Siftome Phase 3L

GSE95277

H3.3K27M cooperates with p53 loss and Pdgfra gain in mouse embryonic neural progenitor cells to induce invasive high-grade gliomas [Human 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
2017-02-23
Last update
2019-05-15
Organization
McGill University
Department
Department of Pediatrics
Public date
2017-10-27
Experiment types
Expression profiling by high throughput sequencing
Platforms
GPL11154 Illumina HiSeq 2000 (Homo sapiens)
Series type
SubSeries
SubSeries
Not available
BioProject
PRJNA376547
Supplementary files
TXT: GSE95277_hg.raw.counts.txt.gz
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
94% 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

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

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
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 10% 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. Neurologic or brain disease context downgraded for colorectal 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 the disease context belongs outside the colorectal tissue specialization.

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 5 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 Exploratory only Dataset can inform exploration but is not strong enough for primary analysis.
  • Supporting fact Tumor vs matched normal · Tissue · suitability 10%. 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 Neurologic or brain disease context downgraded for colorectal 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 the disease context belongs outside the colorectal tissue specialization. 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
GSE95277
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
GSE95277
  • 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
GSE95277
  • 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
GSE95277
  • 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: GSE95277
dataset_title: H3.3K27M cooperates with p53 loss and Pdgfra gain in mouse embryonic neural progenitor cells to induce invasive high-grade gliomas [Human RNA-Seq]
organism: Homo sapiens
assay_type: bulk RNA-seq
processed_data_available: true
raw_data_available: true
submission_date: 2017-02-23
last_update_date: 2019-05-15
organization_name: McGill University
department: Department of Pediatrics
public_date: 2017-10-27
experiment_types: Expression profiling by high throughput sequencing
platforms: GPL11154 Illumina HiSeq 2000 (Homo sapiens)
sub_series: Not available
bioproject: PRJNA376547
supplementary_files: TXT: GSE95277_hg.raw.counts.txt.gz
series_type: SubSeries

Why It Matched

  • Tumor vs matched normal · Tissue · suitability 10%.
  • 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.
  • Neurologic or brain disease context downgraded for colorectal 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 the disease context belongs outside the colorectal tissue specialization.
  • 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

