Siftome Phase 3L

GSE205457

Expression data from chordoma and notochord (RNA-Seq)

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
2022-06-03
Last update
2023-02-09
Organization
Massachusetts General Hospital
Department
Center for Computational and Integrative Biology
Public date
2023-02-07
Experiment types
Expression profiling by high throughput sequencing
Platforms
GPL9115 Illumina Genome Analyzer II (Homo sapiens)
Series type
SubSeries
SubSeries
Not available
BioProject
PRJNA845775
Supplementary files
TAR: GSE205457_RAW.tar
Organism
Homo sapiens
Assay
bulk RNA-seq
Samples
11
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
87% 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

8/15 pts

A small number of samples remain unassigned.

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

  • 2 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 2 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
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 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 3 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 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
GSE205457
Sample records
11 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
GSE205457
  • 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
GSE205457
  • 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
GSE205457
  • 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: GSE205457
dataset_title: Expression data from chordoma and notochord (RNA-Seq)
organism: Homo sapiens
assay_type: bulk RNA-seq
processed_data_available: true
raw_data_available: true
submission_date: 2022-06-03
last_update_date: 2023-02-09
organization_name: Massachusetts General Hospital
department: Center for Computational and Integrative Biology
public_date: 2023-02-07
experiment_types: Expression profiling by high throughput sequencing
platforms: GPL9115 Illumina Genome Analyzer II (Homo sapiens)
sub_series: Not available
bioproject: PRJNA845775
supplementary_files: TAR: GSE205457_RAW.tar
series_type: SubSeries

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 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

11 fields
Field Value Source Origin Confidence Evidence Reason
assay_type bulk RNA-seq dataset GSE205457 Runtime Siftome inference GEO:dataset:GSE205457:50b44cf56fb09dbf657e71f8b1a3e2c37551ffb2da53c8252f1ca1f36ded4c39 high confidence bulk rna-seq dataset_accession: GSE205457 dataset_title: Expression data from chordoma and notochord (RNA-Seq) organism: Homo sapiens assay_type: bulk RNA-seq processed_data_available: true ... keyword match keyword match: bulk rna-seq
organism Homo sapiens dataset GSE205457 Runtime Siftome inference GEO:dataset:GSE205457:50b44cf56fb09dbf657e71f8b1a3e2c37551ffb2da53c8252f1ca1f36ded4c39 high confidence homo sapiens dataset_accession: GSE205457 dataset_title: Expression data from chordoma and notochord (RNA-Seq) organism: Homo sapiens assay_type: bulk RNA-seq processed_data_available: true ... keyword match keyword match: homo sapiens
sample_type tumor sample sample GSM6213097 Runtime Siftome inference GEO:sample:GSM6213097:6c8ccdeaa48ebc139bdf2be21fcad8ee9d87e6aefd9d6d307a5cf46b235355f7 low confidence tumor sample_accession: GSM6213097 sample_title: Chordoma Sample 10 source_name: Chordoma characteristics: tissue: Chordoma; cell type: Tumor Chordoma Sample 10 controlled vocabulary controlled vocabulary sample type match: tumor
sample_type tumor sample sample GSM6213098 Runtime Siftome inference GEO:sample:GSM6213098:7afa3eadf5959c2b8412406d07d0cd269cdb7256b46fe710394fd41aa9f9c00e low confidence tumor sample_accession: GSM6213098 sample_title: Chordoma Sample 11 source_name: Chordoma characteristics: tissue: Chordoma; cell type: Tumor Chordoma Sample 11 controlled vocabulary controlled vocabulary sample type match: tumor
sample_type tumor sample sample GSM6213099 Runtime Siftome inference GEO:sample:GSM6213099:4d1c5f8eecaa4012ee4dbdd0fe300aa82818a0a8f2688f350f36c65fe218b041 low confidence tumor sample_accession: GSM6213099 sample_title: Chordoma Sample 1 source_name: Chordoma characteristics: tissue: Chordoma; cell type: Tumor Chordoma Sample 1 controlled vocabulary controlled vocabulary sample type match: tumor
sample_type tumor sample sample GSM6213100 Runtime Siftome inference GEO:sample:GSM6213100:05009a7c4fb381f31e619b961a1abcc1d6e445e67879b4de6933cc861161826f low confidence tumor sample_accession: GSM6213100 sample_title: Chordoma Sample 3 source_name: Chordoma characteristics: tissue: Chordoma; cell type: Tumor Chordoma Sample 3 controlled vocabulary controlled vocabulary sample type match: tumor
sample_type tumor sample sample GSM6213101 Runtime Siftome inference GEO:sample:GSM6213101:7665c397522e963958b322eb58f60f7e436236b8f360134b691f98bb89133607 low confidence tumor sample_accession: GSM6213101 sample_title: Chordoma Sample 4 source_name: Chordoma characteristics: tissue: Chordoma; cell type: Tumor Chordoma Sample 4 controlled vocabulary controlled vocabulary sample type match: tumor
sample_type tumor sample sample GSM6213102 Runtime Siftome inference GEO:sample:GSM6213102:e3bdc32ede397be569694c864d0eef06ef8d271c34eaf204710b1ebd62f74120 low confidence tumor sample_accession: GSM6213102 sample_title: Chordoma Sample 98 source_name: Chordoma characteristics: tissue: Chordoma; cell type: Tumor Chordoma Sample 98 controlled vocabulary controlled vocabulary sample type match: tumor
sample_type normal tissue sample GSM6213103 Runtime Siftome inference GEO:sample:GSM6213103:9172b8fff163f2faceaba2cce5515f29bae9c1685f7750ad43aaff7ab142cfaa low confidence normal sample_accession: GSM6213103 sample_title: Notochord Sample 1 source_name: Notochord characteristics: tissue: Notochord; cell type: Normal Tissue Notochord Sample 1 controlled vocabulary controlled vocabulary sample type match: normal
sample_type normal tissue sample GSM6213104 Runtime Siftome inference GEO:sample:GSM6213104:1158d87dc2b7347421902035ed60341d6de7c4d6cbfc165d9e427f3682dc9ddb low confidence normal sample_accession: GSM6213104 sample_title: Notochord Sample 2 source_name: Notochord characteristics: tissue: Notochord; cell type: Normal Tissue Notochord Sample 2 controlled vocabulary controlled vocabulary sample type match: normal
sample_type normal tissue sample GSM6213105 Runtime Siftome inference GEO:sample:GSM6213105:dde0a9130b49aa5d2bc7639b14cb796f8ccc0b13f067938c57b4bfbef9eed424 low confidence normal sample_accession: GSM6213105 sample_title: Notochord Sample 3 source_name: Notochord characteristics: tissue: Notochord; cell type: Normal Tissue Notochord Sample 3 controlled vocabulary controlled vocabulary sample type match: normal

