSM4053405 sample_title: COAD-T015 RNA-seq source_name: Tumor characteristics: tissue: Colorectal tumor; patient: COAD-015 COAD-T015 RNA-seq controlled vocabulary controlled vocabulary sample type match: tumor
sample_type tumor sample sample GSM4053406 Runtime Siftome inference GEO:sample:GSM4053406:ab279bb63087f1ae183fd5c9a3cde04d148dcc0ed1d6bfcc76726568f82a33ec low confidence tumor sample_accession: GSM4053406 sample_title: COAD-T016 RNA-seq source_name: Tumor characteristics: tissue: Colorectal tumor; patient: COAD-016 COAD-T016 RNA-seq controlled vocabulary controlled vocabulary sample type match: tumor
sample_type tumor sample sample GSM4053407 Runtime Siftome inference GEO:sample:GSM4053407:e87c797a529c807bb3edd22370da96ce67526710e4992288c559939cc3c41110 low confidence tumor sample_accession: GSM4053407 sample_title: COAD-T017 RNA-seq source_name: Tumor characteristics: tissue: Colorectal tumor; patient: COAD-017 COAD-T017 RNA-seq controlled vocabulary controlled vocabulary sample type match: tumor
sample_type normal tissue sample GSM4053408 Runtime Siftome inference GEO:sample:GSM4053408:83b599b7be4dd65c46ff4aa0a667f0e6735cde19fbd4255bd54de776b65733eb high confidence adjacent normal sample_accession: GSM4053408 sample_title: COAD-N004 RNA-seq source_name: Adjacent Normal characteristics: tissue: Adjacent normal colon; patient: COAD-004 COAD-N004 RNA-seq controlled vocabulary controlled vocabulary sample type match: adjacent normal
sample_type normal tissue sample GSM4053409 Runtime Siftome inference GEO:sample:GSM4053409:788fc7cccd64c14aa82b503464e88bdeb8c24971069d69db1227b03b4ecc0ce9 high confidence adjacent normal sample_accession: GSM4053409 sample_title: COAD-N012 RNA-seq source_name: Adjacent Normal characteristics: tissue: Adjacent normal colon; patient: COAD-012 COAD-N012 RNA-seq controlled vocabulary controlled vocabulary sample type match: adjacent normal
sample_type normal tissue sample GSM4053410 Runtime Siftome inference GEO:sample:GSM4053410:d4e6af26506c15e579d7eabe421e7d85ef9e251160dfefffd0e51c97a4bf2818 high confidence adjacent normal sample_accession: GSM4053410 sample_title: COAD-N014 RNA-seq source_name: Adjacent Normal characteristics: tissue: Adjacent normal colon; patient: COAD-014 COAD-N014 RNA-seq controlled vocabulary controlled vocabulary sample type match: adjacent normal
sample_type normal tissue sample GSM4053411 Runtime Siftome inference GEO:sample:GSM4053411:11a25b4fcbaff42b865687871a372013df9735553c2ab4c00569a27eb9afae21 high confidence adjacent normal sample_accession: GSM4053411 sample_title: COAD-N016 RNA-seq source_name: Adjacent Normal characteristics: tissue: Adjacent normal colon; patient: COAD-016 COAD-N016 RNA-seq controlled vocabulary controlled vocabulary sample type match: adjacent normal
sample_type normal tissue sample GSM4053412 Runtime Siftome inference GEO:sample:GSM4053412:2c3eb103afffcdf8940a4cc5c6b094d7c8d678d7ac6f61ac0cd26d7f5974c4ab high confidence adjacent normal sample_accession: GSM4053412 sample_title: COAD-N017 RNA-seq source_name: Adjacent Normal characteristics: tissue: Adjacent normal colon; patient: COAD-017 COAD-N017 RNA-seq controlled vocabulary controlled vocabulary sample type match: adjacent normal
tissue colon dataset GSE136630 Runtime Siftome inference GEO:dataset:GSE136630:40b96db597f28a3b2efaee9b81dd397da0848cc94555e0942ad7d68c7f336234 medium confidence colorectal dataset_accession: GSE136630 dataset_title: RNA-seq access dataset for epigenomics landscape of colorectal cancer organism: Homo sapiens assay_type: bulk RNA-seq processed_data_... controlled vocabulary controlled vocabulary tissue match: colorectal
tissue colon sample GSM4053401 Runtime Siftome inference GEO:sample:GSM4053401:44e5bd02f99669874801346f61b1ac321beb0ed9ac2f9c234276934bceed1fd8 medium confidence colorectal sample_accession: GSM4053401 sample_title: COAD-T001 RNA-seq source_name: Tumor characteristics: tissue: Colorectal tumor; patient: COAD-001 COAD-T001 RNA-seq controlled vocabulary controlled vocabulary tissue match: colorectal
