Siftome Phase 3L

GSE118206

Reprogramming normal human epithelial tissues to a common, lethal neuroendocrine cancer lineage (RNA-seq)

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
2018-08-07
Last update
2022-02-14
Organization
UCLA
Department
MIMG
Public date
2018-10-05
Experiment types
Expression profiling by high throughput sequencing
Platforms
GPL21290 Illumina HiSeq 3000 (Homo sapiens)
Series type
SubSeries
SubSeries
Not available
BioProject
PRJNA484869
Supplementary files
TAR: GSE118206_RAW.tar
Organism
Homo sapiens
Assay
bulk RNA-seq
Samples
36
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
88% DE readiness

Contrast completeness

25/25 pts

Both case and control groups are present in the proposed grouping.

Minimum group size

20/20 pts

Each contrast group has at least 2 samples.

Processed data availability

20/20 pts

Processed data is marked available in the GEO index.

Sample decision clarity

3/15 pts

Unassigned or review-needed samples remain before analysis.

Blocking warnings

10/10 pts

No dataset warnings are present.

Metadata normalization

10/10 pts

Metadata quality is high enough to support downstream handoff.

Blockers

  • 24 samples are still unassigned.

Next Steps

  • Resolve unassigned or review-needed samples in the grouping table.

Analysis Preparation Checklist

4/6 ready

Group labels reviewed

Needs review

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

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

Minimum sample count met

Ready

Both groups meet the minimum of 2 samples.

Confirm whether the cohort is large enough for the intended statistical analysis.

Processed counts available

Ready

Processed data availability is marked true in the GEO index.

Verify that downloaded processed files contain usable count or expression identifiers.

Ambiguous samples handled

Needs review

0 review-needed samples and 24 unassigned samples remain.

Resolve ambiguous and unassigned samples before finalizing the contrast.

Exclusion decisions recorded

Ready

No hard-excluded samples were detected by the current rules.

Record any manual exclusions in the downstream analysis notes.

Source links preserved

Ready

The dataset and sample accessions can be linked back to GEO.

Keep GEO dataset and sample links with exported metadata.

Bioinformatician Review

Bioinformatician review required

Ask a bioinformatician to review grouping, count availability, exclusions, and design before DE.

  • Analysis readiness has blockers that must be resolved before DE.
  • One or more samples are unassigned and need manual grouping decisions.

Why This Is Ranked Here

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

Score Components

  • relevance 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. Non-colorectal cancer context downgraded for colorectal tumor-vs-normal tissue 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 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 6 samples
  • Likely control group normal tissue 6 samples

Warnings

No ranking warnings are active.

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 0 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.
  • Caution fact Non-colorectal cancer context downgraded for colorectal tumor-vs-normal tissue ranking. Contributed to downgrade or manual-review evidence.
  • Caution fact Missing or unclear metadata: Treatment clarity: No unclear treatment split detected in the sample metadata. Contributed to downgrade or manual-review evidence.
  • Caution fact Overall score capped because comparison suitability is weak for the selected search intent. Contributed to downgrade or manual-review evidence.
  • Caution fact Overall score capped because tumor/normal grouping is from a non-colorectal cancer context. Contributed to downgrade or manual-review evidence.
  • Caution fact Downgraded disease context: 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
GSE118206
Sample records
36 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
GSE118206
  • 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
GSE118206
  • 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
GSE118206
  • 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: GSE118206
dataset_title: Reprogramming normal human epithelial tissues to a common, lethal neuroendocrine cancer lineage (RNA-seq)
organism: Homo sapiens
assay_type: bulk RNA-seq
processed_data_available: true
raw_data_available: true
submission_date: 2018-08-07
last_update_date: 2022-02-14
organization_name: UCLA
department: MIMG
public_date: 2018-10-05
experiment_types: Expression profiling by high throughput sequencing
platforms: GPL21290 Illumina HiSeq 3000 (Homo sapiens)
sub_series: Not available
bioproject: PRJNA484869
supplementary_files: TAR: GSE118206_RAW.tar
series_type: SubSeries

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.

Why It May Not Be Suitable

  • Non-colorectal cancer context downgraded for colorectal tumor-vs-normal tissue 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 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

