Siftome Phase 3L

GSE58375

SMO variants explain the majority of drug resistance in basal cell carcinoma [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
2014-06-10
Last update
2019-05-15
Organization
Stanford University
Department
Dermatology
Public date
2015-03-16
Experiment types
Expression profiling by high throughput sequencing
Platforms
GPL16791 Illumina HiSeq 2500 (Homo sapiens)
Series type
SubSeries
SubSeries
Not available
BioProject
PRJNA252377
Supplementary files
XLSX: GSE58375_RNAseq_Expression_Matrix.xlsx.gz
Organism
Homo sapiens
Assay
bulk RNA-seq
Samples
21
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

Ready after review
97% DE readiness

Contrast completeness

25/25 pts

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

Minimum group size

20/20 pts

Each contrast group has at least 2 samples.

Processed data availability

20/20 pts

Processed data is marked available in the GEO index.

Sample decision clarity

15/15 pts

All samples are assigned to a case or control group.

Blocking warnings

7/10 pts

Warnings are present, but none are critical blockers.

Metadata normalization

10/10 pts

Metadata quality is high enough to support downstream handoff.

Blockers

No readiness blockers detected.

Next Steps

  • Review the sample grouping CSV and contrast CSV before running differential expression.
  • Confirm processed count files and sample identifiers match the exported metadata.

Analysis Preparation Checklist

5/6 ready

Group labels reviewed

Needs review

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

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

Minimum sample count met

Ready

Both groups meet the minimum of 2 samples.

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

Processed counts available

Ready

Processed data availability is marked true in the GEO index.

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

Ambiguous samples handled

Ready

No review-needed or unassigned samples are present in the proposed grouping.

Still scan the grouping table for biology-specific ambiguity.

Exclusion decisions recorded

Ready

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

Record any manual exclusions in the downstream analysis notes.

Source links preserved

Ready

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

Keep GEO dataset and sample links with exported metadata.

Bioinformatician Review

Standard analyst review

Proceed only after the analyst confirms grouping, exclusions, and source files.

No expert-review triggers were detected by Siftome.

Why This Is Ranked Here

Patient tissue tumor-vs-normal
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. 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 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 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 13 samples
  • Likely control group normal tissue 8 samples

Warnings

  • 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 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 1 active warning 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 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: 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 1 warning require review. Contributed to match or upgrade evidence.
  • Caution fact Disease or condition label could not be normalized. Contributed to downgrade or manual-review evidence.
  • Caution fact Non-colorectal cancer context downgraded for colorectal tumor-vs-normal tissue ranking. Contributed to downgrade or manual-review evidence.
  • Caution fact Missing or unclear metadata: Disease clarity: Disease or condition metadata was not normalized. Contributed to downgrade or manual-review evidence.
  • Caution fact Missing or unclear metadata: Treatment clarity: No unclear treatment split detected in the sample metadata. Contributed to downgrade or manual-review evidence.
  • Caution fact Overall score capped because comparison suitability is weak for the selected search intent. Contributed to downgrade or manual-review evidence.
  • Caution fact Overall score capped because tumor/normal grouping is from a non-colorectal cancer context. Contributed to downgrade or manual-review evidence.
  • Caution fact Downgraded disease context: colorectal/GI relevance is unclear. Contributed to downgrade or manual-review evidence.
  • Caution fact Missing or unclear metadata: Downgraded disease context: colorectal/GI relevance is unclear. Contributed to downgrade or manual-review evidence.
  • Caution fact Comparison suitability score is below the Phase 1 recommended threshold. Contributed to downgrade or manual-review evidence.

Manual Corrections

0 active

Source Evidence

4 sources

GEO

Primary source

Original dataset metadata, sample metadata, source links, and GEO data availability flags.

Dataset accession
GSE58375
Sample records
21 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
GSE58375
  • 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
GSE58375
  • 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
GSE58375
  • 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: GSE58375
dataset_title: SMO variants explain the majority of drug resistance in basal cell carcinoma [RNA-Seq]
organism: Homo sapiens
assay_type: bulk RNA-seq
processed_data_available: true
raw_data_available: true
submission_date: 2014-06-10
last_update_date: 2019-05-15
organization_name: Stanford University
department: Dermatology
public_date: 2015-03-16
experiment_types: Expression profiling by high throughput sequencing
platforms: GPL16791 Illumina HiSeq 2500 (Homo sapiens)
sub_series: Not available
bioproject: PRJNA252377
supplementary_files: XLSX: GSE58375_RNAseq_Expression_Matrix.xlsx.gz
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: colorectal/GI relevance is unclear.
  • Processed data is available for downstream review.
  • 1 warning require review.