21 fields
Field Value Source Origin Confidence Evidence Reason
assay_type bulk RNA-seq dataset GSE95277 Runtime Siftome inference GEO:dataset:GSE95277:5a56cb2260634a9ccdb03f076a88a1ff41907947c528656b892535a54ef0ac7c high confidence bulk rna-seq dataset_accession: GSE95277 dataset_title: H3.3K27M cooperates with p53 loss and Pdgfra gain in mouse embryonic neural progenitor cells to induce invasive high-grade gliomas [Hu... keyword match keyword match: bulk rna-seq
normal_tissue_type adjacent normal sample GSM2501173 Runtime Siftome inference GEO:sample:GSM2501173:b402af688d2ecc090297eaf8618796b5ae0338ba115bc8ade06a5342d396f2f1 high confidence matched normal sample_accession: GSM2501173 sample_title: NB 1 source_name: matched normal brain control characteristics: subject status: pediatric brain tumor patient; tissue: normal brain; g... controlled vocabulary controlled vocabulary normal tissue type match: matched normal
normal_tissue_type adjacent normal sample GSM2501174 Runtime Siftome inference GEO:sample:GSM2501174:1eb937cb2fcc41816f2e8da5893c0e64d256e64bebe1ba6db7511e973d0833c8 high confidence matched normal sample_accession: GSM2501174 sample_title: NB 2 source_name: matched normal brain control characteristics: subject status: pediatric brain tumor patient; tissue: normal brain; g... controlled vocabulary controlled vocabulary normal tissue type match: matched normal
normal_tissue_type adjacent normal sample GSM2501175 Runtime Siftome inference GEO:sample:GSM2501175:3ff4f2774d8df87b820ceb1f3517275ca22fd3d1ea0f781be4dad4ddf9417bd2 high confidence matched normal sample_accession: GSM2501175 sample_title: NB 3 source_name: matched normal brain control characteristics: subject status: pediatric brain tumor patient; tissue: normal brain; g... controlled vocabulary controlled vocabulary normal tissue type match: matched normal
organism Homo sapiens dataset GSE95277 Runtime Siftome inference GEO:dataset:GSE95277:5a56cb2260634a9ccdb03f076a88a1ff41907947c528656b892535a54ef0ac7c high confidence homo sapiens dataset_accession: GSE95277 dataset_title: H3.3K27M cooperates with p53 loss and Pdgfra gain in mouse embryonic neural progenitor cells to induce invasive high-grade gliomas [Hu... keyword match keyword match: homo sapiens
organism Mus musculus dataset GSE95277 Runtime Siftome inference GEO:dataset:GSE95277:5a56cb2260634a9ccdb03f076a88a1ff41907947c528656b892535a54ef0ac7c high confidence mouse dataset_accession: GSE95277 dataset_title: H3.3K27M cooperates with p53 loss and Pdgfra gain in mouse embryonic neural progenitor cells to induce invasive high-grade gliomas [Hu... keyword match keyword match: mouse
sample_type normal tissue sample GSM2501173 Runtime Siftome inference GEO:sample:GSM2501173:b402af688d2ecc090297eaf8618796b5ae0338ba115bc8ade06a5342d396f2f1 low confidence normal sample_accession: GSM2501173 sample_title: NB 1 source_name: matched normal brain control characteristics: subject status: pediatric brain tumor patient; tissue: normal brain; g... controlled vocabulary controlled vocabulary sample type match: normal
sample_type tumor sample sample GSM2501173 Runtime Siftome inference GEO:sample:GSM2501173:b402af688d2ecc090297eaf8618796b5ae0338ba115bc8ade06a5342d396f2f1 low confidence tumor sample_accession: GSM2501173 sample_title: NB 1 source_name: matched normal brain control characteristics: subject status: pediatric brain tumor patient; tissue: normal brain; g... controlled vocabulary controlled vocabulary sample type match: tumor
sample_type normal tissue sample GSM2501174 Runtime Siftome inference GEO:sample:GSM2501174:1eb937cb2fcc41816f2e8da5893c0e64d256e64bebe1ba6db7511e973d0833c8 low confidence normal sample_accession: GSM2501174 sample_title: NB 2 source_name: matched normal brain control characteristics: subject status: pediatric brain tumor patient; tissue: normal brain; g... controlled vocabulary controlled vocabulary sample type match: normal
sample_type tumor sample sample GSM2501174 Runtime Siftome inference GEO:sample:GSM2501174:1eb937cb2fcc41816f2e8da5893c0e64d256e64bebe1ba6db7511e973d0833c8 low confidence tumor sample_accession: GSM2501174 sample_title: NB 2 source_name: matched normal brain control characteristics: subject status: pediatric brain tumor patient; tissue: normal brain; g... controlled vocabulary controlled vocabulary sample type match: tumor
sample_type normal tissue sample GSM2501175 Runtime Siftome inference GEO:sample:GSM2501175:3ff4f2774d8df87b820ceb1f3517275ca22fd3d1ea0f781be4dad4ddf9417bd2 low confidence normal sample_accession: GSM2501175 sample_title: NB 3 source_name: matched normal brain control characteristics: subject status: pediatric brain tumor patient; tissue: normal brain; g... controlled vocabulary controlled vocabulary sample type match: normal
sample_type tumor sample sample GSM2501175 Runtime Siftome inference GEO:sample:GSM2501175:3ff4f2774d8df87b820ceb1f3517275ca22fd3d1ea0f781be4dad4ddf9417bd2 low confidence tumor sample_accession: GSM2501175 sample_title: NB 3 source_name: matched normal brain control characteristics: subject status: pediatric brain tumor patient; tissue: normal brain; g... controlled vocabulary controlled vocabulary sample type match: tumor
sample_type tumor sample sample GSM2501176 Runtime Siftome inference GEO:sample:GSM2501176:99d1192edec79b1624b19f44966bf95c3ff9793848698413096ee6c58bd5d382 low confidence tumor sample_accession: GSM2501176 sample_title: WT pHGG 1 source_name: pHGG that are wild-type for H3.3 and TP53 characteristics: subject status: pediatric brain tumor patient; tissu... controlled vocabulary controlled vocabulary sample type match: tumor
sample_type tumor sample sample GSM2501177 Runtime Siftome inference GEO:sample:GSM2501177:1acae94d38c3f990bdd5d032dc629b39116a84e767ba5ebda60b064975b044ec low confidence tumor sample_accession: GSM2501177 sample_title: WT pHGG 2 source_name: pHGG that are wild-type for H3.3 and TP53 characteristics: subject status: pediatric brain tumor patient; tissu... controlled vocabulary controlled vocabulary sample type match: tumor
sample_type tumor sample sample GSM2501178 Runtime Siftome inference GEO:sample:GSM2501178:29ea095ad0095618e58c7c65ee0b8852f1248e510f05a89dd298cf8d721814f5 low confidence tumor sample_accession: GSM2501178 sample_title: WT pHGG 3 source_name: pHGG that are wild-type for H3.3 and TP53 characteristics: subject status: pediatric brain tumor patient; tissu... controlled vocabulary controlled vocabulary sample type match: tumor
sample_type tumor sample sample GSM2501179 Runtime Siftome inference GEO:sample:GSM2501179:c8ac0466c10bd1bec1528c2b1ce95ce39d8df277bee1a6c1d2236b9363c5b3f2 low confidence tumor sample_accession: GSM2501179 sample_title: WT pHGG 4 source_name: pHGG that are wild-type for H3.3 and TP53 characteristics: subject status: pediatric brain tumor patient; tissu... controlled vocabulary controlled vocabulary sample type match: tumor
sample_type tumor sample sample GSM2501180 Runtime Siftome inference GEO:sample:GSM2501180:960786428942e0525fc476a66e7e48edc88c8eaed6a9754a594bcbe9a37c41aa low confidence tumor sample_accession: GSM2501180 sample_title: K27M pHGG 1 source_name: pHGG with H3.3K27M and loss-of-function TP53 mutation characteristics: subject status: pediatric brain tumor ... controlled vocabulary controlled vocabulary sample type match: tumor
sample_type tumor sample sample GSM2501181 Runtime Siftome inference GEO:sample:GSM2501181:018ce82c6c5c3bae4b44c089d6a723c5aa240cb34b0151a72f4a44664e49d585 low confidence tumor sample_accession: GSM2501181 sample_title: K27M pHGG 2 source_name: pHGG with H3.3K27M and loss-of-function TP53 mutation characteristics: subject status: pediatric brain tumor ... controlled vocabulary controlled vocabulary sample type match: tumor
sample_type tumor sample sample GSM2501182 Runtime Siftome inference GEO:sample:GSM2501182:a5fc32fd8457e7b0143351cd451b525f5247ed6513ef872bf10f1e71ced80f56 low confidence tumor sample_accession: GSM2501182 sample_title: K27M pHGG 3 source_name: pHGG with H3.3K27M and loss-of-function TP53 mutation characteristics: subject status: pediatric brain tumor ... controlled vocabulary controlled vocabulary sample type match: tumor
sample_type tumor sample sample GSM2501183 Runtime Siftome inference GEO:sample:GSM2501183:fa488718f380e963563abeee13fb5ff96e5ce6c202e9512918c7dfb73b07f7d7 low confidence tumor sample_accession: GSM2501183 sample_title: K27M pHGG 4 source_name: pHGG with H3.3K27M and loss-of-function TP53 mutation characteristics: subject status: pediatric brain tumor ... controlled vocabulary controlled vocabulary sample type match: tumor
sample_type tumor sample sample GSM2501184 Runtime Siftome inference GEO:sample:GSM2501184:b8356026bc186bb269da824a04ca20b15369f1f54e767708ecde107461cdfa12 low confidence tumor sample_accession: GSM2501184 sample_title: K27M pHGG 5 source_name: pHGG with H3.3K27M and loss-of-function TP53 mutation characteristics: subject status: pediatric brain tumor ... controlled vocabulary controlled vocabulary sample type match: tumor