No warnings

Normalized Fields

50 fields
Field Value Source Origin Confidence Evidence Reason
assay_type bulk RNA-seq dataset GSE118206 Runtime Siftome inference GEO:dataset:GSE118206:64b4f0dbc4bdf1e4d31111f8700c55e13428fe8bba52ef4e4fa7137348532c41 high confidence bulk rna-seq dataset_accession: GSE118206 dataset_title: Reprogramming normal human epithelial tissues to a common, lethal neuroendocrine cancer lineage (RNA-seq) organism: Homo sapiens assa... keyword match keyword match: bulk rna-seq
disease prostate cancer sample GSM3321043 Runtime Siftome inference GEO:sample:GSM3321043:be97ed479c8aab522f9d98dda8758a6bcc6d6fc31bb7b70150c5623893c85666 high confidence prostate cancer sample_accession: GSM3321043 sample_title: prostate: MSKCC-EF1 RNA-seq source_name: prostate characteristics: tissue: prostate; cell type: small cell prostate cancer; transplant... controlled vocabulary controlled vocabulary disease match: prostate cancer
disease prostate cancer sample GSM3321044 Runtime Siftome inference GEO:sample:GSM3321044:ce1401fcea7a11cbc6efc92a719d8e242b9a0587bcf3dbdd677684368eaa9b64 high confidence prostate cancer sample_accession: GSM3321044 sample_title: prostate: NCI-H660 RNA-seq source_name: prostate characteristics: tissue: prostate; cell type: small cell prostate cancer; transplant:... controlled vocabulary controlled vocabulary disease match: prostate cancer
organism Homo sapiens dataset GSE118206 Runtime Siftome inference GEO:dataset:GSE118206:64b4f0dbc4bdf1e4d31111f8700c55e13428fe8bba52ef4e4fa7137348532c41 high confidence homo sapiens dataset_accession: GSE118206 dataset_title: Reprogramming normal human epithelial tissues to a common, lethal neuroendocrine cancer lineage (RNA-seq) organism: Homo sapiens assa... keyword match keyword match: homo sapiens
sample_type normal tissue sample GSM3321022 Runtime Siftome inference GEO:sample:GSM3321022:016b6ceb8ec4d5bb5282a68b6f102159787f5e26b2ff0668c5938485b25408fb low confidence normal sample_accession: GSM3321022 sample_title: prostate: Basal1 RNA-seq source_name: prostate characteristics: tissue: prostate; cell type: normal prostate basal epithelial; transpl... controlled vocabulary controlled vocabulary sample type match: normal
sample_type normal tissue sample GSM3321023 Runtime Siftome inference GEO:sample:GSM3321023:0ac79ca49b1d7619cc21adef2a6b6fcaa88fb0af13ac129619f772f6c9493cce low confidence normal sample_accession: GSM3321023 sample_title: prostate: Basal2 RNA-seq source_name: prostate characteristics: tissue: prostate; cell type: normal prostate basal epithelial; transpl... controlled vocabulary controlled vocabulary sample type match: normal
sample_type normal tissue sample GSM3321024 Runtime Siftome inference GEO:sample:GSM3321024:51e0dd352dd2909f73385890bfae27ed79a78c0d76f0d5bcddd198fe040ff2f6 low confidence normal sample_accession: GSM3321024 sample_title: prostate: Basal3 RNA-seq source_name: prostate characteristics: tissue: prostate; cell type: normal prostate basal epithelial; transpl... controlled vocabulary controlled vocabulary sample type match: normal
sample_type normal tissue sample GSM3321025 Runtime Siftome inference GEO:sample:GSM3321025:41e0713bbd6a36da5094628ba053c05549952c9c1d276dc0d3c94b54aef3f164 low confidence normal sample_accession: GSM3321025 sample_title: lung: NHBE1 RNA-seq source_name: lung characteristics: tissue: lung; cell type: normal bronchial epithelial; transplant: N/A lung: NHB... controlled vocabulary controlled vocabulary sample type match: normal
sample_type normal tissue sample GSM3321026 Runtime Siftome inference GEO:sample:GSM3321026:0249c0dd8ba87de50ec637db4579d76ecd6afb8c36f67ad9d8be46d902de72ae low confidence normal sample_accession: GSM3321026 sample_title: lung: NHBE4 RNA-seq source_name: lung characteristics: tissue: lung; cell type: normal bronchial epithelial; transplant: N/A lung: NHB... controlled vocabulary controlled vocabulary sample type match: normal
sample_type normal tissue sample GSM3321027 Runtime Siftome inference GEO:sample:GSM3321027:f779a6c90f5210d76e4ade8240ad0366de565017afeca6c4aa9db3d1daaaf89e low confidence normal sample_accession: GSM3321027 sample_title: lung: NHBE5 RNA-seq source_name: lung characteristics: tissue: lung; cell type: normal bronchial epithelial; transplant: N/A lung: NHB... controlled vocabulary controlled vocabulary sample type match: normal
sample_type tumor sample sample GSM3321039 Runtime Siftome inference GEO:sample:GSM3321039:7294347d3a7063728bb4d7acae2f5589a5c00e5e035d5bca12256f9390f1df4c medium confidence carcinoma sample_accession: GSM3321039 sample_title: prostate: 22RV1 RNA-seq source_name: prostate characteristics: tissue: prostate; cell type: prostate adenocarcinoma; transplant: N/A p... controlled vocabulary controlled vocabulary sample type match: carcinoma
sample_type tumor sample sample GSM3321040 Runtime Siftome inference GEO:sample:GSM3321040:78499aa940120eb9442b7d638bad1f0971f52460aa4d8ab482bdfd9082f9b739 medium confidence carcinoma sample_accession: GSM3321040 sample_title: prostate: LNCaP RNA-seq source_name: prostate characteristics: tissue: prostate; cell type: prostate adenocarcinoma; transplant: N/A p... controlled vocabulary controlled vocabulary sample type match: carcinoma