Why It May Not Be Suitable

  • Disease or condition label could not be normalized.
  • Non-colorectal cancer context downgraded for colorectal tumor-vs-normal tissue ranking.
  • Missing or unclear metadata: Disease clarity: Disease or condition metadata was not normalized.
  • Missing or unclear metadata: Treatment clarity: No unclear treatment split detected in the sample metadata.
  • Overall score capped because comparison suitability is weak for the selected search intent.
  • Overall score capped because tumor/normal grouping is from a non-colorectal cancer context.
  • Downgraded disease context: colorectal/GI relevance is unclear.
  • Missing or unclear metadata: Downgraded disease context: colorectal/GI relevance is unclear.
  • Comparison suitability score is below the Phase 1 recommended threshold.

Warnings

  • warning DISEASE_LABEL_UNCLEAR Disease or condition label could not be normalized.

Normalized Fields

44 fields
Field Value Source Origin Confidence Evidence Reason
assay_type bulk RNA-seq dataset GSE58375 Runtime Siftome inference GEO:dataset:GSE58375:64a4522828579343806594e8c917534e9593b97d2a0a38b9ecb4e34f3f7998b0 high confidence bulk rna-seq dataset_accession: GSE58375 dataset_title: SMO variants explain the majority of drug resistance in basal cell carcinoma [RNA-Seq] organism: Homo sapiens assay_type: bulk RNA-seq... keyword match keyword match: bulk rna-seq
organism Homo sapiens dataset GSE58375 Runtime Siftome inference GEO:dataset:GSE58375:64a4522828579343806594e8c917534e9593b97d2a0a38b9ecb4e34f3f7998b0 high confidence homo sapiens dataset_accession: GSE58375 dataset_title: SMO variants explain the majority of drug resistance in basal cell carcinoma [RNA-Seq] organism: Homo sapiens assay_type: bulk RNA-seq... keyword match keyword match: homo sapiens
sample_type normal tissue sample GSM1409334 Runtime Siftome inference GEO:sample:GSM1409334:6fb6bbf9c08b4ec074aa389fe42ff7ca1c8d202302b6dc0c06e102dd3eb825f9 low confidence normal sample_accession: GSM1409334 sample_title: RNASeq_Normal1 source_name: normal skin biopsies characteristics: tissue: skin; response to smoothened (smo) inhibitors: Normal RNASeq... controlled vocabulary controlled vocabulary sample type match: normal
sample_type normal tissue sample GSM1409335 Runtime Siftome inference GEO:sample:GSM1409335:56ef4580da8544ab03f68dce694ab8434bd5387162fc93a2b01d6f7836325543 low confidence normal sample_accession: GSM1409335 sample_title: RNASeq_Normal2 source_name: normal skin biopsies characteristics: tissue: skin; response to smoothened (smo) inhibitors: Normal RNASeq... controlled vocabulary controlled vocabulary sample type match: normal
sample_type normal tissue sample GSM1409336 Runtime Siftome inference GEO:sample:GSM1409336:2db0571286314766de52062e2f06a19e823d50c84324e523af8d3dbaf7f30e5d low confidence normal sample_accession: GSM1409336 sample_title: RNASeq_Normal3 source_name: normal skin biopsies characteristics: tissue: skin; response to smoothened (smo) inhibitors: Normal RNASeq... controlled vocabulary controlled vocabulary sample type match: normal
sample_type normal tissue sample GSM1409337 Runtime Siftome inference GEO:sample:GSM1409337:b850bffdd7c87e7b0db71e117fa30bbcd066c30ec82e98923a41263a9da12ca3 low confidence normal sample_accession: GSM1409337 sample_title: RNASeq_Normal4 source_name: normal skin biopsies characteristics: tissue: skin; response to smoothened (smo) inhibitors: Normal RNASeq... controlled vocabulary controlled vocabulary sample type match: normal
sample_type normal tissue sample GSM1409338 Runtime Siftome inference GEO:sample:GSM1409338:13ff00b91af17a144ef7f26062a234a282095c9cb1456db5ccdf64f1c3392c63 low confidence normal sample_accession: GSM1409338 sample_title: RNASeq_Normal5 source_name: normal skin biopsies characteristics: tissue: skin; response to smoothened (smo) inhibitors: Normal RNASeq... controlled vocabulary controlled vocabulary sample type match: normal
