Siftome Phase 3L

GSE24283

Deep transcriptional sequencing analysis of human prostate adenocarcinoma and reference 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
2010-09-22
Last update
2019-05-15
Organization
Genentech, Inc.
Department
Not available
Public date
2010-09-23
Experiment types
Expression profiling by high throughput sequencing
Platforms
GPL9052 Illumina Genome Analyzer (Homo sapiens)
Series type
SubSeries
SubSeries
Not available
BioProject
PRJNA133719
Supplementary files
Not available
Organism
Homo sapiens
Assay
bulk RNA-seq
Samples
8
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
83% 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

0/10 pts

Critical warnings must be resolved before downstream analysis.

Metadata normalization

10/10 pts

Metadata quality is high enough to support downstream handoff.

Blockers

  • 1 samples are still unassigned.
  • Critical dataset warnings must be resolved.

Next Steps

  • Resolve unassigned or review-needed samples in the grouping table.
  • Confirm excluded samples before creating the final analysis metadata file.
  • Resolve critical warnings before downstream analysis.

Analysis Preparation Checklist

3/6 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 1 unassigned samples remain.

Resolve ambiguous and unassigned samples before finalizing the contrast.

Exclusion decisions recorded

Needs review

1 samples have hard exclusion flags in the proposed grouping.

Confirm excluded samples and preserve the reason in the analysis handoff.

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.
  • Critical dataset warnings are present.

Why This Is Ranked Here

Patient tissue tumor-vs-normal
Not suitable Dataset does not meet the current suitability threshold.

Score Components

  • relevance 60% Organism normalized. Assay type normalized. Tissue metadata 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. Neurologic or brain disease context downgraded for colorectal tissue ranking. Animal sample markers downgraded because this is a human dataset ranking.
  • metadata quality 85% 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 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 fewer than ten samples limit cohort confidence. 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 3 samples
  • Likely control group normal tissue 3 samples

Warnings

  • ANIMAL_SAMPLES_IN_HUMAN_DATASET critical Animal sample markers were detected in a human dataset.
  • DISEASE_LABEL_UNCLEAR warning Disease or condition label 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 Animal sample markers were detected in a human dataset. Contributed to downgrade or manual-review evidence.
  • Caution fact Disease or condition label 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 Animal sample markers downgraded because this is a human dataset 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: 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 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
GSE24283
Sample records
8 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
GSE24283
  • 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
GSE24283
  • 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
GSE24283
  • 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: GSE24283
dataset_title: Deep transcriptional sequencing analysis of human prostate adenocarcinoma and reference samples
organism: Homo sapiens
assay_type: bulk RNA-seq
processed_data_available: true
raw_data_available: true
submission_date: 2010-09-22
last_update_date: 2019-05-15
organization_name: Genentech, Inc.
department: Not available
public_date: 2010-09-23
experiment_types: Expression profiling by high throughput sequencing
platforms: GPL9052 Illumina Genome Analyzer (Homo sapiens)
sub_series: Not available
bioproject: PRJNA133719
supplementary_files: Not available
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

  • Animal sample markers were detected in a human dataset.
  • Disease or condition label could not be normalized.
  • Neurologic or brain disease context downgraded for colorectal tissue ranking.
  • Animal sample markers downgraded because this is a human dataset ranking.
  • Missing or unclear metadata: Disease clarity: Disease or condition 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 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

  • critical ANIMAL_SAMPLES_IN_HUMAN_DATASET Animal sample markers were detected in a human dataset.
  • warning DISEASE_LABEL_UNCLEAR Disease or condition label could not be normalized.