sample_type tumor sample sample GSM3321041 Runtime Siftome inference GEO:sample:GSM3321041:71e867e28d09caa2667d5960d7cde9267e8c2ba4e51e579450e6b2aff17d8e90 medium confidence carcinoma sample_accession: GSM3321041 sample_title: prostate: VCaP RNA-seq source_name: prostate characteristics: tissue: prostate; cell type: prostate adenocarcinoma; transplant: N/A pr... controlled vocabulary controlled vocabulary sample type match: carcinoma
sample_type tumor sample sample GSM3321042 Runtime Siftome inference GEO:sample:GSM3321042:b8dbb8e962d65a34135e23113dcaf3699f8606eead5c2a7011ef6f52485e2cca medium confidence carcinoma sample_accession: GSM3321042 sample_title: prostate: DU145 RNA-seq source_name: prostate characteristics: tissue: prostate; cell type: prostate adenocarcinoma; transplant: N/A p... controlled vocabulary controlled vocabulary sample type match: carcinoma
tissue prostate sample GSM3321022 Runtime Siftome inference GEO:sample:GSM3321022:016b6ceb8ec4d5bb5282a68b6f102159787f5e26b2ff0668c5938485b25408fb low confidence prostate sample_accession: GSM3321022 sample_title: prostate: Basal1 RNA-seq source_name: prostate characteristics: tissue: prostate; cell type: normal prostate basal epithelial; transpl... controlled vocabulary controlled vocabulary tissue match: prostate
tissue prostate sample GSM3321023 Runtime Siftome inference GEO:sample:GSM3321023:0ac79ca49b1d7619cc21adef2a6b6fcaa88fb0af13ac129619f772f6c9493cce low confidence prostate sample_accession: GSM3321023 sample_title: prostate: Basal2 RNA-seq source_name: prostate characteristics: tissue: prostate; cell type: normal prostate basal epithelial; transpl... controlled vocabulary controlled vocabulary tissue match: prostate
tissue prostate sample GSM3321024 Runtime Siftome inference GEO:sample:GSM3321024:51e0dd352dd2909f73385890bfae27ed79a78c0d76f0d5bcddd198fe040ff2f6 low confidence prostate sample_accession: GSM3321024 sample_title: prostate: Basal3 RNA-seq source_name: prostate characteristics: tissue: prostate; cell type: normal prostate basal epithelial; transpl... controlled vocabulary controlled vocabulary tissue match: prostate
tissue lung sample GSM3321025 Runtime Siftome inference GEO:sample:GSM3321025:41e0713bbd6a36da5094628ba053c05549952c9c1d276dc0d3c94b54aef3f164 low confidence lung sample_accession: GSM3321025 sample_title: lung: NHBE1 RNA-seq source_name: lung characteristics: tissue: lung; cell type: normal bronchial epithelial; transplant: N/A lung: NHB... controlled vocabulary controlled vocabulary tissue match: lung
tissue lung sample GSM3321026 Runtime Siftome inference GEO:sample:GSM3321026:0249c0dd8ba87de50ec637db4579d76ecd6afb8c36f67ad9d8be46d902de72ae low confidence lung sample_accession: GSM3321026 sample_title: lung: NHBE4 RNA-seq source_name: lung characteristics: tissue: lung; cell type: normal bronchial epithelial; transplant: N/A lung: NHB... controlled vocabulary controlled vocabulary tissue match: lung
tissue lung sample GSM3321027 Runtime Siftome inference GEO:sample:GSM3321027:f779a6c90f5210d76e4ade8240ad0366de565017afeca6c4aa9db3d1daaaf89e low confidence lung sample_accession: GSM3321027 sample_title: lung: NHBE5 RNA-seq source_name: lung characteristics: tissue: lung; cell type: normal bronchial epithelial; transplant: N/A lung: NHB... controlled vocabulary controlled vocabulary tissue match: lung
tissue prostate sample GSM3321028 Runtime Siftome inference GEO:sample:GSM3321028:58842800fa0237a13214d90e9c89b7e420ac58aaaf2e1c86c803519870588e69 low confidence prostate sample_accession: GSM3321028 sample_title: prostate: PARCB1 RNA-seq source_name: prostate characteristics: tissue: prostate; cell type: transformed prostate basal epithelial; tr... controlled vocabulary controlled vocabulary tissue match: prostate
tissue prostate sample GSM3321029 Runtime Siftome inference GEO:sample:GSM3321029:94d9a758836e78ccb57f56ea3c78dd8de0932679600e0010165926034ef827ea low confidence prostate sample_accession: GSM3321029 sample_title: prostate: PARCB2 RNA-seq source_name: prostate characteristics: tissue: prostate; cell type: transformed prostate basal epithelial; tr... controlled vocabulary controlled vocabulary tissue match: prostate
tissue prostate sample GSM3321030 Runtime Siftome inference GEO:sample:GSM3321030:f8de1d5d1e1f8df218a245d488110956957f49d12f7afda75fd939cf69430aee low confidence prostate sample_accession: GSM3321030 sample_title: prostate: PARCB3 RNA-seq source_name: prostate characteristics: tissue: prostate; cell type: transformed prostate basal epithelial; tr... controlled vocabulary controlled vocabulary tissue match: prostate
tissue prostate sample GSM3321031 Runtime Siftome inference GEO:sample:GSM3321031:c7012c66d2c3b535fda887dd40bd3a61368d178f2117d7cf8a5f2f1463baae05 low confidence prostate sample_accession: GSM3321031 sample_title: prostate: PARCB5 RNA-seq source_name: prostate characteristics: tissue: prostate; cell type: transformed prostate basal epithelial; tr... controlled vocabulary controlled vocabulary tissue match: prostate
tissue prostate sample GSM3321032 Runtime Siftome inference GEO:sample:GSM3321032:e0a2701d88c35b3584d72fd5982c7b09de502a0a4b08fbd1bb5bf7c75dc17aa9 low confidence prostate sample_accession: GSM3321032 sample_title: prostate: PARCB6 RNA-seq source_name: prostate characteristics: tissue: prostate; cell type: transformed prostate basal epithelial; tr... controlled vocabulary controlled vocabulary tissue match: prostate