sample_type normal tissue sample GSM1409339 Runtime Siftome inference GEO:sample:GSM1409339:84e2575b5d231029df937389a53694df041f5a0ffd6209477571a38560ed405e low confidence normal sample_accession: GSM1409339 sample_title: RNASeq_Normal6 source_name: normal skin biopsies characteristics: tissue: skin; response to smoothened (smo) inhibitors: Normal RNASeq... controlled vocabulary controlled vocabulary sample type match: normal
sample_type normal tissue sample GSM1409340 Runtime Siftome inference GEO:sample:GSM1409340:293d3fd327c1356f256ab44de3228867c978845a2771e414c45c1c9f46b029b3 low confidence normal sample_accession: GSM1409340 sample_title: RNASeq_Normal7 source_name: normal skin biopsies characteristics: tissue: skin; response to smoothened (smo) inhibitors: Normal RNASeq... controlled vocabulary controlled vocabulary sample type match: normal
sample_type normal tissue sample GSM1409341 Runtime Siftome inference GEO:sample:GSM1409341:f35d1df5f79504e47536d96c9cc450e439d363c1c871b52ab650fb2dd1fc51a8 low confidence normal sample_accession: GSM1409341 sample_title: RNASeq_Normal8 source_name: normal skin biopsies characteristics: tissue: skin; response to smoothened (smo) inhibitors: Normal RNASeq... controlled vocabulary controlled vocabulary sample type match: normal
sample_type tumor sample sample GSM1409342 Runtime Siftome inference GEO:sample:GSM1409342:3d71fbc985cfb414d33bd5a84577e453e3902d2c87d0b5eb2d4e7388b49078ca medium confidence carcinoma sample_accession: GSM1409342 sample_title: RNASeq_Resistance1 source_name: resistant basal cell cancers characteristics: tissue: skin; cell type: basal cell carcinomas (BCCs); r... controlled vocabulary controlled vocabulary sample type match: carcinoma
sample_type tumor sample sample GSM1409343 Runtime Siftome inference GEO:sample:GSM1409343:670e41e7dd0680ca57cb670b46d12d4386e624a5e3329657666a996dd1d2a571 medium confidence carcinoma sample_accession: GSM1409343 sample_title: RNASeq_Resistance2 source_name: resistant basal cell cancers characteristics: tissue: skin; cell type: basal cell carcinomas (BCCs); r... controlled vocabulary controlled vocabulary sample type match: carcinoma
sample_type tumor sample sample GSM1409344 Runtime Siftome inference GEO:sample:GSM1409344:f7ead38c111e31006763610f74c3ec7d90646565b0167960acda4a2f505575f7 medium confidence carcinoma sample_accession: GSM1409344 sample_title: RNASeq_Resistance3 source_name: resistant basal cell cancers characteristics: tissue: skin; cell type: basal cell carcinomas (BCCs); r... controlled vocabulary controlled vocabulary sample type match: carcinoma
sample_type tumor sample sample GSM1409345 Runtime Siftome inference GEO:sample:GSM1409345:02207ccd2fdfd469e0ba14926a5cbb3ec5665b6f3bb88ed36f20680052425a28 medium confidence carcinoma sample_accession: GSM1409345 sample_title: RNASeq_Resistance4 source_name: resistant basal cell cancers characteristics: tissue: skin; cell type: basal cell carcinomas (BCCs); r... controlled vocabulary controlled vocabulary sample type match: carcinoma
sample_type tumor sample sample GSM1409346 Runtime Siftome inference GEO:sample:GSM1409346:5bb9be51378938b23db42aa42bb3092f4d5659ef943f151d67f88a70bac82190 medium confidence carcinoma sample_accession: GSM1409346 sample_title: RNASeq_Resistance5 source_name: resistant basal cell cancers characteristics: tissue: skin; cell type: basal cell carcinomas (BCCs); r... controlled vocabulary controlled vocabulary sample type match: carcinoma
sample_type tumor sample sample GSM1409347 Runtime Siftome inference GEO:sample:GSM1409347:33b2a84190828c24689599295623311a0592335a1fb770faa775c261409ce22c medium confidence carcinoma sample_accession: GSM1409347 sample_title: RNASeq_Resistance6 source_name: resistant basal cell cancers characteristics: tissue: skin; cell type: basal cell carcinomas (BCCs); r... controlled vocabulary controlled vocabulary sample type match: carcinoma