Normalized Fields

18 fields
Field Value Source Origin Confidence Evidence Reason
assay_type bulk RNA-seq dataset GSE24283 Runtime Siftome inference GEO:dataset:GSE24283:075b267cd844947abec1db2f2048ce1ca20d2ff418ad50b7b0f635727206de1a high confidence bulk rna-seq dataset_accession: GSE24283 dataset_title: Deep transcriptional sequencing analysis of human prostate adenocarcinoma and reference samples organism: Homo sapiens assay_type: bul... keyword match keyword match: bulk rna-seq
normal_tissue_type adjacent normal sample GSM597207 Runtime Siftome inference GEO:sample:GSM597207:482867d425cd005771ea98f61c2c19b53158bd06e147eea0733c7fab71218dbb high confidence adjacent normal sample_accession: GSM597207 sample_title: SRC111976 - RNA-Seq source_name: Normal prostate characteristics: sampleID: HF-23732; organ: Prostate; subtype: Adjacent normal prostat... controlled vocabulary controlled vocabulary normal tissue type match: adjacent normal
normal_tissue_type adjacent normal sample GSM597208 Runtime Siftome inference GEO:sample:GSM597208:ed751ccff66beca7c0148629ce7e47f3fa9fe9037cdeda04e248f358601240e0 high confidence adjacent normal sample_accession: GSM597208 sample_title: SRC112036 - RNA-Seq source_name: Normal prostate characteristics: sampleID: HF-23260-(1); organ: Prostate; subtype: Adjacent normal pro... controlled vocabulary controlled vocabulary normal tissue type match: adjacent normal
normal_tissue_type adjacent normal sample GSM597209 Runtime Siftome inference GEO:sample:GSM597209:3a48891243ec586faf41377ef66b0141f9c765bbcaa9346951d251dc61e547da high confidence adjacent normal sample_accession: GSM597209 sample_title: SRC113063 - RNA-Seq source_name: Normal prostate characteristics: sampleID: HF-24127-(1); organ: Prostate; subtype: Adjacent normal pro... controlled vocabulary controlled vocabulary normal tissue type match: adjacent normal
organism Homo sapiens dataset GSE24283 Runtime Siftome inference GEO:dataset:GSE24283:075b267cd844947abec1db2f2048ce1ca20d2ff418ad50b7b0f635727206de1a high confidence homo sapiens dataset_accession: GSE24283 dataset_title: Deep transcriptional sequencing analysis of human prostate adenocarcinoma and reference samples organism: Homo sapiens assay_type: bul... keyword match keyword match: homo sapiens
sample_type tumor sample sample GSM597204 Runtime Siftome inference GEO:sample:GSM597204:19fbd92e19d42a833579e7389ef44f4edf5f78d248e817039f10c6b651b31978 medium confidence carcinoma sample_accession: GSM597204 sample_title: SRC111995 - RNA-Seq source_name: Prostate adenocarcinoma characteristics: sampleID: HF-23751-(1); organ: Prostate; subtype: Prostate ad... controlled vocabulary controlled vocabulary sample type match: carcinoma
sample_type tumor sample sample GSM597205 Runtime Siftome inference GEO:sample:GSM597205:5cbaa97bfd2b179c433fc36391fe7ac484c77846a06f310894abb830455075bc medium confidence carcinoma sample_accession: GSM597205 sample_title: SRC112038 - RNA-Seq source_name: Prostate adenocarcinoma characteristics: sampleID: HF-23261-(1); organ: Prostate; subtype: Prostate ad... controlled vocabulary controlled vocabulary sample type match: carcinoma
sample_type tumor sample sample GSM597206 Runtime Siftome inference GEO:sample:GSM597206:9cc97d9ced8e33853c159407db4b08bff97c6ed6a72df6d5a6f9c19731234bbb medium confidence carcinoma sample_accession: GSM597206 sample_title: SRC113061 - RNA-Seq source_name: Prostate adenocarcinoma characteristics: sampleID: HF-24126-(1); organ: Prostate; subtype: Prostate ad... controlled vocabulary controlled vocabulary sample type match: carcinoma
sample_type normal tissue sample GSM597207 Runtime Siftome inference GEO:sample:GSM597207:482867d425cd005771ea98f61c2c19b53158bd06e147eea0733c7fab71218dbb high confidence adjacent normal sample_accession: GSM597207 sample_title: SRC111976 - RNA-Seq source_name: Normal prostate characteristics: sampleID: HF-23732; organ: Prostate; subtype: Adjacent normal prostat... controlled vocabulary controlled vocabulary sample type match: adjacent normal
