Siftome Phase 3L

GSE80400

Small RNA sequencing of human prostate cancer 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
2016-04-18
Last update
2019-05-15
Organization
Erasmus MC
Department
Urology
Public date
2016-04-19
Experiment types
Non-coding RNA profiling by high throughput sequencing
Platforms
GPL9052 Illumina Genome Analyzer (Homo sapiens)
Series type
Series
SubSeries
Not available
BioProject
PRJNA318802
Supplementary files
TXT: GSE80400_Processed_data_matrix.txt.gz
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

12/15 pts

All non-excluded samples are assigned; excluded samples should still be confirmed.

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

  • Critical dataset warnings must be resolved.
  • Secondary RNA assay context should be analyzed separately from ordinary bulk RNA-seq.

Next Steps

  • Confirm excluded samples before creating the final analysis metadata file.
  • Resolve critical warnings before downstream analysis.

Analysis Preparation Checklist

4/6 ready

Group labels reviewed

Needs review

Siftome proposed case and control labels, but no reviewer confirmation is stored yet.

Open the sample grouping CSV and confirm group labels before analysis.

Minimum sample count met

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

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.
  • Critical dataset warnings are present.
  • Assay context may require expert handling before DESeq2-style analysis.

Why This Is Ranked Here

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

Score Components

  • relevance 100% Disease or condition metadata normalized. Organism normalized. Assay type normalized. Tissue metadata normalized.
  • comparison suitability 0% 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. Small RNA, miRNA, circRNA, or extracellular-vesicle RNA context downgraded for primary mRNA tissue ranking. Non-colorectal cancer context downgraded for colorectal tumor-vs-normal tissue ranking. Animal sample markers downgraded because this is a human dataset ranking.
  • metadata quality 100% 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 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 secondary RNA assays are not primary mRNA tissue RNA-seq. 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 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 8 samples
  • Likely control group normal tissue 2 samples

Warnings

  • ANIMAL_SAMPLES_IN_HUMAN_DATASET critical Animal sample markers were detected in a human dataset.
  • SECONDARY_ASSAY_CONTEXT warning Secondary RNA assay context such as small RNA, miRNA, circRNA, or non-coding RNA was detected.

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: not a colorectal/GI cancer cohort. 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 unmatched normal · Tissue · suitability 0%. 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: not a colorectal/GI cancer cohort. 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 Secondary RNA assay context such as small RNA, miRNA, circRNA, or non-coding RNA was detected. Contributed to downgrade or manual-review evidence.
  • Caution fact Small RNA, miRNA, circRNA, or extracellular-vesicle RNA context downgraded for primary mRNA tissue ranking. 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 Animal sample markers downgraded because this is a human dataset ranking. 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 secondary RNA assays are not primary mRNA tissue RNA-seq. 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: not a colorectal/GI cancer cohort. 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
GSE80400
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
GSE80400
  • 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
GSE80400
  • 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
GSE80400
  • 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: GSE80400
dataset_title: Small RNA sequencing of human prostate cancer samples
organism: Homo sapiens
assay_type: bulk RNA-seq
processed_data_available: true
raw_data_available: true
submission_date: 2016-04-18
last_update_date: 2019-05-15
organization_name: Erasmus MC
department: Urology
public_date: 2016-04-19
experiment_types: Non-coding RNA profiling by high throughput sequencing
platforms: GPL9052 Illumina Genome Analyzer (Homo sapiens)
sub_series: Not available
bioproject: PRJNA318802
supplementary_files: TXT: GSE80400_Processed_data_matrix.txt.gz
series_type: Series

Why It Matched

  • Tumor vs unmatched normal · Tissue · suitability 0%.
  • Prioritized assay: bulk RNA-seq is the active assay expectation.
  • Downgraded disease context: not a colorectal/GI cancer cohort.
  • 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.
  • Secondary RNA assay context such as small RNA, miRNA, circRNA, or non-coding RNA was detected.
  • Small RNA, miRNA, circRNA, or extracellular-vesicle RNA context downgraded for primary mRNA tissue ranking.
  • Non-colorectal cancer context downgraded for colorectal tumor-vs-normal tissue ranking.
  • Animal sample markers downgraded because this is a human dataset ranking.
  • 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 secondary RNA assays are not primary mRNA tissue RNA-seq.
  • Overall score capped because tumor/normal grouping is from a non-colorectal cancer context.
  • Downgraded disease context: not a colorectal/GI cancer cohort.
  • 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 SECONDARY_ASSAY_CONTEXT Secondary RNA assay context such as small RNA, miRNA, circRNA, or non-coding RNA was detected.