sample_type tumor sample sample GSM1409348 Runtime Siftome inference GEO:sample:GSM1409348:972db80ace25f05fa3d85adf9537b2b4654247df68c539422cc5fdcf280c1b40 medium confidence carcinoma sample_accession: GSM1409348 sample_title: RNASeq_Resistance7 source_name: resistant basal cell cancers characteristics: tissue: skin; cell type: basal cell carcinomas (BCCs); r... controlled vocabulary controlled vocabulary sample type match: carcinoma
sample_type tumor sample sample GSM1409349 Runtime Siftome inference GEO:sample:GSM1409349:8f06fc6714248c0687cdec92bb9aebd00c948d089247f9bbd97524daf1ecc099 medium confidence carcinoma sample_accession: GSM1409349 sample_title: RNASeq_Resistance8 source_name: resistant basal cell cancers characteristics: tissue: skin; cell type: basal cell carcinomas (BCCs); r... controlled vocabulary controlled vocabulary sample type match: carcinoma
sample_type tumor sample sample GSM1409350 Runtime Siftome inference GEO:sample:GSM1409350:19828af3a5e5d1df82acc4142031424641ed2611f9695b92232a0ff152ee881c medium confidence carcinoma sample_accession: GSM1409350 sample_title: RNASeq_Resistance9 source_name: resistant basal cell cancers characteristics: tissue: skin; cell type: basal cell carcinomas (BCCs); r... controlled vocabulary controlled vocabulary sample type match: carcinoma
sample_type tumor sample sample GSM1409351 Runtime Siftome inference GEO:sample:GSM1409351:8bec819ce2c810650a5b2dcb58d93b3567d27fcec32a6566b956f4485cf6f024 medium confidence carcinoma sample_accession: GSM1409351 sample_title: RNASeq_Sensitive1 source_name: sensitive basal cell cancers characteristics: tissue: skin; cell type: basal cell carcinomas (BCCs); re... controlled vocabulary controlled vocabulary sample type match: carcinoma
sample_type tumor sample sample GSM1409352 Runtime Siftome inference GEO:sample:GSM1409352:c7338df8d84a6a97749cf3a30b91e4be52e01f3b731d9049a8f9c2fddfac7ea2 medium confidence carcinoma sample_accession: GSM1409352 sample_title: RNASeq_Sensitive2 source_name: sensitive basal cell cancers characteristics: tissue: skin; cell type: basal cell carcinomas (BCCs); re... controlled vocabulary controlled vocabulary sample type match: carcinoma
sample_type tumor sample sample GSM1409353 Runtime Siftome inference GEO:sample:GSM1409353:9296f1e4bcc386587a7a0e6ace4289bceaddecf0b967e3a4d4186959f36854e3 medium confidence carcinoma sample_accession: GSM1409353 sample_title: RNASeq_Sensitive3 source_name: sensitive basal cell cancers characteristics: tissue: skin; cell type: basal cell carcinomas (BCCs); re... controlled vocabulary controlled vocabulary sample type match: carcinoma
sample_type tumor sample sample GSM1409354 Runtime Siftome inference GEO:sample:GSM1409354:4c15352814907969db0c59e3171136a9451cfa9404cd83f0be4b88bcc8123e1c medium confidence carcinoma sample_accession: GSM1409354 sample_title: RNASeq_Sensitive4 source_name: sensitive basal cell cancers characteristics: tissue: skin; cell type: basal cell carcinomas (BCCs); re... controlled vocabulary controlled vocabulary sample type match: carcinoma
tissue skin sample GSM1409334 Runtime Siftome inference GEO:sample:GSM1409334:6fb6bbf9c08b4ec074aa389fe42ff7ca1c8d202302b6dc0c06e102dd3eb825f9 low confidence skin sample_accession: GSM1409334 sample_title: RNASeq_Normal1 source_name: normal skin biopsies characteristics: tissue: skin; response to smoothened (smo) inhibitors: Normal RNASeq... controlled vocabulary controlled vocabulary tissue match: skin
tissue skin sample GSM1409335 Runtime Siftome inference GEO:sample:GSM1409335:56ef4580da8544ab03f68dce694ab8434bd5387162fc93a2b01d6f7836325543 low confidence skin sample_accession: GSM1409335 sample_title: RNASeq_Normal2 source_name: normal skin biopsies characteristics: tissue: skin; response to smoothened (smo) inhibitors: Normal RNASeq... controlled vocabulary controlled vocabulary tissue match: skin
