Siftome Phase 3L

GSE138340

Differential expression analysis of primary AML cells treated with AC220 vs DMSO in endothelial cell co-culture.

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
2019-10-02
Last update
2021-06-21
Organization
Fred Hutchinson Cancer Research Center
Department
Clinical Research Division
Public date
2019-10-03
Experiment types
Expression profiling by high throughput sequencing
Platforms
GPL16791 Illumina HiSeq 2500 (Homo sapiens)
Series type
Series
SubSeries
Not available
BioProject
PRJNA575538
Supplementary files
TXT: GSE138340_edgeR_analysis.txt.gz
Organism
Homo sapiens
Assay
bulk RNA-seq
Samples
7
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
82% DE readiness

Contrast completeness

25/25 pts

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

Minimum group size

8/20 pts

A contrast exists, but at least one group is below the minimum sample count.

Processed data availability

20/20 pts

Processed data is marked available in the GEO index.

Sample decision clarity

15/15 pts

All samples are assigned to a case or control group.

Blocking warnings

7/10 pts

Warnings are present, but none are critical blockers.

Metadata normalization

7/10 pts

Metadata quality is usable, but still deserves review.

Blockers

  • At least one contrast group is below the minimum sample count.

Next Steps

  • Review blockers and update sample grouping or dataset selection before analysis.

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

Blocked

At least one group has fewer than 2 samples.

Choose a larger dataset or merge only scientifically valid groups.

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

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.
  • Analysis preparation checklist contains blocked items.
  • At least one comparison group has fewer than two samples.

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 50% Organism normalized. Assay type normalized.
  • comparison suitability 5% Tumor and normal sample groups detected. No excluded sample type flags detected. Tumor/normal design boosted for colorectal tumor-vs-normal tissue triage. Patient tissue or biopsy specimens boosted for tissue comparison triage. Missing colorectal disease context downgraded for tumor-vs-normal tissue ranking.
  • metadata quality 70% Sample source clarity: All samples have source metadata and clear GSE/GSM accessions. Group clarity: Rule-based grouping found both case and control samples. Disease clarity: Disease or condition metadata was not normalized. Tissue clarity: Tissue metadata was not normalized. Treatment clarity: No unclear treatment split detected in the sample metadata. Replicate clarity: No pooled sample or technical replicate flags detected. Data availability clarity: Dataset-level processed or raw data availability is explicit.
  • data availability 100% Processed data available. Raw data available.
  • overall 45% Weighted score: 30% relevance, 30% comparison suitability, 25% metadata quality, 15% data availability. Overall score capped because comparison suitability is weak for the selected search intent. Overall score capped because fewer than ten samples limit cohort confidence. Overall score capped because colorectal/CRC disease context is not explicit.

Derived Classifications

  • Organism Homo sapiens Organism remains rule-derived: Homo sapiens.
  • Assay bulk RNA-seq Assay remains rule-derived: bulk RNA-seq.
  • Study design Tumor vs unmatched normal Study design remains rule-derived: Tumor vs unmatched normal.
  • Specimen/source Tissue Specimen/source remains rule-derived: Tissue.
  • Likely case group tumor sample 6 samples
  • Likely control group normal tissue 1 samples

Warnings

  • DISEASE_LABEL_UNCLEAR warning Disease or condition label could not be normalized.
  • TISSUE_TYPE_MISSING warning Tissue or cell type could not be normalized.

Intent Interpretation

  • Active intent Patient tissue tumor-vs-normal Ranks human colorectal tissue or biopsy cohorts where tumor samples can be compared with normal controls.
  • Organism expectation Homo sapiens Dataset organism is interpreted as Homo sapiens.
  • Assay expectation bulk RNA-seq Dataset assay is interpreted as bulk RNA-seq.
  • Specimen assumption patient tissue or biopsy Derived specimen/source is Tissue.
  • Control-group assumption matched normal, adjacent normal, paired normal, healthy tissue control, or otherwise normal tissue control Derived study design is Tumor vs unmatched normal; likely groups are tumor sample vs normal tissue.
  • Score caps Applied when matching conditions are present non-human datasets stay below the primary recommendation band, missing colorectal/colon/rectal/CRC context stays below the primary recommendation band, biofluid and model-system datasets cannot reach Recommended by default, microarray and secondary assays are capped unless explicitly enabled, or small cohorts are capped below high-confidence recommendations
  • Warning rules 2 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 Downgraded disease context: colorectal/GI relevance is unclear. Derived from current-intent ranking reasons and warnings.