Normalized Fields

34 fields
Field Value Source Origin Confidence Evidence Reason
assay_type bulk RNA-seq dataset GSE80400 Runtime Siftome inference GEO:dataset:GSE80400:44cd78b579d4d74f5d3d9f060338ddeb5b3b0f5a3d9c62ce46d5394ea12c604d high confidence bulk rna-seq dataset_accession: GSE80400 dataset_title: Small RNA sequencing of human prostate cancer samples organism: Homo sapiens assay_type: bulk RNA-seq processed_data_available: true r... keyword match keyword match: bulk rna-seq
disease prostate cancer dataset GSE80400 Runtime Siftome inference GEO:dataset:GSE80400:44cd78b579d4d74f5d3d9f060338ddeb5b3b0f5a3d9c62ce46d5394ea12c604d high confidence prostate cancer dataset_accession: GSE80400 dataset_title: Small RNA sequencing of human prostate cancer samples organism: Homo sapiens assay_type: bulk RNA-seq processed_data_available: true r... controlled vocabulary controlled vocabulary disease match: prostate cancer
organism Homo sapiens dataset GSE80400 Runtime Siftome inference GEO:dataset:GSE80400:44cd78b579d4d74f5d3d9f060338ddeb5b3b0f5a3d9c62ce46d5394ea12c604d high confidence homo sapiens dataset_accession: GSE80400 dataset_title: Small RNA sequencing of human prostate cancer samples organism: Homo sapiens assay_type: bulk RNA-seq processed_data_available: true r... keyword match keyword match: homo sapiens
sample_type normal tissue sample GSM2125974 Runtime Siftome inference GEO:sample:GSM2125974:f1b2b62866bc0d179d83a0c5f69cbde6c388887f99b7eaf58285f44eb759041c low confidence normal sample_accession: GSM2125974 sample_title: Group 1 NAP source_name: prostate characteristics: organ: prostate; status: normal; source: n.a.; storage: fresh-frozen Group 1 NAP controlled vocabulary controlled vocabulary sample type match: normal
sample_type normal tissue sample GSM2125975 Runtime Siftome inference GEO:sample:GSM2125975:4b7c4f2f11e5d06e49c52eed365ba5e939acdc7e7b757272290e513640843dd1 low confidence normal sample_accession: GSM2125975 sample_title: Group 2. BPH source_name: prostate characteristics: organ: prostate; status: normal; source: n.a.; storage: fresh-frozen Group 2. BPH controlled vocabulary controlled vocabulary sample type match: normal
sample_type tumor sample sample GSM2125976 Runtime Siftome inference GEO:sample:GSM2125976:e1bdde31619c174a5f818b3e02be75f66f2814cddd84ed735eaa72c70ac17fd9 low confidence tumor sample_accession: GSM2125976 sample_title: Group 3. PCa 6 cured source_name: prostate characteristics: organ: prostate; status: tumor; source: primary tumor; storage: fresh-froz... controlled vocabulary controlled vocabulary sample type match: tumor
sample_type tumor sample sample GSM2125977 Runtime Siftome inference GEO:sample:GSM2125977:0ee445dec2ab6beb5c0ca41758baf6a9fc1a15abfcccdd4e36c411d35d73ae0a low confidence tumor sample_accession: GSM2125977 sample_title: Group 4. PCa 6 recurrent source_name: prostate characteristics: organ: prostate; status: tumor; source: primary tumor; storage: fresh-... controlled vocabulary controlled vocabulary sample type match: tumor
sample_type tumor sample sample GSM2125978 Runtime Siftome inference GEO:sample:GSM2125978:f4b074d380f25fc2fd5382e4db98128733f35167392083c7aa6e09f405ed43d7 low confidence tumor sample_accession: GSM2125978 sample_title: Group 5. PCa 7 recurrent source_name: prostate characteristics: organ: prostate; status: tumor; source: primary tumor; storage: fresh-... controlled vocabulary controlled vocabulary sample type match: tumor