tissue prostate sample GSM3321033 Runtime Siftome inference GEO:sample:GSM3321033:d0a6e49eaaebc6c911986ce8d4a6d020128abf89089cbbc55c6b6930a00c63e2 low confidence prostate sample_accession: GSM3321033 sample_title: prostate: PARCB8 RNA-seq source_name: prostate characteristics: tissue: prostate; cell type: transformed prostate basal epithelial; tr... controlled vocabulary controlled vocabulary tissue match: prostate
tissue lung sample GSM3321034 Runtime Siftome inference GEO:sample:GSM3321034:6d8f45bd4dd09c6ff29fc31e106f2e5f32d74973bbfbdc90dce49d0c549e04f8 low confidence lung sample_accession: GSM3321034 sample_title: lung: NHBE1-PARCB1 RNA-seq source_name: lung characteristics: tissue: lung; cell type: transformed bronchial epithelial; transplant: N... controlled vocabulary controlled vocabulary tissue match: lung
tissue lung sample GSM3321035 Runtime Siftome inference GEO:sample:GSM3321035:9f032f54e4a1db8cd6abe075add19e34cc6611c4927aa65642e4e9463c5312b1 low confidence lung sample_accession: GSM3321035 sample_title: lung: NHBE1-PARCB2 RNA-seq source_name: lung characteristics: tissue: lung; cell type: transformed bronchial epithelial; transplant: N... controlled vocabulary controlled vocabulary tissue match: lung
tissue lung sample GSM3321036 Runtime Siftome inference GEO:sample:GSM3321036:a5f4d0a4694d1b6fe227255e6a260e30533e4c735ae2ea80a5a1afc051d2cb9e low confidence lung sample_accession: GSM3321036 sample_title: lung: NHBE4-PARCB1 RNA-seq source_name: lung characteristics: tissue: lung; cell type: transformed bronchial epithelial; transplant: N... controlled vocabulary controlled vocabulary tissue match: lung
tissue lung sample GSM3321037 Runtime Siftome inference GEO:sample:GSM3321037:598566d173590abc9120cd5172a1a98c5fb0f8ec841909e2c843630712fdfe14 low confidence lung sample_accession: GSM3321037 sample_title: lung: NHBE4-PARCB2 RNA-seq source_name: lung characteristics: tissue: lung; cell type: transformed bronchial epithelial; transplant: N... controlled vocabulary controlled vocabulary tissue match: lung
tissue lung sample GSM3321038 Runtime Siftome inference GEO:sample:GSM3321038:2e08d9c2a8f9651368cd9d8b606ee0d63c99b189aadab29c32b52b3b3e440b92 low confidence lung sample_accession: GSM3321038 sample_title: lung: NHBE5-PARCB RNA-seq source_name: lung characteristics: tissue: lung; cell type: transformed bronchial epithelial; transplant: NS... controlled vocabulary controlled vocabulary tissue match: lung
tissue prostate sample GSM3321039 Runtime Siftome inference GEO:sample:GSM3321039:7294347d3a7063728bb4d7acae2f5589a5c00e5e035d5bca12256f9390f1df4c low confidence prostate sample_accession: GSM3321039 sample_title: prostate: 22RV1 RNA-seq source_name: prostate characteristics: tissue: prostate; cell type: prostate adenocarcinoma; transplant: N/A p... controlled vocabulary controlled vocabulary tissue match: prostate
tissue prostate sample GSM3321040 Runtime Siftome inference GEO:sample:GSM3321040:78499aa940120eb9442b7d638bad1f0971f52460aa4d8ab482bdfd9082f9b739 low confidence prostate sample_accession: GSM3321040 sample_title: prostate: LNCaP RNA-seq source_name: prostate characteristics: tissue: prostate; cell type: prostate adenocarcinoma; transplant: N/A p... controlled vocabulary controlled vocabulary tissue match: prostate
tissue prostate sample GSM3321041 Runtime Siftome inference GEO:sample:GSM3321041:71e867e28d09caa2667d5960d7cde9267e8c2ba4e51e579450e6b2aff17d8e90 low confidence prostate sample_accession: GSM3321041 sample_title: prostate: VCaP RNA-seq source_name: prostate characteristics: tissue: prostate; cell type: prostate adenocarcinoma; transplant: N/A pr... controlled vocabulary controlled vocabulary tissue match: prostate
tissue prostate sample GSM3321042 Runtime Siftome inference GEO:sample:GSM3321042:b8dbb8e962d65a34135e23113dcaf3699f8606eead5c2a7011ef6f52485e2cca low confidence prostate sample_accession: GSM3321042 sample_title: prostate: DU145 RNA-seq source_name: prostate characteristics: tissue: prostate; cell type: prostate adenocarcinoma; transplant: N/A p... controlled vocabulary controlled vocabulary tissue match: prostate
tissue prostate sample GSM3321043 Runtime Siftome inference GEO:sample:GSM3321043:be97ed479c8aab522f9d98dda8758a6bcc6d6fc31bb7b70150c5623893c85666 low confidence prostate sample_accession: GSM3321043 sample_title: prostate: MSKCC-EF1 RNA-seq source_name: prostate characteristics: tissue: prostate; cell type: small cell prostate cancer; transplant... controlled vocabulary controlled vocabulary tissue match: prostate
tissue prostate sample GSM3321044 Runtime Siftome inference GEO:sample:GSM3321044:ce1401fcea7a11cbc6efc92a719d8e242b9a0587bcf3dbdd677684368eaa9b64 low confidence prostate sample_accession: GSM3321044 sample_title: prostate: NCI-H660 RNA-seq source_name: prostate characteristics: tissue: prostate; cell type: small cell prostate cancer; transplant:... controlled vocabulary controlled vocabulary tissue match: prostate
