Siftome Phase 3L

GSE141438

RNA-seq dataset for MPNST patient tissue samples

Not suitable Dataset does not meet the current suitability threshold.
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
2019-12-04
Last update
2021-07-22
Organization
Broad Institute of MIT and Harvard
Department
Epigenomics Program
Public date
2021-06-28
Experiment types
Expression profiling by high throughput sequencing
Platforms
GPL11154 Illumina HiSeq 2000 (Homo sapiens)
Series type
SubSeries
SubSeries
Not available
BioProject
PRJNA593503
Supplementary files
TXT: GSE141438_DEGS_MPNST-Normal.txt.gz; TAR: GSE141438_RAW.tar
Organism
Homo sapiens
Assay
bulk RNA-seq
Samples
17
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

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

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

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

  • 3 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 3 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
Not suitable Dataset does not meet the current suitability threshold.

Score Components

  • relevance 50% Organism normalized. Assay type normalized.
  • comparison suitability 0% 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. Non-colorectal cancer context downgraded for colorectal 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 34% 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 tumor/normal grouping is from a non-colorectal cancer context.

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 7 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 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 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 Not suitable Dataset does not meet the current suitability threshold.
  • Supporting fact Tumor vs matched normal · Tissue · suitability 0%. 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 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 Non-colorectal cancer context downgraded for colorectal 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 tumor/normal grouping is from a non-colorectal cancer context. 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
GSE141438
Sample records
17 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
GSE141438
  • 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
GSE141438
  • 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
GSE141438
  • 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: GSE141438
dataset_title: RNA-seq dataset for MPNST patient tissue samples
organism: Homo sapiens
assay_type: bulk RNA-seq
processed_data_available: true
raw_data_available: true
submission_date: 2019-12-04
last_update_date: 2021-07-22
organization_name: Broad Institute of MIT and Harvard
department: Epigenomics Program
public_date: 2021-06-28
experiment_types: Expression profiling by high throughput sequencing
platforms: GPL11154 Illumina HiSeq 2000 (Homo sapiens)
sub_series: Not available
bioproject: PRJNA593503
supplementary_files: TXT: GSE141438_DEGS_MPNST-Normal.txt.gz; TAR: GSE141438_RAW.tar
series_type: SubSeries

Why It Matched

  • Tumor vs matched normal · Tissue · suitability 0%.
  • Prioritized for patient tissue tumor-vs-normal triage.
  • 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.
  • Non-colorectal cancer context downgraded for colorectal 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 tumor/normal grouping is from a non-colorectal cancer context.
  • 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