sample_type tumor sample sample GSM2125979 Runtime Siftome inference GEO:sample:GSM2125979:4281266b0c18bd77cddabb7876387543c8282810b84ef2fd53af92260a50c167 low confidence tumor sample_accession: GSM2125979 sample_title: Group 6. PCa 8 recurrent source_name: prostate characteristics: organ: prostate; status: tumor; source: primary tumor; storage: fresh-... controlled vocabulary controlled vocabulary sample type match: tumor
sample_type tumor sample sample GSM2125980 Runtime Siftome inference GEO:sample:GSM2125980:9437e967e53a1390546b35bfcc188c3a2bc775bd12622115a16cc9dc51019447 low confidence tumor sample_accession: GSM2125980 sample_title: Group 7. PCa TURP hormone refractory disease source_name: prostate characteristics: organ: prostate; status: tumor; source: primary tu... controlled vocabulary controlled vocabulary sample type match: tumor
sample_type tumor sample sample GSM2125981 Runtime Siftome inference GEO:sample:GSM2125981:2e008619a6db79e635c9c26b127a38a184ec7ae7d45b05c20ec2f9d20bee5c58 low confidence tumor sample_accession: GSM2125981 sample_title: Group 8. LN-PCa source_name: lymph node characteristics: organ: lymph node; status: tumor; source: metastatic lesion; storage: fresh-f... controlled vocabulary controlled vocabulary sample type match: tumor
sample_type tumor sample sample GSM2125982 Runtime Siftome inference GEO:sample:GSM2125982:a7a4a1aa13344f68f82cd90878490d8d7a493a271d3962e5910c258cc5ddea08 low confidence tumor sample_accession: GSM2125982 sample_title: Group 9. PCa 6 recurrent no chromosomal alterations source_name: prostate characteristics: organ: prostate; status: tumor; source: pri... controlled vocabulary controlled vocabulary sample type match: tumor
sample_type tumor sample sample GSM2125983 Runtime Siftome inference GEO:sample:GSM2125983:f843cc38d371c14965f205fd5c723b6d895229fcd61eba526be5d99e7ecbe5b4 low confidence tumor sample_accession: GSM2125983 sample_title: Group 10. PCa 6 TMPRSS2-ERG fusion source_name: prostate characteristics: organ: prostate; status: tumor; source: primary tumor; stora... controlled vocabulary controlled vocabulary sample type match: tumor
sample_type tumor sample sample GSM2125984 Runtime Siftome inference GEO:sample:GSM2125984:b55c6239b50dcabe15e9aacac93174df8840868151956f345baaa1170a47ff5f low confidence tumor sample_accession: GSM2125984 sample_title: Group 11. FFPE of group 3 source_name: prostate characteristics: organ: prostate; status: tumor; source: primary tumor; storage: FFPE ... controlled vocabulary controlled vocabulary sample type match: tumor
tissue prostate dataset GSE80400 Runtime Siftome inference GEO:dataset:GSE80400:44cd78b579d4d74f5d3d9f060338ddeb5b3b0f5a3d9c62ce46d5394ea12c604d low confidence prostate dataset_accession: GSE80400 dataset_title: Small RNA sequencing of human prostate cancer samples organism: Homo sapiens assay_type: bulk RNA-seq processed_data_available: true r... controlled vocabulary controlled vocabulary tissue match: prostate
tissue prostate sample GSM2125974 Runtime Siftome inference GEO:sample:GSM2125974:f1b2b62866bc0d179d83a0c5f69cbde6c388887f99b7eaf58285f44eb759041c low confidence prostate sample_accession: GSM2125974 sample_title: Group 1 NAP source_name: prostate characteristics: organ: prostate; status: normal; source: n.a.; storage: fresh-frozen Group 1 NAP controlled vocabulary controlled vocabulary tissue match: prostate
tissue prostate sample GSM2125975 Runtime Siftome inference GEO:sample:GSM2125975:4b7c4f2f11e5d06e49c52eed365ba5e939acdc7e7b757272290e513640843dd1 low confidence prostate sample_accession: GSM2125975 sample_title: Group 2. BPH source_name: prostate characteristics: organ: prostate; status: normal; source: n.a.; storage: fresh-frozen Group 2. BPH controlled vocabulary controlled vocabulary tissue match: prostate