tissue prostate sample GSM3321045 Runtime Siftome inference GEO:sample:GSM3321045:4cc0c7b6e1020a1b271a2320dbb9f1bc3abcdc8b3648a2c74296903a51e9f20d low confidence prostate sample_accession: GSM3321045 sample_title: prostate: ACB1 RNA-seq source_name: prostate characteristics: tissue: prostate; cell type: transformed prostate basal epithelial; tran... controlled vocabulary controlled vocabulary tissue match: prostate
tissue prostate sample GSM3321046 Runtime Siftome inference GEO:sample:GSM3321046:af365e3528691ee5d3430156781d9d4b26a13cf15c820727edf2880f1f3c8551 low confidence prostate sample_accession: GSM3321046 sample_title: prostate: ACB2 RNA-seq source_name: prostate characteristics: tissue: prostate; cell type: transformed prostate basal epithelial; tran... controlled vocabulary controlled vocabulary tissue match: prostate
tissue prostate sample GSM3321047 Runtime Siftome inference GEO:sample:GSM3321047:d4dc66fa1a5c5a55f849c1cf846a71ffbb68b9778032534708939c7753dc925a low confidence prostate sample_accession: GSM3321047 sample_title: prostate: ACB3 RNA-seq source_name: prostate characteristics: tissue: prostate; cell type: transformed prostate basal epithelial; tran... controlled vocabulary controlled vocabulary tissue match: prostate
tissue prostate sample GSM3321048 Runtime Siftome inference GEO:sample:GSM3321048:59b8c912413130c5fc1b543730a7cfe8abd6dbd1605085a800cb77750efed98f low confidence prostate sample_accession: GSM3321048 sample_title: prostate: ACB4 RNA-seq source_name: prostate characteristics: tissue: prostate; cell type: transformed prostate basal epithelial; tran... controlled vocabulary controlled vocabulary tissue match: prostate
tissue prostate sample GSM3321049 Runtime Siftome inference GEO:sample:GSM3321049:bfb2975ac0596cc5369085b8e4cdbf75183197597d1d1f2ac4d9efc9e86811d4 low confidence prostate sample_accession: GSM3321049 sample_title: prostate: ACB5 RNA-seq source_name: prostate characteristics: tissue: prostate; cell type: transformed prostate basal epithelial; tran... controlled vocabulary controlled vocabulary tissue match: prostate
tissue prostate sample GSM3321050 Runtime Siftome inference GEO:sample:GSM3321050:1b6167a34c8af66f58353203a20543da2704b4926538794da3ee11f0297cc217 low confidence prostate sample_accession: GSM3321050 sample_title: prostate: PACB1 RNA-seq source_name: prostate characteristics: tissue: prostate; cell type: transformed prostate basal epithelial; tra... controlled vocabulary controlled vocabulary tissue match: prostate
tissue prostate sample GSM3321051 Runtime Siftome inference GEO:sample:GSM3321051:10b8c469dc17a14c51d7854943870794b67dc4ece90fca53d111d3413e8421b9 low confidence prostate sample_accession: GSM3321051 sample_title: prostate: PACB3 RNA-seq source_name: prostate characteristics: tissue: prostate; cell type: transformed prostate basal epithelial; tra... controlled vocabulary controlled vocabulary tissue match: prostate
tissue prostate sample GSM3321052 Runtime Siftome inference GEO:sample:GSM3321052:66d4d030446c91847d1f8f6b242d74b2b88dfbad75e003ad3f708bc850290d5b low confidence prostate sample_accession: GSM3321052 sample_title: prostate: PACB4 RNA-seq source_name: prostate characteristics: tissue: prostate; cell type: transformed prostate basal epithelial; tra... controlled vocabulary controlled vocabulary tissue match: prostate
tissue prostate sample GSM3321053 Runtime Siftome inference GEO:sample:GSM3321053:3b262791d2b993b3306073b2437dd3de2dc5cb2b82c8af90cd9625dec7ed5bb2 low confidence prostate sample_accession: GSM3321053 sample_title: prostate: PACB5 RNA-seq source_name: prostate characteristics: tissue: prostate; cell type: transformed prostate basal epithelial; tra... controlled vocabulary controlled vocabulary tissue match: prostate
tissue prostate sample GSM3321054 Runtime Siftome inference GEO:sample:GSM3321054:c96548ef558f99f9ba38a62d26d2d6ae69a39fff22f8e47697289b92f148f169 low confidence prostate sample_accession: GSM3321054 sample_title: prostate: ARCB1 RNA-seq source_name: prostate characteristics: tissue: prostate; cell type: transformed prostate basal epithelial; tra... controlled vocabulary controlled vocabulary tissue match: prostate
tissue prostate sample GSM3321055 Runtime Siftome inference GEO:sample:GSM3321055:cae7c0a21c72a1aeebbed3f52a4c2758f4325dbc8446f4eb9b793bb7d3399fbb low confidence prostate sample_accession: GSM3321055 sample_title: prostate: ARCB4 RNA-seq source_name: prostate characteristics: tissue: prostate; cell type: transformed prostate basal epithelial; tra... controlled vocabulary controlled vocabulary tissue match: prostate
tissue prostate sample GSM3321056 Runtime Siftome inference GEO:sample:GSM3321056:90c84c523b55fa980ce601328be34c2c60209d2e27a54497d39c937042c24b44 low confidence prostate sample_accession: GSM3321056 sample_title: prostate: ARCB5 RNA-seq source_name: prostate characteristics: tissue: prostate; cell type: transformed prostate basal epithelial; tra... controlled vocabulary controlled vocabulary tissue match: prostate
tissue prostate sample GSM3321057 Runtime Siftome inference GEO:sample:GSM3321057:ba5daec7771dff7fcc3fa0320b6f6f0796abf47ac9898ac641ffb003f6d23173 low confidence prostate sample_accession: GSM3321057 sample_title: prostate: ARCB6 RNA-seq source_name: prostate characteristics: tissue: prostate; cell type: transformed prostate basal epithelial; tra... controlled vocabulary controlled vocabulary tissue match: prostate