tissue skin sample GSM1409336 Runtime Siftome inference GEO:sample:GSM1409336:2db0571286314766de52062e2f06a19e823d50c84324e523af8d3dbaf7f30e5d low confidence skin sample_accession: GSM1409336 sample_title: RNASeq_Normal3 source_name: normal skin biopsies characteristics: tissue: skin; response to smoothened (smo) inhibitors: Normal RNASeq... controlled vocabulary controlled vocabulary tissue match: skin
tissue skin sample GSM1409337 Runtime Siftome inference GEO:sample:GSM1409337:b850bffdd7c87e7b0db71e117fa30bbcd066c30ec82e98923a41263a9da12ca3 low confidence skin sample_accession: GSM1409337 sample_title: RNASeq_Normal4 source_name: normal skin biopsies characteristics: tissue: skin; response to smoothened (smo) inhibitors: Normal RNASeq... controlled vocabulary controlled vocabulary tissue match: skin
tissue skin sample GSM1409338 Runtime Siftome inference GEO:sample:GSM1409338:13ff00b91af17a144ef7f26062a234a282095c9cb1456db5ccdf64f1c3392c63 low confidence skin sample_accession: GSM1409338 sample_title: RNASeq_Normal5 source_name: normal skin biopsies characteristics: tissue: skin; response to smoothened (smo) inhibitors: Normal RNASeq... controlled vocabulary controlled vocabulary tissue match: skin
tissue skin sample GSM1409339 Runtime Siftome inference GEO:sample:GSM1409339:84e2575b5d231029df937389a53694df041f5a0ffd6209477571a38560ed405e low confidence skin sample_accession: GSM1409339 sample_title: RNASeq_Normal6 source_name: normal skin biopsies characteristics: tissue: skin; response to smoothened (smo) inhibitors: Normal RNASeq... controlled vocabulary controlled vocabulary tissue match: skin
tissue skin sample GSM1409340 Runtime Siftome inference GEO:sample:GSM1409340:293d3fd327c1356f256ab44de3228867c978845a2771e414c45c1c9f46b029b3 low confidence skin sample_accession: GSM1409340 sample_title: RNASeq_Normal7 source_name: normal skin biopsies characteristics: tissue: skin; response to smoothened (smo) inhibitors: Normal RNASeq... controlled vocabulary controlled vocabulary tissue match: skin
tissue skin sample GSM1409341 Runtime Siftome inference GEO:sample:GSM1409341:f35d1df5f79504e47536d96c9cc450e439d363c1c871b52ab650fb2dd1fc51a8 low confidence skin sample_accession: GSM1409341 sample_title: RNASeq_Normal8 source_name: normal skin biopsies characteristics: tissue: skin; response to smoothened (smo) inhibitors: Normal RNASeq... controlled vocabulary controlled vocabulary tissue match: skin
tissue skin sample GSM1409342 Runtime Siftome inference GEO:sample:GSM1409342:3d71fbc985cfb414d33bd5a84577e453e3902d2c87d0b5eb2d4e7388b49078ca low confidence skin sample_accession: GSM1409342 sample_title: RNASeq_Resistance1 source_name: resistant basal cell cancers characteristics: tissue: skin; cell type: basal cell carcinomas (BCCs); r... controlled vocabulary controlled vocabulary tissue match: skin
tissue skin sample GSM1409343 Runtime Siftome inference GEO:sample:GSM1409343:670e41e7dd0680ca57cb670b46d12d4386e624a5e3329657666a996dd1d2a571 low confidence skin sample_accession: GSM1409343 sample_title: RNASeq_Resistance2 source_name: resistant basal cell cancers characteristics: tissue: skin; cell type: basal cell carcinomas (BCCs); r... controlled vocabulary controlled vocabulary tissue match: skin
tissue skin sample GSM1409344 Runtime Siftome inference GEO:sample:GSM1409344:f7ead38c111e31006763610f74c3ec7d90646565b0167960acda4a2f505575f7 low confidence skin sample_accession: GSM1409344 sample_title: RNASeq_Resistance3 source_name: resistant basal cell cancers characteristics: tissue: skin; cell type: basal cell carcinomas (BCCs); r... controlled vocabulary controlled vocabulary tissue match: skin