tissue prostate sample GSM2125976 Runtime Siftome inference GEO:sample:GSM2125976:e1bdde31619c174a5f818b3e02be75f66f2814cddd84ed735eaa72c70ac17fd9 low confidence prostate sample_accession: GSM2125976 sample_title: Group 3. PCa 6 cured source_name: prostate characteristics: organ: prostate; status: tumor; source: primary tumor; storage: fresh-froz... controlled vocabulary controlled vocabulary tissue match: prostate
tissue prostate sample GSM2125977 Runtime Siftome inference GEO:sample:GSM2125977:0ee445dec2ab6beb5c0ca41758baf6a9fc1a15abfcccdd4e36c411d35d73ae0a low confidence prostate sample_accession: GSM2125977 sample_title: Group 4. PCa 6 recurrent source_name: prostate characteristics: organ: prostate; status: tumor; source: primary tumor; storage: fresh-... controlled vocabulary controlled vocabulary tissue match: prostate
tissue prostate sample GSM2125978 Runtime Siftome inference GEO:sample:GSM2125978:f4b074d380f25fc2fd5382e4db98128733f35167392083c7aa6e09f405ed43d7 low confidence prostate sample_accession: GSM2125978 sample_title: Group 5. PCa 7 recurrent source_name: prostate characteristics: organ: prostate; status: tumor; source: primary tumor; storage: fresh-... controlled vocabulary controlled vocabulary tissue match: prostate
tissue prostate sample GSM2125979 Runtime Siftome inference GEO:sample:GSM2125979:4281266b0c18bd77cddabb7876387543c8282810b84ef2fd53af92260a50c167 low confidence prostate sample_accession: GSM2125979 sample_title: Group 6. PCa 8 recurrent source_name: prostate characteristics: organ: prostate; status: tumor; source: primary tumor; storage: fresh-... controlled vocabulary controlled vocabulary tissue match: prostate
tissue prostate sample GSM2125980 Runtime Siftome inference GEO:sample:GSM2125980:9437e967e53a1390546b35bfcc188c3a2bc775bd12622115a16cc9dc51019447 low confidence prostate sample_accession: GSM2125980 sample_title: Group 7. PCa TURP hormone refractory disease source_name: prostate characteristics: organ: prostate; status: tumor; source: primary tu... controlled vocabulary controlled vocabulary tissue match: prostate
tissue prostate sample GSM2125982 Runtime Siftome inference GEO:sample:GSM2125982:a7a4a1aa13344f68f82cd90878490d8d7a493a271d3962e5910c258cc5ddea08 low confidence prostate sample_accession: GSM2125982 sample_title: Group 9. PCa 6 recurrent no chromosomal alterations source_name: prostate characteristics: organ: prostate; status: tumor; source: pri... controlled vocabulary controlled vocabulary tissue match: prostate
tissue prostate sample GSM2125983 Runtime Siftome inference GEO:sample:GSM2125983:f843cc38d371c14965f205fd5c723b6d895229fcd61eba526be5d99e7ecbe5b4 low confidence prostate sample_accession: GSM2125983 sample_title: Group 10. PCa 6 TMPRSS2-ERG fusion source_name: prostate characteristics: organ: prostate; status: tumor; source: primary tumor; stora... controlled vocabulary controlled vocabulary tissue match: prostate
tissue prostate sample GSM2125984 Runtime Siftome inference GEO:sample:GSM2125984:b55c6239b50dcabe15e9aacac93174df8840868151956f345baaa1170a47ff5f low confidence prostate sample_accession: GSM2125984 sample_title: Group 11. FFPE of group 3 source_name: prostate characteristics: organ: prostate; status: tumor; source: primary tumor; storage: FFPE ... controlled vocabulary controlled vocabulary tissue match: prostate
tumor_type primary tumor sample GSM2125976 Runtime Siftome inference GEO:sample:GSM2125976:e1bdde31619c174a5f818b3e02be75f66f2814cddd84ed735eaa72c70ac17fd9 high confidence primary tumor sample_accession: GSM2125976 sample_title: Group 3. PCa 6 cured source_name: prostate characteristics: organ: prostate; status: tumor; source: primary tumor; storage: fresh-froz... controlled vocabulary controlled vocabulary tumor type match: primary tumor