Sample Group Preview

Possible case samples

Samples currently treated as the comparison case group.

6
  • GSM3321039 prostate: 22RV1 RNA-seq tumor sample Case marker detected. prostate tissue: prostate; cell type: prostate adenocarcinoma; transplant: N/A
  • GSM3321040 prostate: LNCaP RNA-seq tumor sample Case marker detected. prostate tissue: prostate; cell type: prostate adenocarcinoma; transplant: N/A
  • GSM3321041 prostate: VCaP RNA-seq tumor sample Case marker detected. prostate tissue: prostate; cell type: prostate adenocarcinoma; transplant: N/A
  • GSM3321042 prostate: DU145 RNA-seq tumor sample Case marker detected. prostate tissue: prostate; cell type: prostate adenocarcinoma; transplant: N/A
  • GSM3321043 prostate: MSKCC-EF1 RNA-seq prostate cancer Case marker detected. prostate tissue: prostate; cell type: small cell prostate cancer; transplant: N/A
  • GSM3321044 prostate: NCI-H660 RNA-seq prostate cancer Case marker detected. prostate tissue: prostate; cell type: small cell prostate cancer; transplant: N/A

Possible control samples

Samples currently treated as controls or baseline.

6
  • GSM3321022 prostate: Basal1 RNA-seq normal tissue Control marker detected. prostate tissue: prostate; cell type: normal prostate basal epithelial; transplant: N/A
  • GSM3321023 prostate: Basal2 RNA-seq normal tissue Control marker detected. prostate tissue: prostate; cell type: normal prostate basal epithelial; transplant: N/A
  • GSM3321024 prostate: Basal3 RNA-seq normal tissue Control marker detected. prostate tissue: prostate; cell type: normal prostate basal epithelial; transplant: N/A
  • GSM3321025 lung: NHBE1 RNA-seq normal tissue Control marker detected. lung tissue: lung; cell type: normal bronchial epithelial; transplant: N/A
  • GSM3321026 lung: NHBE4 RNA-seq normal tissue Control marker detected. lung tissue: lung; cell type: normal bronchial epithelial; transplant: N/A
  • GSM3321027 lung: NHBE5 RNA-seq normal tissue Control marker detected. lung tissue: lung; cell type: normal bronchial epithelial; transplant: N/A

Unassigned samples

Samples with no explicit case or control marker.