Sample Group Preview

Possible case samples

Samples currently treated as the comparison case group.

6
  • GSM6213097 Chordoma Sample 10 tumor sample Case marker detected. Chordoma tissue: Chordoma; cell type: Tumor
  • GSM6213098 Chordoma Sample 11 tumor sample Case marker detected. Chordoma tissue: Chordoma; cell type: Tumor
  • GSM6213099 Chordoma Sample 1 tumor sample Case marker detected. Chordoma tissue: Chordoma; cell type: Tumor
  • GSM6213100 Chordoma Sample 3 tumor sample Case marker detected. Chordoma tissue: Chordoma; cell type: Tumor
  • GSM6213101 Chordoma Sample 4 tumor sample Case marker detected. Chordoma tissue: Chordoma; cell type: Tumor
  • GSM6213102 Chordoma Sample 98 tumor sample Case marker detected. Chordoma tissue: Chordoma; cell type: Tumor

Possible control samples

Samples currently treated as controls or baseline.

3
  • GSM6213103 Notochord Sample 1 normal tissue Control marker detected. Notochord tissue: Notochord; cell type: Normal Tissue
  • GSM6213104 Notochord Sample 2 normal tissue Control marker detected. Notochord tissue: Notochord; cell type: Normal Tissue
  • GSM6213105 Notochord Sample 3 normal tissue Control marker detected. Notochord tissue: Notochord; cell type: Normal Tissue

Unassigned samples

Samples with no explicit case or control marker.

2
  • GSM6213106 Nugen Control 1 unassigned No explicit case or control marker detected. Nugen Total RNA Control tissue: Nugen Total RNA Control
  • GSM6213107 Nugen Control 2 unassigned No explicit case or control marker detected. Nugen Total RNA Control tissue: Nugen Total RNA Control

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
  • GSM6213097 Chordoma Sample 10 Chordoma tissue: Chordoma; cell type: Tumor
  • GSM6213098 Chordoma Sample 11 Chordoma tissue: Chordoma; cell type: Tumor
  • GSM6213099 Chordoma Sample 1 Chordoma tissue: Chordoma; cell type: Tumor
  • GSM6213100 Chordoma Sample 3 Chordoma tissue: Chordoma; cell type: Tumor
  • GSM6213101 Chordoma Sample 4 Chordoma tissue: Chordoma; cell type: Tumor
  • GSM6213102 Chordoma Sample 98 Chordoma tissue: Chordoma; cell type: Tumor

normal tissue

3 samples
  • GSM6213103 Notochord Sample 1 Notochord tissue: Notochord; cell type: Normal Tissue
  • GSM6213104 Notochord Sample 2 Notochord tissue: Notochord; cell type: Normal Tissue
  • GSM6213105 Notochord Sample 3 Notochord tissue: Notochord; cell type: Normal Tissue

unassigned

2 samples
  • GSM6213106 Nugen Control 1 Nugen Total RNA Control tissue: Nugen Total RNA Control
  • GSM6213107 Nugen Control 2 Nugen Total RNA Control tissue: Nugen Total RNA Control

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 colorectal/CRC disease context is not explicit.

Sample Links

11 samples

Review Audit Trail

0 decisions

No review decisions have been stored for this dataset.