tumor_type primary tumor sample GSM2125977 Runtime Siftome inference GEO:sample:GSM2125977:0ee445dec2ab6beb5c0ca41758baf6a9fc1a15abfcccdd4e36c411d35d73ae0a high confidence primary tumor sample_accession: GSM2125977 sample_title: Group 4. PCa 6 recurrent source_name: prostate characteristics: organ: prostate; status: tumor; source: primary tumor; storage: fresh-... controlled vocabulary controlled vocabulary tumor type match: primary tumor
tumor_type primary tumor sample GSM2125978 Runtime Siftome inference GEO:sample:GSM2125978:f4b074d380f25fc2fd5382e4db98128733f35167392083c7aa6e09f405ed43d7 high confidence primary tumor sample_accession: GSM2125978 sample_title: Group 5. PCa 7 recurrent source_name: prostate characteristics: organ: prostate; status: tumor; source: primary tumor; storage: fresh-... controlled vocabulary controlled vocabulary tumor type match: primary tumor
tumor_type primary tumor sample GSM2125979 Runtime Siftome inference GEO:sample:GSM2125979:4281266b0c18bd77cddabb7876387543c8282810b84ef2fd53af92260a50c167 high confidence primary tumor sample_accession: GSM2125979 sample_title: Group 6. PCa 8 recurrent source_name: prostate characteristics: organ: prostate; status: tumor; source: primary tumor; storage: fresh-... controlled vocabulary controlled vocabulary tumor type match: primary tumor
tumor_type primary tumor sample GSM2125980 Runtime Siftome inference GEO:sample:GSM2125980:9437e967e53a1390546b35bfcc188c3a2bc775bd12622115a16cc9dc51019447 high confidence primary tumor sample_accession: GSM2125980 sample_title: Group 7. PCa TURP hormone refractory disease source_name: prostate characteristics: organ: prostate; status: tumor; source: primary tu... controlled vocabulary controlled vocabulary tumor type match: primary tumor
tumor_type metastatic tumor sample GSM2125981 Runtime Siftome inference GEO:sample:GSM2125981:2e008619a6db79e635c9c26b127a38a184ec7ae7d45b05c20ec2f9d20bee5c58 high confidence metastatic lesion sample_accession: GSM2125981 sample_title: Group 8. LN-PCa source_name: lymph node characteristics: organ: lymph node; status: tumor; source: metastatic lesion; storage: fresh-f... controlled vocabulary controlled vocabulary tumor type match: metastatic lesion
tumor_type primary tumor sample GSM2125982 Runtime Siftome inference GEO:sample:GSM2125982:a7a4a1aa13344f68f82cd90878490d8d7a493a271d3962e5910c258cc5ddea08 high confidence primary tumor sample_accession: GSM2125982 sample_title: Group 9. PCa 6 recurrent no chromosomal alterations source_name: prostate characteristics: organ: prostate; status: tumor; source: pri... controlled vocabulary controlled vocabulary tumor type match: primary tumor
tumor_type primary tumor sample GSM2125983 Runtime Siftome inference GEO:sample:GSM2125983:f843cc38d371c14965f205fd5c723b6d895229fcd61eba526be5d99e7ecbe5b4 high confidence primary tumor sample_accession: GSM2125983 sample_title: Group 10. PCa 6 TMPRSS2-ERG fusion source_name: prostate characteristics: organ: prostate; status: tumor; source: primary tumor; stora... controlled vocabulary controlled vocabulary tumor type match: primary tumor
tumor_type primary tumor sample GSM2125984 Runtime Siftome inference GEO:sample:GSM2125984:b55c6239b50dcabe15e9aacac93174df8840868151956f345baaa1170a47ff5f high confidence primary tumor sample_accession: GSM2125984 sample_title: Group 11. FFPE of group 3 source_name: prostate characteristics: organ: prostate; status: tumor; source: primary tumor; storage: FFPE ... controlled vocabulary controlled vocabulary tumor type match: primary tumor