24
  • GSM3321028 prostate: PARCB1 RNA-seq unassigned No explicit case or control marker detected. prostate tissue: prostate; cell type: transformed prostate basal epithelial; transplant: NSG mice
  • GSM3321029 prostate: PARCB2 RNA-seq unassigned No explicit case or control marker detected. prostate tissue: prostate; cell type: transformed prostate basal epithelial; transplant: NSG mice
  • GSM3321030 prostate: PARCB3 RNA-seq unassigned No explicit case or control marker detected. prostate tissue: prostate; cell type: transformed prostate basal epithelial; transplant: NSG mice
  • GSM3321031 prostate: PARCB5 RNA-seq unassigned No explicit case or control marker detected. prostate tissue: prostate; cell type: transformed prostate basal epithelial; transplant: NSG mice
  • GSM3321032 prostate: PARCB6 RNA-seq unassigned No explicit case or control marker detected. prostate tissue: prostate; cell type: transformed prostate basal epithelial; transplant: NSG mice
  • GSM3321033 prostate: PARCB8 RNA-seq unassigned No explicit case or control marker detected. prostate tissue: prostate; cell type: transformed prostate basal epithelial; transplant: NSG mice
  • GSM3321034 lung: NHBE1-PARCB1 RNA-seq unassigned No explicit case or control marker detected. lung tissue: lung; cell type: transformed bronchial epithelial; transplant: NSG mice
  • GSM3321035 lung: NHBE1-PARCB2 RNA-seq unassigned No explicit case or control marker detected. lung tissue: lung; cell type: transformed bronchial epithelial; transplant: NSG mice
  • GSM3321036 lung: NHBE4-PARCB1 RNA-seq unassigned No explicit case or control marker detected. lung tissue: lung; cell type: transformed bronchial epithelial; transplant: NSG mice
  • GSM3321037 lung: NHBE4-PARCB2 RNA-seq unassigned No explicit case or control marker detected. lung tissue: lung; cell type: transformed bronchial epithelial; transplant: NSG mice
  • GSM3321038 lung: NHBE5-PARCB RNA-seq unassigned No explicit case or control marker detected. lung tissue: lung; cell type: transformed bronchial epithelial; transplant: NSG mice
  • GSM3321045 prostate: ACB1 RNA-seq unassigned No explicit case or control marker detected. prostate tissue: prostate; cell type: transformed prostate basal epithelial; transplant: NSG mice
  • GSM3321046 prostate: ACB2 RNA-seq unassigned No explicit case or control marker detected. prostate tissue: prostate; cell type: transformed prostate basal epithelial; transplant: NSG mice
  • GSM3321047 prostate: ACB3 RNA-seq unassigned No explicit case or control marker detected. prostate tissue: prostate; cell type: transformed prostate basal epithelial; transplant: NSG mice
  • GSM3321048 prostate: ACB4 RNA-seq unassigned No explicit case or control marker detected. prostate tissue: prostate; cell type: transformed prostate basal epithelial; transplant: NSG mice
  • GSM3321049 prostate: ACB5 RNA-seq unassigned No explicit case or control marker detected. prostate tissue: prostate; cell type: transformed prostate basal epithelial; transplant: NSG mice
  • GSM3321050 prostate: PACB1 RNA-seq unassigned No explicit case or control marker detected. prostate tissue: prostate; cell type: transformed prostate basal epithelial; transplant: NSG mice
  • GSM3321051 prostate: PACB3 RNA-seq unassigned No explicit case or control marker detected. prostate tissue: prostate; cell type: transformed prostate basal epithelial; transplant: NSG mice
  • GSM3321052 prostate: PACB4 RNA-seq unassigned No explicit case or control marker detected. prostate tissue: prostate; cell type: transformed prostate basal epithelial; transplant: NSG mice
  • GSM3321053 prostate: PACB5 RNA-seq unassigned No explicit case or control marker detected. prostate tissue: prostate; cell type: transformed prostate basal epithelial; transplant: NSG mice
  • GSM3321054 prostate: ARCB1 RNA-seq unassigned No explicit case or control marker detected. prostate tissue: prostate; cell type: transformed prostate basal epithelial; transplant: NSG mice
  • GSM3321055 prostate: ARCB4 RNA-seq unassigned No explicit case or control marker detected. prostate tissue: prostate; cell type: transformed prostate basal epithelial; transplant: NSG mice
  • GSM3321056 prostate: ARCB5 RNA-seq unassigned No explicit case or control marker detected. prostate tissue: prostate; cell type: transformed prostate basal epithelial; transplant: NSG mice
  • GSM3321057 prostate: ARCB6 RNA-seq unassigned No explicit case or control marker detected. prostate tissue: prostate; cell type: transformed prostate basal epithelial; transplant: NSG mice