Applied Review Decisions

No active review decisions affect this ranking.

Ranking Facts

  • Recommendation Exploratory only Dataset can inform exploration but is not strong enough for primary analysis.
  • Supporting fact Tumor vs unmatched normal · Tissue · suitability 5%. Contributed to match or upgrade evidence.
  • Supporting fact Prioritized assay: bulk RNA-seq is the active assay expectation. Contributed to match or upgrade evidence.
  • Supporting fact Downgraded disease context: colorectal/GI relevance is unclear. Contributed to match or upgrade evidence.
  • Supporting fact Processed data is available for downstream review. Contributed to match or upgrade evidence.
  • Supporting fact 2 warnings require review. Contributed to match or upgrade evidence.
  • Caution fact Disease or condition label could not be normalized. Contributed to downgrade or manual-review evidence.
  • Caution fact Tissue or cell type could not be normalized. Contributed to downgrade or manual-review evidence.
  • Caution fact Missing colorectal disease context downgraded for tumor-vs-normal tissue ranking. Contributed to downgrade or manual-review evidence.
  • Caution fact Missing or unclear metadata: Missing colorectal disease context downgraded for tumor-vs-normal tissue ranking. Contributed to downgrade or manual-review evidence.
  • Caution fact Missing or unclear metadata: Disease clarity: Disease or condition metadata was not normalized. Contributed to downgrade or manual-review evidence.
  • Caution fact Missing or unclear metadata: Tissue clarity: Tissue metadata was not normalized. Contributed to downgrade or manual-review evidence.
  • Caution fact Missing or unclear metadata: Treatment clarity: No unclear treatment split detected in the sample metadata. Contributed to downgrade or manual-review evidence.
  • Caution fact Overall score capped because comparison suitability is weak for the selected search intent. Contributed to downgrade or manual-review evidence.
  • Caution fact Overall score capped because fewer than ten samples limit cohort confidence. Contributed to downgrade or manual-review evidence.
  • Caution fact Overall score capped because colorectal/CRC disease context is not explicit. Contributed to downgrade or manual-review evidence.
  • Caution fact Downgraded disease context: colorectal/GI relevance is unclear. Contributed to downgrade or manual-review evidence.
  • Caution fact Missing or unclear metadata: Downgraded disease context: colorectal/GI relevance is unclear. Contributed to downgrade or manual-review evidence.
  • Caution fact Comparison suitability score is below the Phase 1 recommended threshold. Contributed to downgrade or manual-review evidence.

Manual Corrections

0 active

Source Evidence

4 sources

GEO

Primary source

Original dataset metadata, sample metadata, source links, and GEO data availability flags.

Dataset accession
GSE138340
Sample records
7 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
GSE138340
  • 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
GSE138340
  • 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
GSE138340
  • 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: GSE138340
dataset_title: Differential expression analysis of primary AML cells treated with AC220 vs DMSO in endothelial cell co-culture.
organism: Homo sapiens
assay_type: bulk RNA-seq
processed_data_available: true
raw_data_available: true
submission_date: 2019-10-02
last_update_date: 2021-06-21
organization_name: Fred Hutchinson Cancer Research Center
department: Clinical Research Division
public_date: 2019-10-03
experiment_types: Expression profiling by high throughput sequencing
platforms: GPL16791 Illumina HiSeq 2500 (Homo sapiens)
sub_series: Not available
bioproject: PRJNA575538
supplementary_files: TXT: GSE138340_edgeR_analysis.txt.gz
series_type: Series

Why It Matched

  • Tumor vs unmatched normal · Tissue · suitability 5%.
  • Prioritized assay: bulk RNA-seq is the active assay expectation.
  • Downgraded disease context: colorectal/GI relevance is unclear.
  • Processed data is available for downstream review.
  • 2 warnings require review.