tissue skin sample GSM1409345 Runtime Siftome inference GEO:sample:GSM1409345:02207ccd2fdfd469e0ba14926a5cbb3ec5665b6f3bb88ed36f20680052425a28 low confidence skin sample_accession: GSM1409345 sample_title: RNASeq_Resistance4 source_name: resistant basal cell cancers characteristics: tissue: skin; cell type: basal cell carcinomas (BCCs); r... controlled vocabulary controlled vocabulary tissue match: skin
tissue skin sample GSM1409346 Runtime Siftome inference GEO:sample:GSM1409346:5bb9be51378938b23db42aa42bb3092f4d5659ef943f151d67f88a70bac82190 low confidence skin sample_accession: GSM1409346 sample_title: RNASeq_Resistance5 source_name: resistant basal cell cancers characteristics: tissue: skin; cell type: basal cell carcinomas (BCCs); r... controlled vocabulary controlled vocabulary tissue match: skin
tissue skin sample GSM1409347 Runtime Siftome inference GEO:sample:GSM1409347:33b2a84190828c24689599295623311a0592335a1fb770faa775c261409ce22c low confidence skin sample_accession: GSM1409347 sample_title: RNASeq_Resistance6 source_name: resistant basal cell cancers characteristics: tissue: skin; cell type: basal cell carcinomas (BCCs); r... controlled vocabulary controlled vocabulary tissue match: skin
tissue skin sample GSM1409348 Runtime Siftome inference GEO:sample:GSM1409348:972db80ace25f05fa3d85adf9537b2b4654247df68c539422cc5fdcf280c1b40 low confidence skin sample_accession: GSM1409348 sample_title: RNASeq_Resistance7 source_name: resistant basal cell cancers characteristics: tissue: skin; cell type: basal cell carcinomas (BCCs); r... controlled vocabulary controlled vocabulary tissue match: skin
tissue skin sample GSM1409349 Runtime Siftome inference GEO:sample:GSM1409349:8f06fc6714248c0687cdec92bb9aebd00c948d089247f9bbd97524daf1ecc099 low confidence skin sample_accession: GSM1409349 sample_title: RNASeq_Resistance8 source_name: resistant basal cell cancers characteristics: tissue: skin; cell type: basal cell carcinomas (BCCs); r... controlled vocabulary controlled vocabulary tissue match: skin
tissue skin sample GSM1409350 Runtime Siftome inference GEO:sample:GSM1409350:19828af3a5e5d1df82acc4142031424641ed2611f9695b92232a0ff152ee881c low confidence skin sample_accession: GSM1409350 sample_title: RNASeq_Resistance9 source_name: resistant basal cell cancers characteristics: tissue: skin; cell type: basal cell carcinomas (BCCs); r... controlled vocabulary controlled vocabulary tissue match: skin
tissue skin sample GSM1409351 Runtime Siftome inference GEO:sample:GSM1409351:8bec819ce2c810650a5b2dcb58d93b3567d27fcec32a6566b956f4485cf6f024 low confidence skin sample_accession: GSM1409351 sample_title: RNASeq_Sensitive1 source_name: sensitive basal cell cancers characteristics: tissue: skin; cell type: basal cell carcinomas (BCCs); re... controlled vocabulary controlled vocabulary tissue match: skin
tissue skin sample GSM1409352 Runtime Siftome inference GEO:sample:GSM1409352:c7338df8d84a6a97749cf3a30b91e4be52e01f3b731d9049a8f9c2fddfac7ea2 low confidence skin sample_accession: GSM1409352 sample_title: RNASeq_Sensitive2 source_name: sensitive basal cell cancers characteristics: tissue: skin; cell type: basal cell carcinomas (BCCs); re... controlled vocabulary controlled vocabulary tissue match: skin
tissue skin sample GSM1409353 Runtime Siftome inference GEO:sample:GSM1409353:9296f1e4bcc386587a7a0e6ace4289bceaddecf0b967e3a4d4186959f36854e3 low confidence skin sample_accession: GSM1409353 sample_title: RNASeq_Sensitive3 source_name: sensitive basal cell cancers characteristics: tissue: skin; cell type: basal cell carcinomas (BCCs); re... controlled vocabulary controlled vocabulary tissue match: skin
tissue skin sample GSM1409354 Runtime Siftome inference GEO:sample:GSM1409354:4c15352814907969db0c59e3171136a9451cfa9404cd83f0be4b88bcc8123e1c low confidence skin sample_accession: GSM1409354 sample_title: RNASeq_Sensitive4 source_name: sensitive basal cell cancers characteristics: tissue: skin; cell type: basal cell carcinomas (BCCs); re... controlled vocabulary controlled vocabulary tissue match: skin