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

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

6 samples
  • GSM3321022 prostate: Basal1 RNA-seq prostate tissue: prostate; cell type: normal prostate basal epithelial; transplant: N/A
  • GSM3321023 prostate: Basal2 RNA-seq prostate tissue: prostate; cell type: normal prostate basal epithelial; transplant: N/A
  • GSM3321024 prostate: Basal3 RNA-seq prostate tissue: prostate; cell type: normal prostate basal epithelial; transplant: N/A
  • GSM3321025 lung: NHBE1 RNA-seq lung tissue: lung; cell type: normal bronchial epithelial; transplant: N/A
  • GSM3321026 lung: NHBE4 RNA-seq lung tissue: lung; cell type: normal bronchial epithelial; transplant: N/A
  • GSM3321027 lung: NHBE5 RNA-seq lung tissue: lung; cell type: normal bronchial epithelial; transplant: N/A

unassigned

24 samples
  • GSM3321028 prostate: PARCB1 RNA-seq prostate tissue: prostate; cell type: transformed prostate basal epithelial; transplant: NSG mice
  • GSM3321029 prostate: PARCB2 RNA-seq prostate tissue: prostate; cell type: transformed prostate basal epithelial; transplant: NSG mice
  • GSM3321030 prostate: PARCB3 RNA-seq prostate tissue: prostate; cell type: transformed prostate basal epithelial; transplant: NSG mice
  • GSM3321031 prostate: PARCB5 RNA-seq prostate tissue: prostate; cell type: transformed prostate basal epithelial; transplant: NSG mice
  • GSM3321032 prostate: PARCB6 RNA-seq prostate tissue: prostate; cell type: transformed prostate basal epithelial; transplant: NSG mice
  • GSM3321033 prostate: PARCB8 RNA-seq prostate tissue: prostate; cell type: transformed prostate basal epithelial; transplant: NSG mice
  • GSM3321034 lung: NHBE1-PARCB1 RNA-seq lung tissue: lung; cell type: transformed bronchial epithelial; transplant: NSG mice
  • GSM3321035 lung: NHBE1-PARCB2 RNA-seq lung tissue: lung; cell type: transformed bronchial epithelial; transplant: NSG mice
  • GSM3321036 lung: NHBE4-PARCB1 RNA-seq lung tissue: lung; cell type: transformed bronchial epithelial; transplant: NSG mice
  • GSM3321037 lung: NHBE4-PARCB2 RNA-seq lung tissue: lung; cell type: transformed bronchial epithelial; transplant: NSG mice
  • GSM3321038 lung: NHBE5-PARCB RNA-seq lung tissue: lung; cell type: transformed bronchial epithelial; transplant: NSG mice
  • GSM3321045 prostate: ACB1 RNA-seq prostate tissue: prostate; cell type: transformed prostate basal epithelial; transplant: NSG mice
  • GSM3321046 prostate: ACB2 RNA-seq prostate tissue: prostate; cell type: transformed prostate basal epithelial; transplant: NSG mice
  • GSM3321047 prostate: ACB3 RNA-seq prostate tissue: prostate; cell type: transformed prostate basal epithelial; transplant: NSG mice
  • GSM3321048 prostate: ACB4 RNA-seq prostate tissue: prostate; cell type: transformed prostate basal epithelial; transplant: NSG mice
  • GSM3321049 prostate: ACB5 RNA-seq prostate tissue: prostate; cell type: transformed prostate basal epithelial; transplant: NSG mice
  • GSM3321050 prostate: PACB1 RNA-seq prostate tissue: prostate; cell type: transformed prostate basal epithelial; transplant: NSG mice
  • GSM3321051 prostate: PACB3 RNA-seq prostate tissue: prostate; cell type: transformed prostate basal epithelial; transplant: NSG mice
  • GSM3321052 prostate: PACB4 RNA-seq prostate tissue: prostate; cell type: transformed prostate basal epithelial; transplant: NSG mice
  • GSM3321053 prostate: PACB5 RNA-seq prostate tissue: prostate; cell type: transformed prostate basal epithelial; transplant: NSG mice
  • GSM3321054 prostate: ARCB1 RNA-seq prostate tissue: prostate; cell type: transformed prostate basal epithelial; transplant: NSG mice
  • GSM3321055 prostate: ARCB4 RNA-seq prostate tissue: prostate; cell type: transformed prostate basal epithelial; transplant: NSG mice
  • GSM3321056 prostate: ARCB5 RNA-seq prostate tissue: prostate; cell type: transformed prostate basal epithelial; transplant: NSG mice
  • GSM3321057 prostate: ARCB6 RNA-seq prostate tissue: prostate; cell type: transformed prostate basal epithelial; transplant: NSG mice

tumor sample

4 samples
  • GSM3321039 prostate: 22RV1 RNA-seq prostate tissue: prostate; cell type: prostate adenocarcinoma; transplant: N/A
  • GSM3321040 prostate: LNCaP RNA-seq prostate tissue: prostate; cell type: prostate adenocarcinoma; transplant: N/A
  • GSM3321041 prostate: VCaP RNA-seq prostate tissue: prostate; cell type: prostate adenocarcinoma; transplant: N/A
  • GSM3321042 prostate: DU145 RNA-seq prostate tissue: prostate; cell type: prostate adenocarcinoma; transplant: N/A

prostate cancer

2 samples
  • GSM3321043 prostate: MSKCC-EF1 RNA-seq prostate tissue: prostate; cell type: small cell prostate cancer; transplant: N/A
  • GSM3321044 prostate: NCI-H660 RNA-seq prostate tissue: prostate; cell type: small cell prostate cancer; transplant: N/A

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.
  • Non-colorectal cancer context downgraded for colorectal tumor-vs-normal tissue 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 tumor/normal grouping is from a non-colorectal cancer context.

Sample Links

36 samples

Review Audit Trail

0 decisions

No review decisions have been stored for this dataset.