Why It May Not Be Suitable

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

Warnings

  • warning DISEASE_LABEL_UNCLEAR Disease or condition label could not be normalized.
  • warning TISSUE_TYPE_MISSING Tissue or cell type could not be normalized.

Normalized Fields

10 fields
Field Value Source Origin Confidence Evidence Reason
assay_type bulk RNA-seq dataset GSE138340 Runtime Siftome inference GEO:dataset:GSE138340:51a66aaede621190aedb897e0f87c2fd20a51f41de9f1354ab738fcc1fccbeb6 high confidence bulk rna-seq dataset_accession: GSE138340 dataset_title: Differential expression analysis of primary AML cells treated with AC220 vs DMSO in endothelial cell co-culture. organism: Homo sapie... keyword match keyword match: bulk rna-seq
organism Homo sapiens dataset GSE138340 Runtime Siftome inference GEO:dataset:GSE138340:51a66aaede621190aedb897e0f87c2fd20a51f41de9f1354ab738fcc1fccbeb6 high confidence homo sapiens dataset_accession: GSE138340 dataset_title: Differential expression analysis of primary AML cells treated with AC220 vs DMSO in endothelial cell co-culture. organism: Homo sapie... keyword match keyword match: homo sapiens
sample_type tumor sample sample GSM4105692 Runtime Siftome inference GEO:sample:GSM4105692:91ba27deedce57fa98835aa1c56bd142ee06206f404c1dd3fa87733388511b0a low confidence tumor sample_accession: GSM4105692 sample_title: A37927_AE source_name: primary AML characteristics: tissue: hematopoietic; tumor stage: AML A37927_AE controlled vocabulary controlled vocabulary sample type match: tumor
sample_type tumor sample sample GSM4105693 Runtime Siftome inference GEO:sample:GSM4105693:4c4cb4d97ce6eda128237beb5842236171dc6f963b8a4e9dd87dcc86a82fc3d7 low confidence tumor sample_accession: GSM4105693 sample_title: A37927_DE source_name: primary AML characteristics: tissue: hematopoietic; tumor stage: AML A37927_DE controlled vocabulary controlled vocabulary sample type match: tumor
sample_type tumor sample sample GSM4105694 Runtime Siftome inference GEO:sample:GSM4105694:c2ce0d3d2245f058498f20607328aeefb2a78f2f1c43ce771941675b4298aece low confidence tumor sample_accession: GSM4105694 sample_title: A59733_AE source_name: primary AML characteristics: tissue: hematopoietic; tumor stage: AML A59733_AE controlled vocabulary controlled vocabulary sample type match: tumor
sample_type tumor sample sample GSM4105695 Runtime Siftome inference GEO:sample:GSM4105695:df5da18aae3a1fb7b8cbc759b5921fafdcd16467f63b54f4691448621d48891c low confidence tumor sample_accession: GSM4105695 sample_title: A59733_DE source_name: primary AML characteristics: tissue: hematopoietic; tumor stage: AML A59733_DE controlled vocabulary controlled vocabulary sample type match: tumor
sample_type tumor sample sample GSM4105696 Runtime Siftome inference GEO:sample:GSM4105696:2893901b0fe15f41d4d93c1922bc73600989f7e592c284b1efa8cd64e8b1e76a low confidence tumor sample_accession: GSM4105696 sample_title: AERNAB03E16 source_name: primary AML characteristics: tissue: hematopoietic; tumor stage: AML AERNAB03E16 controlled vocabulary controlled vocabulary sample type match: tumor
sample_type tumor sample sample GSM4105697 Runtime Siftome inference GEO:sample:GSM4105697:db6513c7e38d034824969e67f308ab39a6903d669d96961dc095cb6731fd3646 low confidence tumor sample_accession: GSM4105697 sample_title: DERNAB03E16 source_name: primary AML characteristics: tissue: hematopoietic; tumor stage: AML DERNAB03E16 controlled vocabulary controlled vocabulary sample type match: tumor
sample_type normal tissue sample GSM4105698 Runtime Siftome inference GEO:sample:GSM4105698:f8e0ff718833fcc7ca14286ec85e0121612f3a54d60b87536b38ae55f4e449b2 low confidence normal sample_accession: GSM4105698 sample_title: EC source_name: HUVEC characteristics: tissue: Endothelium; tumor stage: normal EC controlled vocabulary controlled vocabulary sample type match: normal
sample_type tumor sample sample GSM4105698 Runtime Siftome inference GEO:sample:GSM4105698:f8e0ff718833fcc7ca14286ec85e0121612f3a54d60b87536b38ae55f4e449b2 low confidence tumor sample_accession: GSM4105698 sample_title: EC source_name: HUVEC characteristics: tissue: Endothelium; tumor stage: normal EC controlled vocabulary controlled vocabulary sample type match: tumor