23 fields
Field Value Source Origin Confidence Evidence Reason
assay_type bulk RNA-seq dataset GSE141438 Runtime Siftome inference GEO:dataset:GSE141438:a004d58800d1116397821e37ca74d15883d7d760345c2547d5fbbbdced239565 high confidence bulk rna-seq dataset_accession: GSE141438 dataset_title: RNA-seq dataset for MPNST patient tissue samples organism: Homo sapiens assay_type: bulk RNA-seq processed_data_available: true raw_d... keyword match keyword match: bulk rna-seq
normal_tissue_type adjacent normal sample GSM4202876 Runtime Siftome inference GEO:sample:GSM4202876:1f4dc077523e70ffbbe634a46fd97ced0df2ccf07e228687a5c814e47819f4a7 high confidence adjacent normal sample_accession: GSM4202876 sample_title: Sample_32N RNA-seq source_name: Adjacent Normal characteristics: tissue: Fat; genotype: PRC2 mutant; patient diagnosis: MPNST Sample_3... controlled vocabulary controlled vocabulary normal tissue type match: adjacent normal
normal_tissue_type adjacent normal sample GSM4202877 Runtime Siftome inference GEO:sample:GSM4202877:8086552f772f1972e1f961c79fcf065099be83ac6c4538307db63210a4e9c231 high confidence adjacent normal sample_accession: GSM4202877 sample_title: Sample_7BN RNA-seq source_name: Adjacent Normal characteristics: tissue: Muscle; genotype: PRC2 mutant; patient diagnosis: MPNST Sampl... controlled vocabulary controlled vocabulary normal tissue type match: adjacent normal
normal_tissue_type adjacent normal sample GSM4202878 Runtime Siftome inference GEO:sample:GSM4202878:67859cea1718828dd01b860bf9a8390a24377012bebaf0308891cd0ddbf75e45 high confidence adjacent normal sample_accession: GSM4202878 sample_title: Sample_N26 RNA-seq source_name: Adjacent Normal characteristics: tissue: Fat; genotype: PRC2 mutant; patient diagnosis: MPNST Sample_N... controlled vocabulary controlled vocabulary normal tissue type match: adjacent normal
normal_tissue_type adjacent normal sample GSM4202879 Runtime Siftome inference GEO:sample:GSM4202879:f0ef74180f2a9d31e81de026c3cf0cdf86510b8c07bcfe151e684615bbcdd8d3 high confidence adjacent normal sample_accession: GSM4202879 sample_title: Sample_N27 RNA-seq source_name: Adjacent Normal characteristics: tissue: Muscle; genotype: PRC2 mutant; patient diagnosis: MPNST Sampl... controlled vocabulary controlled vocabulary normal tissue type match: adjacent normal
normal_tissue_type adjacent normal sample GSM4202880 Runtime Siftome inference GEO:sample:GSM4202880:04d25696bc08ee556f53606e923277ac9ffc7ed68c02ddaab4393cda8558428b high confidence adjacent normal sample_accession: GSM4202880 sample_title: Sample_N3 RNA-seq source_name: Adjacent Normal characteristics: tissue: Muscle; genotype: PRC2 mutant; patient diagnosis: MPNST Sample... controlled vocabulary controlled vocabulary normal tissue type match: adjacent normal
normal_tissue_type adjacent normal sample GSM4202881 Runtime Siftome inference GEO:sample:GSM4202881:1f7a4769b50b3f87aef42fcb9f4c844d4b2d3ae138a98059eafd98a055446883 high confidence adjacent normal sample_accession: GSM4202881 sample_title: Sample_N6 RNA-seq source_name: Adjacent Normal characteristics: tissue: Muscle; genotype: PRC2 mutant; patient diagnosis: MPNST Sample... controlled vocabulary controlled vocabulary normal tissue type match: adjacent normal
normal_tissue_type adjacent normal sample GSM4202882 Runtime Siftome inference GEO:sample:GSM4202882:a334531507dc69aaf725291e5228c345e07c19cf83b4709e6594553b65182c92 high confidence adjacent normal sample_accession: GSM4202882 sample_title: Sample_N9 RNA-seq source_name: Adjacent Normal characteristics: tissue: Muscle; genotype: PRC2 mutant; patient diagnosis: MPNST Sample... controlled vocabulary controlled vocabulary normal tissue type match: adjacent normal
organism Homo sapiens dataset GSE141438 Runtime Siftome inference GEO:dataset:GSE141438:a004d58800d1116397821e37ca74d15883d7d760345c2547d5fbbbdced239565 high confidence homo sapiens dataset_accession: GSE141438 dataset_title: RNA-seq dataset for MPNST patient tissue samples organism: Homo sapiens assay_type: bulk RNA-seq processed_data_available: true raw_d... keyword match keyword match: homo sapiens
sample_type normal tissue sample GSM4202876 Runtime Siftome inference GEO:sample:GSM4202876:1f4dc077523e70ffbbe634a46fd97ced0df2ccf07e228687a5c814e47819f4a7 high confidence adjacent normal sample_accession: GSM4202876 sample_title: Sample_32N RNA-seq source_name: Adjacent Normal characteristics: tissue: Fat; genotype: PRC2 mutant; patient diagnosis: MPNST Sample_3... controlled vocabulary controlled vocabulary sample type match: adjacent normal
sample_type normal tissue sample GSM4202877 Runtime Siftome inference GEO:sample:GSM4202877:8086552f772f1972e1f961c79fcf065099be83ac6c4538307db63210a4e9c231 high confidence adjacent normal sample_accession: GSM4202877 sample_title: Sample_7BN RNA-seq source_name: Adjacent Normal characteristics: tissue: Muscle; genotype: PRC2 mutant; patient diagnosis: MPNST Sampl... controlled vocabulary controlled vocabulary sample type match: adjacent normal