Sample Group Preview

Possible case samples

Samples currently treated as the comparison case group.

5
  • GSM2501180 K27M pHGG 1 tumor sample Case marker detected. pHGG with H3.3K27M and loss-of-function TP53 mutation subject status: pediatric brain tumor patient; tissue: pediatric high-grade gliomas (pHGG); genotype/variation: H3.3K27M; Tp53 mut; High Pdgfra
  • GSM2501181 K27M pHGG 2 tumor sample Case marker detected. pHGG with H3.3K27M and loss-of-function TP53 mutation subject status: pediatric brain tumor patient; tissue: pediatric high-grade gliomas (pHGG); genotype/variation: H3.3K27M; Tp53 mut; High Pdgfra
  • GSM2501182 K27M pHGG 3 tumor sample Case marker detected. pHGG with H3.3K27M and loss-of-function TP53 mutation subject status: pediatric brain tumor patient; tissue: pediatric high-grade gliomas (pHGG); genotype/variation: H3.3K27M; Tp53 mut; High Pdgfra
  • GSM2501183 K27M pHGG 4 tumor sample Case marker detected. pHGG with H3.3K27M and loss-of-function TP53 mutation subject status: pediatric brain tumor patient; tissue: pediatric high-grade gliomas (pHGG); genotype/variation: H3.3K27M; Tp53 mut; High Pdgfra
  • GSM2501184 K27M pHGG 5 tumor sample Case marker detected. pHGG with H3.3K27M and loss-of-function TP53 mutation subject status: pediatric brain tumor patient; tissue: pediatric high-grade gliomas (pHGG); genotype/variation: H3.3K27M; Tp53 mut; High Pdgfra

Possible control samples

Samples currently treated as controls or baseline.