Sample Group Preview

Possible case samples

Samples currently treated as the comparison case group.

6
  • GSM4105692 A37927_AE tumor sample Case marker detected. primary AML tissue: hematopoietic; tumor stage: AML
  • GSM4105693 A37927_DE tumor sample Case marker detected. primary AML tissue: hematopoietic; tumor stage: AML
  • GSM4105694 A59733_AE tumor sample Case marker detected. primary AML tissue: hematopoietic; tumor stage: AML
  • GSM4105695 A59733_DE tumor sample Case marker detected. primary AML tissue: hematopoietic; tumor stage: AML
  • GSM4105696 AERNAB03E16 tumor sample Case marker detected. primary AML tissue: hematopoietic; tumor stage: AML
  • GSM4105697 DERNAB03E16 tumor sample Case marker detected. primary AML tissue: hematopoietic; tumor stage: AML

Possible control samples

Samples currently treated as controls or baseline.

1
  • GSM4105698 EC normal tissue Control marker detected. HUVEC tissue: Endothelium; tumor stage: normal

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

70 pts
Clarity
70%
Weight
100 pts

Sample source clarity: All samples have source metadata and clear GSE/GSM accessions. Group clarity: Rule-based grouping found both case and control samples. Disease clarity: Disease or condition metadata was not normalized. Tissue clarity: Tissue metadata was not 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

6 samples
  • GSM4105692 A37927_AE primary AML tissue: hematopoietic; tumor stage: AML
  • GSM4105693 A37927_DE primary AML tissue: hematopoietic; tumor stage: AML
  • GSM4105694 A59733_AE primary AML tissue: hematopoietic; tumor stage: AML
  • GSM4105695 A59733_DE primary AML tissue: hematopoietic; tumor stage: AML
  • GSM4105696 AERNAB03E16 primary AML tissue: hematopoietic; tumor stage: AML
  • GSM4105697 DERNAB03E16 primary AML tissue: hematopoietic; tumor stage: AML

normal tissue

1 sample
  • GSM4105698 EC HUVEC tissue: Endothelium; tumor stage: normal

Score Breakdown

50%

relevance

  • Organism normalized.
  • Assay type normalized.
5%

comparison suitability

  • Tumor and normal sample groups detected.
  • No excluded sample type flags detected.
  • Tumor/normal design boosted for colorectal tumor-vs-normal tissue triage.
  • Patient tissue or biopsy specimens boosted for tissue comparison triage.
  • Missing colorectal disease context downgraded for tumor-vs-normal tissue ranking.
70%

metadata quality

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

data availability

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

overall

  • Weighted score: 30% relevance, 30% comparison suitability, 25% metadata quality, 15% data availability.
  • Overall score capped because comparison suitability is weak for the selected search intent.
  • Overall score capped because fewer than ten samples limit cohort confidence.
  • Overall score capped because colorectal/CRC disease context is not explicit.

Sample Links

7 samples

Review Audit Trail

0 decisions

No review decisions have been stored for this dataset.