sample_type normal tissue sample GSM597208 Runtime Siftome inference GEO:sample:GSM597208:ed751ccff66beca7c0148629ce7e47f3fa9fe9037cdeda04e248f358601240e0 high confidence adjacent normal sample_accession: GSM597208 sample_title: SRC112036 - RNA-Seq source_name: Normal prostate characteristics: sampleID: HF-23260-(1); organ: Prostate; subtype: Adjacent normal pro... controlled vocabulary controlled vocabulary sample type match: adjacent normal
sample_type normal tissue sample GSM597209 Runtime Siftome inference GEO:sample:GSM597209:3a48891243ec586faf41377ef66b0141f9c765bbcaa9346951d251dc61e547da high confidence adjacent normal sample_accession: GSM597209 sample_title: SRC113063 - RNA-Seq source_name: Normal prostate characteristics: sampleID: HF-24127-(1); organ: Prostate; subtype: Adjacent normal pro... controlled vocabulary controlled vocabulary sample type match: adjacent normal
tissue prostate dataset GSE24283 Runtime Siftome inference GEO:dataset:GSE24283:075b267cd844947abec1db2f2048ce1ca20d2ff418ad50b7b0f635727206de1a low confidence prostate dataset_accession: GSE24283 dataset_title: Deep transcriptional sequencing analysis of human prostate adenocarcinoma and reference samples organism: Homo sapiens assay_type: bul... controlled vocabulary controlled vocabulary tissue match: prostate
tissue prostate sample GSM597204 Runtime Siftome inference GEO:sample:GSM597204:19fbd92e19d42a833579e7389ef44f4edf5f78d248e817039f10c6b651b31978 low confidence prostate sample_accession: GSM597204 sample_title: SRC111995 - RNA-Seq source_name: Prostate adenocarcinoma characteristics: sampleID: HF-23751-(1); organ: Prostate; subtype: Prostate ad... controlled vocabulary controlled vocabulary tissue match: prostate
tissue prostate sample GSM597205 Runtime Siftome inference GEO:sample:GSM597205:5cbaa97bfd2b179c433fc36391fe7ac484c77846a06f310894abb830455075bc low confidence prostate sample_accession: GSM597205 sample_title: SRC112038 - RNA-Seq source_name: Prostate adenocarcinoma characteristics: sampleID: HF-23261-(1); organ: Prostate; subtype: Prostate ad... controlled vocabulary controlled vocabulary tissue match: prostate
tissue prostate sample GSM597206 Runtime Siftome inference GEO:sample:GSM597206:9cc97d9ced8e33853c159407db4b08bff97c6ed6a72df6d5a6f9c19731234bbb low confidence prostate sample_accession: GSM597206 sample_title: SRC113061 - RNA-Seq source_name: Prostate adenocarcinoma characteristics: sampleID: HF-24126-(1); organ: Prostate; subtype: Prostate ad... controlled vocabulary controlled vocabulary tissue match: prostate
tissue prostate sample GSM597207 Runtime Siftome inference GEO:sample:GSM597207:482867d425cd005771ea98f61c2c19b53158bd06e147eea0733c7fab71218dbb low confidence prostate sample_accession: GSM597207 sample_title: SRC111976 - RNA-Seq source_name: Normal prostate characteristics: sampleID: HF-23732; organ: Prostate; subtype: Adjacent normal prostat... controlled vocabulary controlled vocabulary tissue match: prostate
tissue prostate sample GSM597208 Runtime Siftome inference GEO:sample:GSM597208:ed751ccff66beca7c0148629ce7e47f3fa9fe9037cdeda04e248f358601240e0 low confidence prostate sample_accession: GSM597208 sample_title: SRC112036 - RNA-Seq source_name: Normal prostate characteristics: sampleID: HF-23260-(1); organ: Prostate; subtype: Adjacent normal pro... controlled vocabulary controlled vocabulary tissue match: prostate
tissue prostate sample GSM597209 Runtime Siftome inference GEO:sample:GSM597209:3a48891243ec586faf41377ef66b0141f9c765bbcaa9346951d251dc61e547da low confidence prostate sample_accession: GSM597209 sample_title: SRC113063 - RNA-Seq source_name: Normal prostate characteristics: sampleID: HF-24127-(1); organ: Prostate; subtype: Adjacent normal pro... controlled vocabulary controlled vocabulary tissue match: prostate