7
  • GSM2501173 NB 1 normal tissue Control marker detected. matched normal brain control subject status: pediatric brain tumor patient; tissue: normal brain; genotype/variation: H3.3WT; Low pdgfra
  • GSM2501174 NB 2 normal tissue Control marker detected. matched normal brain control subject status: pediatric brain tumor patient; tissue: normal brain; genotype/variation: H3.3WT; Low pdgfra
  • GSM2501175 NB 3 normal tissue Control marker detected. matched normal brain control subject status: pediatric brain tumor patient; tissue: normal brain; genotype/variation: H3.3WT; Low pdgfra
  • GSM2501176 WT pHGG 1 control Control marker detected. pHGG that are wild-type for H3.3 and TP53 subject status: pediatric brain tumor patient; tissue: pediatric high-grade gliomas (pHGG); genotype/variation: H3.3WT; Low pdgfra
  • GSM2501177 WT pHGG 2 control Control marker detected. pHGG that are wild-type for H3.3 and TP53 subject status: pediatric brain tumor patient; tissue: pediatric high-grade gliomas (pHGG); genotype/variation: H3.3WT; Low pdgfra
  • GSM2501178 WT pHGG 3 control Control marker detected. pHGG that are wild-type for H3.3 and TP53 subject status: pediatric brain tumor patient; tissue: pediatric high-grade gliomas (pHGG); genotype/variation: H3.3WT; Low pdgfra
  • GSM2501179 WT pHGG 4 control Control marker detected. pHGG that are wild-type for H3.3 and TP53 subject status: pediatric brain tumor patient; tissue: pediatric high-grade gliomas (pHGG); genotype/variation: H3.3WT; Low pdgfra

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

normal tissue

3 samples
  • GSM2501173 NB 1 matched normal brain control subject status: pediatric brain tumor patient; tissue: normal brain; genotype/variation: H3.3WT; Low pdgfra
  • GSM2501174 NB 2 matched normal brain control subject status: pediatric brain tumor patient; tissue: normal brain; genotype/variation: H3.3WT; Low pdgfra
  • GSM2501175 NB 3 matched normal brain control subject status: pediatric brain tumor patient; tissue: normal brain; genotype/variation: H3.3WT; Low pdgfra

control

4 samples
  • GSM2501176 WT pHGG 1 pHGG that are wild-type for H3.3 and TP53 subject status: pediatric brain tumor patient; tissue: pediatric high-grade gliomas (pHGG); genotype/variation: H3.3WT; Low pdgfra
  • GSM2501177 WT pHGG 2 pHGG that are wild-type for H3.3 and TP53 subject status: pediatric brain tumor patient; tissue: pediatric high-grade gliomas (pHGG); genotype/variation: H3.3WT; Low pdgfra
  • GSM2501178 WT pHGG 3 pHGG that are wild-type for H3.3 and TP53 subject status: pediatric brain tumor patient; tissue: pediatric high-grade gliomas (pHGG); genotype/variation: H3.3WT; Low pdgfra
  • GSM2501179 WT pHGG 4 pHGG that are wild-type for H3.3 and TP53 subject status: pediatric brain tumor patient; tissue: pediatric high-grade gliomas (pHGG); genotype/variation: H3.3WT; Low pdgfra

tumor sample

5 samples
  • GSM2501180 K27M pHGG 1 pHGG with H3.3K27M and loss-of-function TP53 mutation subject status: pediatric brain tumor patient; tissue: pediatric high-grade gliomas (pHGG); genotype/variation: H3.3K27M; Tp53 mut; High Pdgfra
  • GSM2501181 K27M pHGG 2 pHGG with H3.3K27M and loss-of-function TP53 mutation subject status: pediatric brain tumor patient; tissue: pediatric high-grade gliomas (pHGG); genotype/variation: H3.3K27M; Tp53 mut; High Pdgfra
  • GSM2501182 K27M pHGG 3 pHGG with H3.3K27M and loss-of-function TP53 mutation subject status: pediatric brain tumor patient; tissue: pediatric high-grade gliomas (pHGG); genotype/variation: H3.3K27M; Tp53 mut; High Pdgfra
  • GSM2501183 K27M pHGG 4 pHGG with H3.3K27M and loss-of-function TP53 mutation subject status: pediatric brain tumor patient; tissue: pediatric high-grade gliomas (pHGG); genotype/variation: H3.3K27M; Tp53 mut; High Pdgfra
  • GSM2501184 K27M pHGG 5 pHGG with H3.3K27M and loss-of-function TP53 mutation subject status: pediatric brain tumor patient; tissue: pediatric high-grade gliomas (pHGG); genotype/variation: H3.3K27M; Tp53 mut; High Pdgfra

Score Breakdown

50%

relevance

  • Organism normalized.
  • Assay type normalized.
10%

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.
  • Neurologic or brain disease context downgraded for colorectal 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 the disease context belongs outside the colorectal tissue specialization.

Sample Links

12 samples

Review Audit Trail

0 decisions

No review decisions have been stored for this dataset.