sample_type normal tissue sample GSM4202878 Runtime Siftome inference GEO:sample:GSM4202878:67859cea1718828dd01b860bf9a8390a24377012bebaf0308891cd0ddbf75e45 high confidence adjacent normal sample_accession: GSM4202878 sample_title: Sample_N26 RNA-seq source_name: Adjacent Normal characteristics: tissue: Fat; genotype: PRC2 mutant; patient diagnosis: MPNST Sample_N... controlled vocabulary controlled vocabulary sample type match: adjacent normal
sample_type normal tissue sample GSM4202879 Runtime Siftome inference GEO:sample:GSM4202879:f0ef74180f2a9d31e81de026c3cf0cdf86510b8c07bcfe151e684615bbcdd8d3 high confidence adjacent normal sample_accession: GSM4202879 sample_title: Sample_N27 RNA-seq source_name: Adjacent Normal characteristics: tissue: Muscle; genotype: PRC2 mutant; patient diagnosis: MPNST Sampl... controlled vocabulary controlled vocabulary sample type match: adjacent normal
sample_type normal tissue sample GSM4202880 Runtime Siftome inference GEO:sample:GSM4202880:04d25696bc08ee556f53606e923277ac9ffc7ed68c02ddaab4393cda8558428b high confidence adjacent normal sample_accession: GSM4202880 sample_title: Sample_N3 RNA-seq source_name: Adjacent Normal characteristics: tissue: Muscle; genotype: PRC2 mutant; patient diagnosis: MPNST Sample... controlled vocabulary controlled vocabulary sample type match: adjacent normal
sample_type normal tissue sample GSM4202881 Runtime Siftome inference GEO:sample:GSM4202881:1f7a4769b50b3f87aef42fcb9f4c844d4b2d3ae138a98059eafd98a055446883 high confidence adjacent normal sample_accession: GSM4202881 sample_title: Sample_N6 RNA-seq source_name: Adjacent Normal characteristics: tissue: Muscle; genotype: PRC2 mutant; patient diagnosis: MPNST Sample... controlled vocabulary controlled vocabulary sample type match: adjacent normal
sample_type normal tissue sample GSM4202882 Runtime Siftome inference GEO:sample:GSM4202882:a334531507dc69aaf725291e5228c345e07c19cf83b4709e6594553b65182c92 high confidence adjacent normal sample_accession: GSM4202882 sample_title: Sample_N9 RNA-seq source_name: Adjacent Normal characteristics: tissue: Muscle; genotype: PRC2 mutant; patient diagnosis: MPNST Sample... controlled vocabulary controlled vocabulary sample type match: adjacent normal
sample_type tumor sample sample GSM4202883 Runtime Siftome inference GEO:sample:GSM4202883:b0c575c6f604a18b600763dcf724a50749fd1862e282c0968aa1131b6e066f35 low confidence tumor sample_accession: GSM4202883 sample_title: Sample_32T RNA-seq source_name: Tumor characteristics: tissue: MPNST; genotype: PRC2 mutant; patient diagnosis: MPNST Sample_32T RNA-seq controlled vocabulary controlled vocabulary sample type match: tumor
sample_type tumor sample sample GSM4202884 Runtime Siftome inference GEO:sample:GSM4202884:2d00b30302db3971c7e0a137222a1fbbb99b4c31c8b24e83b3718f3441421d92 low confidence tumor sample_accession: GSM4202884 sample_title: Sample_7BT RNA-seq source_name: Tumor characteristics: tissue: MPNST; genotype: PRC2 mutant; patient diagnosis: MPNST Sample_7BT RNA-seq controlled vocabulary controlled vocabulary sample type match: tumor
sample_type tumor sample sample GSM4202885 Runtime Siftome inference GEO:sample:GSM4202885:d45a60f2a0bfeeb18a612f62b2892cea52f8873185255b00fab5129f30a55a36 low confidence tumor sample_accession: GSM4202885 sample_title: Sample_T26 RNA-seq source_name: Tumor characteristics: tissue: MPNST; genotype: PRC2 mutant; patient diagnosis: MPNST Sample_T26 RNA-seq controlled vocabulary controlled vocabulary sample type match: tumor
sample_type tumor sample sample GSM4202886 Runtime Siftome inference GEO:sample:GSM4202886:0d322b9ecdd3ed479fd3e12194c83d05a14411610bc952d2f23e6e55fbe178da low confidence tumor sample_accession: GSM4202886 sample_title: Sample_T27 RNA-seq source_name: Tumor characteristics: tissue: MPNST; genotype: PRC2 mutant; patient diagnosis: MPNST Sample_T27 RNA-seq controlled vocabulary controlled vocabulary sample type match: tumor
sample_type tumor sample sample GSM4202887 Runtime Siftome inference GEO:sample:GSM4202887:164339694fb5a0184161e14ee6ff1f7198974c99b92de367c840f5b5b18a0d32 low confidence tumor sample_accession: GSM4202887 sample_title: Sample_T3 RNA-seq source_name: Tumor characteristics: tissue: MPNST; genotype: PRC2 mutant; patient diagnosis: MPNST Sample_T3 RNA-seq controlled vocabulary controlled vocabulary sample type match: tumor
sample_type tumor sample sample GSM4202888 Runtime Siftome inference GEO:sample:GSM4202888:07ab15ed1df7423303f29c6d255412261aea89ac8c0c117a88b61853789b7f12 low confidence tumor sample_accession: GSM4202888 sample_title: Sample_T6 RNA-seq source_name: Tumor characteristics: tissue: MPNST; genotype: PRC2 mutant; patient diagnosis: MPNST Sample_T6 RNA-seq controlled vocabulary controlled vocabulary sample type match: tumor
sample_type tumor sample sample GSM4202889 Runtime Siftome inference GEO:sample:GSM4202889:515df63a61a00182c5e1b7914f38de4004e36e87876d50468b380088d8e3ce45 low confidence tumor sample_accession: GSM4202889 sample_title: Sample_T9 RNA-seq source_name: Tumor characteristics: tissue: MPNST; genotype: PRC2 mutant; patient diagnosis: MPNST Sample_T9 RNA-seq controlled vocabulary controlled vocabulary sample type match: tumor