tissue colon sample GSM4053402 Runtime Siftome inference GEO:sample:GSM4053402:68bf001ac09bdfb295c312801c6fa80df212b83187061b0d5e022fd7135fd7e1 medium confidence colorectal sample_accession: GSM4053402 sample_title: COAD-T004 RNA-seq source_name: Tumor characteristics: tissue: Colorectal tumor; patient: COAD-004 COAD-T004 RNA-seq controlled vocabulary controlled vocabulary tissue match: colorectal
tissue colon sample GSM4053403 Runtime Siftome inference GEO:sample:GSM4053403:3080555d8eed302ef5f9d5b3936202f4f10dad227ddeb57ebfdda869fde8e81e medium confidence colorectal sample_accession: GSM4053403 sample_title: COAD-T012 RNA-seq source_name: Tumor characteristics: tissue: Colorectal tumor; patient: COAD-012 COAD-T012 RNA-seq controlled vocabulary controlled vocabulary tissue match: colorectal
tissue colon sample GSM4053404 Runtime Siftome inference GEO:sample:GSM4053404:a1a6afc791f9e53c459e73e6432efb8c122d27a28fc7e59eefd4407a718abe99 medium confidence colorectal sample_accession: GSM4053404 sample_title: COAD-T014 RNA-seq source_name: Tumor characteristics: tissue: Colorectal tumor; patient: COAD-014 COAD-T014 RNA-seq controlled vocabulary controlled vocabulary tissue match: colorectal
tissue colon sample GSM4053405 Runtime Siftome inference GEO:sample:GSM4053405:3732037b2caea051e17ec4e49baecc0f40fb7082e4fa5d99c94b216cc96122ac medium confidence colorectal sample_accession: GSM4053405 sample_title: COAD-T015 RNA-seq source_name: Tumor characteristics: tissue: Colorectal tumor; patient: COAD-015 COAD-T015 RNA-seq controlled vocabulary controlled vocabulary tissue match: colorectal
tissue colon sample GSM4053406 Runtime Siftome inference GEO:sample:GSM4053406:ab279bb63087f1ae183fd5c9a3cde04d148dcc0ed1d6bfcc76726568f82a33ec medium confidence colorectal sample_accession: GSM4053406 sample_title: COAD-T016 RNA-seq source_name: Tumor characteristics: tissue: Colorectal tumor; patient: COAD-016 COAD-T016 RNA-seq controlled vocabulary controlled vocabulary tissue match: colorectal
tissue colon sample GSM4053407 Runtime Siftome inference GEO:sample:GSM4053407:e87c797a529c807bb3edd22370da96ce67526710e4992288c559939cc3c41110 medium confidence colorectal sample_accession: GSM4053407 sample_title: COAD-T017 RNA-seq source_name: Tumor characteristics: tissue: Colorectal tumor; patient: COAD-017 COAD-T017 RNA-seq controlled vocabulary controlled vocabulary tissue match: colorectal
tissue colon sample GSM4053408 Runtime Siftome inference GEO:sample:GSM4053408:83b599b7be4dd65c46ff4aa0a667f0e6735cde19fbd4255bd54de776b65733eb low confidence colon sample_accession: GSM4053408 sample_title: COAD-N004 RNA-seq source_name: Adjacent Normal characteristics: tissue: Adjacent normal colon; patient: COAD-004 COAD-N004 RNA-seq controlled vocabulary controlled vocabulary tissue match: colon
tissue colon sample GSM4053409 Runtime Siftome inference GEO:sample:GSM4053409:788fc7cccd64c14aa82b503464e88bdeb8c24971069d69db1227b03b4ecc0ce9 low confidence colon sample_accession: GSM4053409 sample_title: COAD-N012 RNA-seq source_name: Adjacent Normal characteristics: tissue: Adjacent normal colon; patient: COAD-012 COAD-N012 RNA-seq controlled vocabulary controlled vocabulary tissue match: colon
tissue colon sample GSM4053410 Runtime Siftome inference GEO:sample:GSM4053410:d4e6af26506c15e579d7eabe421e7d85ef9e251160dfefffd0e51c97a4bf2818 low confidence colon sample_accession: GSM4053410 sample_title: COAD-N014 RNA-seq source_name: Adjacent Normal characteristics: tissue: Adjacent normal colon; patient: COAD-014 COAD-N014 RNA-seq controlled vocabulary controlled vocabulary tissue match: colon
tissue colon sample GSM4053411 Runtime Siftome inference GEO:sample:GSM4053411:11a25b4fcbaff42b865687871a372013df9735553c2ab4c00569a27eb9afae21 low confidence colon sample_accession: GSM4053411 sample_title: COAD-N016 RNA-seq source_name: Adjacent Normal characteristics: tissue: Adjacent normal colon; patient: COAD-016 COAD-N016 RNA-seq controlled vocabulary controlled vocabulary tissue match: colon
tissue colon sample GSM4053412 Runtime Siftome inference GEO:sample:GSM4053412:2c3eb103afffcdf8940a4cc5c6b094d7c8d678d7ac6f61ac0cd26d7f5974c4ab low confidence colon sample_accession: GSM4053412 sample_title: COAD-N017 RNA-seq source_name: Adjacent Normal characteristics: tissue: Adjacent normal colon; patient: COAD-017 COAD-N017 RNA-seq controlled vocabulary controlled vocabulary tissue match: colon