Sample Group Preview

Possible case samples

Samples currently treated as the comparison case group.

3
  • GSM597204 SRC111995 - RNA-Seq tumor sample Case marker detected. Prostate adenocarcinoma sampleID: HF-23751-(1); organ: Prostate; subtype: Prostate adenocarcinoma
  • GSM597205 SRC112038 - RNA-Seq tumor sample Case marker detected. Prostate adenocarcinoma sampleID: HF-23261-(1); organ: Prostate; subtype: Prostate adenocarcinoma
  • GSM597206 SRC113061 - RNA-Seq tumor sample Case marker detected. Prostate adenocarcinoma sampleID: HF-24126-(1); organ: Prostate; subtype: Prostate adenocarcinoma

Possible control samples

Samples currently treated as controls or baseline.

3
  • GSM597207 SRC111976 - RNA-Seq normal tissue Control marker detected. Normal prostate sampleID: HF-23732; organ: Prostate; subtype: Adjacent normal prostate
  • GSM597208 SRC112036 - RNA-Seq normal tissue Control marker detected. Normal prostate sampleID: HF-23260-(1); organ: Prostate; subtype: Adjacent normal prostate
  • GSM597209 SRC113063 - RNA-Seq normal tissue Control marker detected. Normal prostate sampleID: HF-24127-(1); organ: Prostate; subtype: Adjacent normal prostate

Unassigned samples

Samples with no explicit case or control marker.

1
  • GSM597210 Brain - RNA-Seq unassigned No explicit case or control marker detected. Brain sampleID: Ambion 6050; organ: Brain; subtype: Brain reference

Excluded samples

Samples excluded from grouping by hard exclusion rules.

1
  • GSM597211 Universal reference - RNA-Seq excluded: animal sample in human dataset animal sample in human dataset: Animal sample marker detected in a human dataset. Universal reference sampleID: Stratagene 740000; organ: Multiple; subtype: Universal reference

Ambiguous samples

Samples that need manual review before trusting grouping.

0

No samples

Metadata Quality Components

Persisted metadata quality

85 pts
Clarity
85%
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 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

3 samples
  • GSM597204 SRC111995 - RNA-Seq Prostate adenocarcinoma sampleID: HF-23751-(1); organ: Prostate; subtype: Prostate adenocarcinoma
  • GSM597205 SRC112038 - RNA-Seq Prostate adenocarcinoma sampleID: HF-23261-(1); organ: Prostate; subtype: Prostate adenocarcinoma
  • GSM597206 SRC113061 - RNA-Seq Prostate adenocarcinoma sampleID: HF-24126-(1); organ: Prostate; subtype: Prostate adenocarcinoma

normal tissue

3 samples
  • GSM597207 SRC111976 - RNA-Seq Normal prostate sampleID: HF-23732; organ: Prostate; subtype: Adjacent normal prostate
  • GSM597208 SRC112036 - RNA-Seq Normal prostate sampleID: HF-23260-(1); organ: Prostate; subtype: Adjacent normal prostate
  • GSM597209 SRC113063 - RNA-Seq Normal prostate sampleID: HF-24127-(1); organ: Prostate; subtype: Adjacent normal prostate

unassigned

1 sample
  • GSM597210 Brain - RNA-Seq Brain sampleID: Ambion 6050; organ: Brain; subtype: Brain reference

excluded: animal sample in human dataset

1 sample
  • GSM597211 Universal reference - RNA-Seq Universal reference sampleID: Stratagene 740000; organ: Multiple; subtype: Universal reference

Score Breakdown

60%

relevance

  • Organism normalized.
  • Assay type normalized.
  • Tissue metadata 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.
  • Neurologic or brain disease context downgraded for colorectal tissue ranking.
  • Animal sample markers downgraded because this is a human dataset ranking.
85%

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 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 fewer than ten samples limit cohort confidence.
  • Overall score capped because the disease context belongs outside the colorectal tissue specialization.

Sample Links

8 samples

Review Audit Trail

0 decisions

No review decisions have been stored for this dataset.