Sample Group Preview

Possible case samples

Samples currently treated as the comparison case group.

7
  • GSM4202883 Sample_32T RNA-seq tumor sample Case marker detected. Tumor tissue: MPNST; genotype: PRC2 mutant; patient diagnosis: MPNST
  • GSM4202884 Sample_7BT RNA-seq tumor sample Case marker detected. Tumor tissue: MPNST; genotype: PRC2 mutant; patient diagnosis: MPNST
  • GSM4202885 Sample_T26 RNA-seq tumor sample Case marker detected. Tumor tissue: MPNST; genotype: PRC2 mutant; patient diagnosis: MPNST
  • GSM4202886 Sample_T27 RNA-seq tumor sample Case marker detected. Tumor tissue: MPNST; genotype: PRC2 mutant; patient diagnosis: MPNST
  • GSM4202887 Sample_T3 RNA-seq tumor sample Case marker detected. Tumor tissue: MPNST; genotype: PRC2 mutant; patient diagnosis: MPNST
  • GSM4202888 Sample_T6 RNA-seq tumor sample Case marker detected. Tumor tissue: MPNST; genotype: PRC2 mutant; patient diagnosis: MPNST
  • GSM4202889 Sample_T9 RNA-seq tumor sample Case marker detected. Tumor tissue: MPNST; genotype: PRC2 mutant; patient diagnosis: MPNST

Possible control samples

Samples currently treated as controls or baseline.