Sample Group Preview

Possible case samples

Samples currently treated as the comparison case group.

8
  • GSM2125976 Group 3. PCa 6 cured tumor sample Case marker detected. prostate organ: prostate; status: tumor; source: primary tumor; storage: fresh-frozen
  • GSM2125977 Group 4. PCa 6 recurrent tumor sample Case marker detected. prostate organ: prostate; status: tumor; source: primary tumor; storage: fresh-frozen
  • GSM2125978 Group 5. PCa 7 recurrent tumor sample Case marker detected. prostate organ: prostate; status: tumor; source: primary tumor; storage: fresh-frozen
  • GSM2125979 Group 6. PCa 8 recurrent tumor sample Case marker detected. prostate organ: prostate; status: tumor; source: primary tumor; storage: fresh-frozen
  • GSM2125980 Group 7. PCa TURP hormone refractory disease tumor sample Case marker detected. prostate organ: prostate; status: tumor; source: primary tumor; storage: fresh-frozen
  • GSM2125981 Group 8. LN-PCa tumor sample Case marker detected. lymph node organ: lymph node; status: tumor; source: metastatic lesion; storage: fresh-frozen
  • GSM2125983 Group 10. PCa 6 TMPRSS2-ERG fusion tumor sample Case marker detected. prostate organ: prostate; status: tumor; source: primary tumor; storage: fresh-frozen
  • GSM2125984 Group 11. FFPE of group 3 tumor sample Case marker detected. prostate organ: prostate; status: tumor; source: primary tumor; storage: FFPE

Possible control samples

Samples currently treated as controls or baseline.

2
  • GSM2125974 Group 1 NAP normal tissue Control marker detected. prostate organ: prostate; status: normal; source: n.a.; storage: fresh-frozen
  • GSM2125975 Group 2. BPH normal tissue Control marker detected. prostate organ: prostate; status: normal; source: n.a.; storage: fresh-frozen

Unassigned samples

Samples with no explicit case or control marker.

0

No samples

Excluded samples

Samples excluded from grouping by hard exclusion rules.

1
  • GSM2125982 Group 9. PCa 6 recurrent no chromosomal alterations excluded: animal sample in human dataset animal sample in human dataset: Animal sample marker detected in a human dataset. prostate organ: prostate; status: tumor; source: primary tumor; storage: fresh-frozen

Ambiguous samples

Samples that need manual review before trusting grouping.

0

No samples

Metadata Quality Components

Persisted metadata quality

100 pts
Clarity
100%
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 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

normal tissue

2 samples
  • GSM2125974 Group 1 NAP prostate organ: prostate; status: normal; source: n.a.; storage: fresh-frozen
  • GSM2125975 Group 2. BPH prostate organ: prostate; status: normal; source: n.a.; storage: fresh-frozen

tumor sample

8 samples
  • GSM2125976 Group 3. PCa 6 cured prostate organ: prostate; status: tumor; source: primary tumor; storage: fresh-frozen
  • GSM2125977 Group 4. PCa 6 recurrent prostate organ: prostate; status: tumor; source: primary tumor; storage: fresh-frozen
  • GSM2125978 Group 5. PCa 7 recurrent prostate organ: prostate; status: tumor; source: primary tumor; storage: fresh-frozen
  • GSM2125979 Group 6. PCa 8 recurrent prostate organ: prostate; status: tumor; source: primary tumor; storage: fresh-frozen
  • GSM2125980 Group 7. PCa TURP hormone refractory disease prostate organ: prostate; status: tumor; source: primary tumor; storage: fresh-frozen
  • GSM2125981 Group 8. LN-PCa lymph node organ: lymph node; status: tumor; source: metastatic lesion; storage: fresh-frozen
  • GSM2125983 Group 10. PCa 6 TMPRSS2-ERG fusion prostate organ: prostate; status: tumor; source: primary tumor; storage: fresh-frozen
  • GSM2125984 Group 11. FFPE of group 3 prostate organ: prostate; status: tumor; source: primary tumor; storage: FFPE

excluded: animal sample in human dataset

1 sample
  • GSM2125982 Group 9. PCa 6 recurrent no chromosomal alterations prostate organ: prostate; status: tumor; source: primary tumor; storage: fresh-frozen

Score Breakdown

100%

relevance

  • Disease or condition metadata normalized.
  • Organism normalized.
  • Assay type normalized.
  • Tissue metadata normalized.
0%

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.
  • Small RNA, miRNA, circRNA, or extracellular-vesicle RNA context downgraded for primary mRNA tissue ranking.
  • Non-colorectal cancer context downgraded for colorectal tumor-vs-normal tissue ranking.
  • Animal sample markers downgraded because this is a human dataset ranking.
100%

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 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 secondary RNA assays are not primary mRNA tissue RNA-seq.
  • Overall score capped because tumor/normal grouping is from a non-colorectal cancer context.

Sample Links

11 samples

Review Audit Trail

0 decisions

No review decisions have been stored for this dataset.