Sample Group Preview

Possible case samples

Samples currently treated as the comparison case group.

7
  • GSM4053401 COAD-T001 RNA-seq tumor sample Case marker detected. Tumor tissue: Colorectal tumor; patient: COAD-001
  • GSM4053402 COAD-T004 RNA-seq tumor sample Case marker detected. Tumor tissue: Colorectal tumor; patient: COAD-004
  • GSM4053403 COAD-T012 RNA-seq tumor sample Case marker detected. Tumor tissue: Colorectal tumor; patient: COAD-012
  • GSM4053404 COAD-T014 RNA-seq tumor sample Case marker detected. Tumor tissue: Colorectal tumor; patient: COAD-014
  • GSM4053405 COAD-T015 RNA-seq tumor sample Case marker detected. Tumor tissue: Colorectal tumor; patient: COAD-015
  • GSM4053406 COAD-T016 RNA-seq tumor sample Case marker detected. Tumor tissue: Colorectal tumor; patient: COAD-016
  • GSM4053407 COAD-T017 RNA-seq tumor sample Case marker detected. Tumor tissue: Colorectal tumor; patient: COAD-017

Possible control samples

Samples currently treated as controls or baseline.

5
  • GSM4053408 COAD-N004 RNA-seq normal tissue Control marker detected. Adjacent Normal tissue: Adjacent normal colon; patient: COAD-004
  • GSM4053409 COAD-N012 RNA-seq normal tissue Control marker detected. Adjacent Normal tissue: Adjacent normal colon; patient: COAD-012
  • GSM4053410 COAD-N014 RNA-seq normal tissue Control marker detected. Adjacent Normal tissue: Adjacent normal colon; patient: COAD-014
  • GSM4053411 COAD-N016 RNA-seq normal tissue Control marker detected. Adjacent Normal tissue: Adjacent normal colon; patient: COAD-016
  • GSM4053412 COAD-N017 RNA-seq normal tissue Control marker detected. Adjacent Normal tissue: Adjacent normal colon; patient: COAD-017

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

tumor sample

7 samples
  • GSM4053401 COAD-T001 RNA-seq Tumor tissue: Colorectal tumor; patient: COAD-001
  • GSM4053402 COAD-T004 RNA-seq Tumor tissue: Colorectal tumor; patient: COAD-004
  • GSM4053403 COAD-T012 RNA-seq Tumor tissue: Colorectal tumor; patient: COAD-012
  • GSM4053404 COAD-T014 RNA-seq Tumor tissue: Colorectal tumor; patient: COAD-014
  • GSM4053405 COAD-T015 RNA-seq Tumor tissue: Colorectal tumor; patient: COAD-015
  • GSM4053406 COAD-T016 RNA-seq Tumor tissue: Colorectal tumor; patient: COAD-016
  • GSM4053407 COAD-T017 RNA-seq Tumor tissue: Colorectal tumor; patient: COAD-017

normal tissue

5 samples
  • GSM4053408 COAD-N004 RNA-seq Adjacent Normal tissue: Adjacent normal colon; patient: COAD-004
  • GSM4053409 COAD-N012 RNA-seq Adjacent Normal tissue: Adjacent normal colon; patient: COAD-012
  • GSM4053410 COAD-N014 RNA-seq Adjacent Normal tissue: Adjacent normal colon; patient: COAD-014
  • GSM4053411 COAD-N016 RNA-seq Adjacent Normal tissue: Adjacent normal colon; patient: COAD-016
  • GSM4053412 COAD-N017 RNA-seq Adjacent Normal tissue: Adjacent normal colon; patient: COAD-017

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.
  • 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.
100%

overall

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

Sample Links

12 samples

Review Audit Trail

0 decisions

No review decisions have been stored for this dataset.