Sample Group Preview

Possible case samples

Samples currently treated as the comparison case group.

13
  • GSM1409342 RNASeq_Resistance1 tumor sample Case marker detected. resistant basal cell cancers tissue: skin; cell type: basal cell carcinomas (BCCs); response to smoothened (smo) inhibitors: Resistance
  • GSM1409343 RNASeq_Resistance2 tumor sample Case marker detected. resistant basal cell cancers tissue: skin; cell type: basal cell carcinomas (BCCs); response to smoothened (smo) inhibitors: Resistance
  • GSM1409344 RNASeq_Resistance3 tumor sample Case marker detected. resistant basal cell cancers tissue: skin; cell type: basal cell carcinomas (BCCs); response to smoothened (smo) inhibitors: Resistance
  • GSM1409345 RNASeq_Resistance4 tumor sample Case marker detected. resistant basal cell cancers tissue: skin; cell type: basal cell carcinomas (BCCs); response to smoothened (smo) inhibitors: Resistance
  • GSM1409346 RNASeq_Resistance5 tumor sample Case marker detected. resistant basal cell cancers tissue: skin; cell type: basal cell carcinomas (BCCs); response to smoothened (smo) inhibitors: Resistance
  • GSM1409347 RNASeq_Resistance6 tumor sample Case marker detected. resistant basal cell cancers tissue: skin; cell type: basal cell carcinomas (BCCs); response to smoothened (smo) inhibitors: Resistance
  • GSM1409348 RNASeq_Resistance7 tumor sample Case marker detected. resistant basal cell cancers tissue: skin; cell type: basal cell carcinomas (BCCs); response to smoothened (smo) inhibitors: Resistance
  • GSM1409349 RNASeq_Resistance8 tumor sample Case marker detected. resistant basal cell cancers tissue: skin; cell type: basal cell carcinomas (BCCs); response to smoothened (smo) inhibitors: Resistance
  • GSM1409350 RNASeq_Resistance9 tumor sample Case marker detected. resistant basal cell cancers tissue: skin; cell type: basal cell carcinomas (BCCs); response to smoothened (smo) inhibitors: Resistance
  • GSM1409351 RNASeq_Sensitive1 tumor sample Case marker detected. sensitive basal cell cancers tissue: skin; cell type: basal cell carcinomas (BCCs); response to smoothened (smo) inhibitors: Sensitive
  • GSM1409352 RNASeq_Sensitive2 tumor sample Case marker detected. sensitive basal cell cancers tissue: skin; cell type: basal cell carcinomas (BCCs); response to smoothened (smo) inhibitors: Sensitive
  • GSM1409353 RNASeq_Sensitive3 tumor sample Case marker detected. sensitive basal cell cancers tissue: skin; cell type: basal cell carcinomas (BCCs); response to smoothened (smo) inhibitors: Sensitive
  • GSM1409354 RNASeq_Sensitive4 tumor sample Case marker detected. sensitive basal cell cancers tissue: skin; cell type: basal cell carcinomas (BCCs); response to smoothened (smo) inhibitors: Sensitive

Possible control samples

Samples currently treated as controls or baseline.

8
  • GSM1409334 RNASeq_Normal1 normal tissue Control marker detected. normal skin biopsies tissue: skin; response to smoothened (smo) inhibitors: Normal
  • GSM1409335 RNASeq_Normal2 normal tissue Control marker detected. normal skin biopsies tissue: skin; response to smoothened (smo) inhibitors: Normal
  • GSM1409336 RNASeq_Normal3 normal tissue Control marker detected. normal skin biopsies tissue: skin; response to smoothened (smo) inhibitors: Normal
  • GSM1409337 RNASeq_Normal4 normal tissue Control marker detected. normal skin biopsies tissue: skin; response to smoothened (smo) inhibitors: Normal
  • GSM1409338 RNASeq_Normal5 normal tissue Control marker detected. normal skin biopsies tissue: skin; response to smoothened (smo) inhibitors: Normal
  • GSM1409339 RNASeq_Normal6 normal tissue Control marker detected. normal skin biopsies tissue: skin; response to smoothened (smo) inhibitors: Normal
  • GSM1409340 RNASeq_Normal7 normal tissue Control marker detected. normal skin biopsies tissue: skin; response to smoothened (smo) inhibitors: Normal
  • GSM1409341 RNASeq_Normal8 normal tissue Control marker detected. normal skin biopsies tissue: skin; response to smoothened (smo) inhibitors: Normal

Unassigned samples

Samples with no explicit case or control marker.