7
  • GSM4202876 Sample_32N RNA-seq normal tissue Control marker detected. Adjacent Normal tissue: Fat; genotype: PRC2 mutant; patient diagnosis: MPNST
  • GSM4202877 Sample_7BN RNA-seq normal tissue Control marker detected. Adjacent Normal tissue: Muscle; genotype: PRC2 mutant; patient diagnosis: MPNST
  • GSM4202878 Sample_N26 RNA-seq normal tissue Control marker detected. Adjacent Normal tissue: Fat; genotype: PRC2 mutant; patient diagnosis: MPNST
  • GSM4202879 Sample_N27 RNA-seq normal tissue Control marker detected. Adjacent Normal tissue: Muscle; genotype: PRC2 mutant; patient diagnosis: MPNST
  • GSM4202880 Sample_N3 RNA-seq normal tissue Control marker detected. Adjacent Normal tissue: Muscle; genotype: PRC2 mutant; patient diagnosis: MPNST
  • GSM4202881 Sample_N6 RNA-seq normal tissue Control marker detected. Adjacent Normal tissue: Muscle; genotype: PRC2 mutant; patient diagnosis: MPNST
  • GSM4202882 Sample_N9 RNA-seq normal tissue Control marker detected. Adjacent Normal tissue: Muscle; genotype: PRC2 mutant; patient diagnosis: MPNST

Unassigned samples

Samples with no explicit case or control marker.

3
  • GSM5272695 Sample_31T RNA-seq unassigned No explicit case or control marker detected. Neurofibroma tissue: Neurofibroma
  • GSM5272696 Sample_NF4T RNA-seq unassigned No explicit case or control marker detected. Neurofibroma tissue: Neurofibroma
  • GSM5272697 Sample_NF5T RNA-seq unassigned No explicit case or control marker detected. Neurofibroma tissue: Neurofibroma

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

normal tissue

7 samples
  • GSM4202876 Sample_32N RNA-seq Adjacent Normal tissue: Fat; genotype: PRC2 mutant; patient diagnosis: MPNST
  • GSM4202877 Sample_7BN RNA-seq Adjacent Normal tissue: Muscle; genotype: PRC2 mutant; patient diagnosis: MPNST
  • GSM4202878 Sample_N26 RNA-seq Adjacent Normal tissue: Fat; genotype: PRC2 mutant; patient diagnosis: MPNST
  • GSM4202879 Sample_N27 RNA-seq Adjacent Normal tissue: Muscle; genotype: PRC2 mutant; patient diagnosis: MPNST
  • GSM4202880 Sample_N3 RNA-seq Adjacent Normal tissue: Muscle; genotype: PRC2 mutant; patient diagnosis: MPNST
  • GSM4202881 Sample_N6 RNA-seq Adjacent Normal tissue: Muscle; genotype: PRC2 mutant; patient diagnosis: MPNST
  • GSM4202882 Sample_N9 RNA-seq Adjacent Normal tissue: Muscle; genotype: PRC2 mutant; patient diagnosis: MPNST

tumor sample

7 samples
  • GSM4202883 Sample_32T RNA-seq Tumor tissue: MPNST; genotype: PRC2 mutant; patient diagnosis: MPNST
  • GSM4202884 Sample_7BT RNA-seq Tumor tissue: MPNST; genotype: PRC2 mutant; patient diagnosis: MPNST
  • GSM4202885 Sample_T26 RNA-seq Tumor tissue: MPNST; genotype: PRC2 mutant; patient diagnosis: MPNST
  • GSM4202886 Sample_T27 RNA-seq Tumor tissue: MPNST; genotype: PRC2 mutant; patient diagnosis: MPNST
  • GSM4202887 Sample_T3 RNA-seq Tumor tissue: MPNST; genotype: PRC2 mutant; patient diagnosis: MPNST
  • GSM4202888 Sample_T6 RNA-seq Tumor tissue: MPNST; genotype: PRC2 mutant; patient diagnosis: MPNST
  • GSM4202889 Sample_T9 RNA-seq Tumor tissue: MPNST; genotype: PRC2 mutant; patient diagnosis: MPNST

unassigned

3 samples
  • GSM5272695 Sample_31T RNA-seq Neurofibroma tissue: Neurofibroma
  • GSM5272696 Sample_NF4T RNA-seq Neurofibroma tissue: Neurofibroma
  • GSM5272697 Sample_NF5T RNA-seq Neurofibroma tissue: Neurofibroma

Score Breakdown

50%

relevance

  • Organism normalized.
  • Assay type normalized.
0%

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.
  • Non-colorectal cancer context downgraded for colorectal 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.
34%

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 tumor/normal grouping is from a non-colorectal cancer context.

Sample Links

17 samples

Review Audit Trail

0 decisions

No review decisions have been stored for this dataset.