0

No samples

Excluded samples

Samples excluded from grouping by hard exclusion rules.

0

No samples

Ambiguous samples

Samples that need manual review before trusting grouping.

0

No samples

Metadata Quality Components

Persisted metadata quality

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

normal tissue

8 samples
  • GSM1409334 RNASeq_Normal1 normal skin biopsies tissue: skin; response to smoothened (smo) inhibitors: Normal
  • GSM1409335 RNASeq_Normal2 normal skin biopsies tissue: skin; response to smoothened (smo) inhibitors: Normal
  • GSM1409336 RNASeq_Normal3 normal skin biopsies tissue: skin; response to smoothened (smo) inhibitors: Normal
  • GSM1409337 RNASeq_Normal4 normal skin biopsies tissue: skin; response to smoothened (smo) inhibitors: Normal
  • GSM1409338 RNASeq_Normal5 normal skin biopsies tissue: skin; response to smoothened (smo) inhibitors: Normal
  • GSM1409339 RNASeq_Normal6 normal skin biopsies tissue: skin; response to smoothened (smo) inhibitors: Normal
  • GSM1409340 RNASeq_Normal7 normal skin biopsies tissue: skin; response to smoothened (smo) inhibitors: Normal
  • GSM1409341 RNASeq_Normal8 normal skin biopsies tissue: skin; response to smoothened (smo) inhibitors: Normal

tumor sample

13 samples
  • GSM1409342 RNASeq_Resistance1 resistant basal cell cancers tissue: skin; cell type: basal cell carcinomas (BCCs); response to smoothened (smo) inhibitors: Resistance
  • GSM1409343 RNASeq_Resistance2 resistant basal cell cancers tissue: skin; cell type: basal cell carcinomas (BCCs); response to smoothened (smo) inhibitors: Resistance
  • GSM1409344 RNASeq_Resistance3 resistant basal cell cancers tissue: skin; cell type: basal cell carcinomas (BCCs); response to smoothened (smo) inhibitors: Resistance
  • GSM1409345 RNASeq_Resistance4 resistant basal cell cancers tissue: skin; cell type: basal cell carcinomas (BCCs); response to smoothened (smo) inhibitors: Resistance
  • GSM1409346 RNASeq_Resistance5 resistant basal cell cancers tissue: skin; cell type: basal cell carcinomas (BCCs); response to smoothened (smo) inhibitors: Resistance
  • GSM1409347 RNASeq_Resistance6 resistant basal cell cancers tissue: skin; cell type: basal cell carcinomas (BCCs); response to smoothened (smo) inhibitors: Resistance
  • GSM1409348 RNASeq_Resistance7 resistant basal cell cancers tissue: skin; cell type: basal cell carcinomas (BCCs); response to smoothened (smo) inhibitors: Resistance
  • GSM1409349 RNASeq_Resistance8 resistant basal cell cancers tissue: skin; cell type: basal cell carcinomas (BCCs); response to smoothened (smo) inhibitors: Resistance
  • GSM1409350 RNASeq_Resistance9 resistant basal cell cancers tissue: skin; cell type: basal cell carcinomas (BCCs); response to smoothened (smo) inhibitors: Resistance
  • GSM1409351 RNASeq_Sensitive1 sensitive basal cell cancers tissue: skin; cell type: basal cell carcinomas (BCCs); response to smoothened (smo) inhibitors: Sensitive
  • GSM1409352 RNASeq_Sensitive2 sensitive basal cell cancers tissue: skin; cell type: basal cell carcinomas (BCCs); response to smoothened (smo) inhibitors: Sensitive
  • GSM1409353 RNASeq_Sensitive3 sensitive basal cell cancers tissue: skin; cell type: basal cell carcinomas (BCCs); response to smoothened (smo) inhibitors: Sensitive
  • GSM1409354 RNASeq_Sensitive4 sensitive basal cell cancers tissue: skin; cell type: basal cell carcinomas (BCCs); response to smoothened (smo) inhibitors: Sensitive

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

Sample Links

21 samples

Review Audit Trail

0 decisions

No review decisions have been stored for this dataset.