Siftome Phase 3L

GSE149390

Importance of RAD6B in activation of canonical WNT signaling in melanoma development

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
2020-04-27
Last update
2021-01-26
Organization
Wayne State University
Department
Oncology
Public date
2020-10-27
Experiment types
Expression profiling by high throughput sequencing
Platforms
GPL16791 Illumina HiSeq 2500 (Homo sapiens)
Series type
Series
SubSeries
Not available
BioProject
PRJNA628598
Supplementary files
CSV: GSE149390_Melanoma_melanocyte_M14_Rad6BKO_Diff_Expression_mshekhar.csv.gz; CSV: GSE149390_Melanoma_melanocyte_M14_Rad6BKO_HEMaLP_Diff_Expression_mshekhar.csv.gz; CSV: GSE149390_Melanoma_melanocyte_M14_Rad6BKO_HEMaLP_counts_mshekhar.csv.gz; CSV: GSE149390_Melanoma_melanocyte_M14_Rad6BKO_counts_mshekhar.csv.gz
Organism
Homo sapiens
Assay
bulk RNA-seq
Samples
9
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

  • 3 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 3 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 fewer than ten samples limit cohort confidence. 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 3 samples
  • Likely control group normal tissue 3 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 fewer than ten samples limit cohort confidence. 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
GSE149390
Sample records
9 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
GSE149390
  • 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
GSE149390
  • 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
GSE149390
  • 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: GSE149390
dataset_title: Importance of RAD6B in activation of canonical WNT signaling in melanoma development
organism: Homo sapiens
assay_type: bulk RNA-seq
processed_data_available: true
raw_data_available: true
submission_date: 2020-04-27
last_update_date: 2021-01-26
organization_name: Wayne State University
department: Oncology
public_date: 2020-10-27
experiment_types: Expression profiling by high throughput sequencing
platforms: GPL16791 Illumina HiSeq 2500 (Homo sapiens)
sub_series: Not available
bioproject: PRJNA628598
supplementary_files: CSV: GSE149390_Melanoma_melanocyte_M14_Rad6BKO_Diff_Expression_mshekhar.csv.gz; CSV: GSE149390_Melanoma_melanocyte_M14_Rad6BKO_HEMaLP_Diff_Expression_mshekhar.csv.gz; CSV: GSE149390_Melanoma_melanocyte_M14_Rad6BKO_HEMaLP_counts_mshekhar.csv.gz; CSV: GSE149390_Melanoma_melanocyte_M14_Rad6BKO_counts_mshekhar.csv.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.

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 fewer than ten samples limit cohort confidence.
  • 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

15 fields
Field Value Source Origin Confidence Evidence Reason
assay_type bulk RNA-seq dataset GSE149390 Runtime Siftome inference GEO:dataset:GSE149390:ddc877f22d88e7ef6119d40a3fbf91bccc356a09fdccc6380b2f4a3e6de0d6b0 high confidence bulk rna-seq dataset_accession: GSE149390 dataset_title: Importance of RAD6B in activation of canonical WNT signaling in melanoma development organism: Homo sapiens assay_type: bulk RNA-seq ... keyword match keyword match: bulk rna-seq
disease melanoma dataset GSE149390 Runtime Siftome inference GEO:dataset:GSE149390:ddc877f22d88e7ef6119d40a3fbf91bccc356a09fdccc6380b2f4a3e6de0d6b0 high confidence melanoma dataset_accession: GSE149390 dataset_title: Importance of RAD6B in activation of canonical WNT signaling in melanoma development organism: Homo sapiens assay_type: bulk RNA-seq ... controlled vocabulary controlled vocabulary disease match: melanoma
disease melanoma sample GSM4498881 Runtime Siftome inference GEO:sample:GSM4498881:91fcd1c1b655e146e4735a3c951e0dd922c832d902429383123473cfdcdb0707 high confidence melanoma sample_accession: GSM4498881 sample_title: CtrlM14 1: Control M14 melanoma source_name: Metastatic melanoma line characteristics: tissue: Metastatic melanoma line CtrlM14 1: Con... controlled vocabulary controlled vocabulary disease match: melanoma
disease melanoma sample GSM4498882 Runtime Siftome inference GEO:sample:GSM4498882:64cca730be83cfaa3380fc9528fcf6d50bbf1ccfa294fca60ae049e068622ef5 high confidence melanoma sample_accession: GSM4498882 sample_title: CtrlM14 2: Control M14 melanoma source_name: Metastatic melanoma line characteristics: tissue: Metastatic melanoma line CtrlM14 2: Con... controlled vocabulary controlled vocabulary disease match: melanoma
disease melanoma sample GSM4498883 Runtime Siftome inference GEO:sample:GSM4498883:85c3dd4dc7914203f86c43b1c21e4ec772bbd1cca1e0b8c310bf66dd90c3c40f high confidence melanoma sample_accession: GSM4498883 sample_title: CtrlM14 3: Control M14 melanoma source_name: Metastatic melanoma line characteristics: tissue: Metastatic melanoma line CtrlM14 3: Con... controlled vocabulary controlled vocabulary disease match: melanoma
organism Homo sapiens dataset GSE149390 Runtime Siftome inference GEO:dataset:GSE149390:ddc877f22d88e7ef6119d40a3fbf91bccc356a09fdccc6380b2f4a3e6de0d6b0 high confidence homo sapiens dataset_accession: GSE149390 dataset_title: Importance of RAD6B in activation of canonical WNT signaling in melanoma development organism: Homo sapiens assay_type: bulk RNA-seq ... keyword match keyword match: homo sapiens
sample_type tumor sample sample GSM4498881 Runtime Siftome inference GEO:sample:GSM4498881:91fcd1c1b655e146e4735a3c951e0dd922c832d902429383123473cfdcdb0707 medium confidence metastatic sample_accession: GSM4498881 sample_title: CtrlM14 1: Control M14 melanoma source_name: Metastatic melanoma line characteristics: tissue: Metastatic melanoma line CtrlM14 1: Con... controlled vocabulary controlled vocabulary sample type match: metastatic
sample_type tumor sample sample GSM4498882 Runtime Siftome inference GEO:sample:GSM4498882:64cca730be83cfaa3380fc9528fcf6d50bbf1ccfa294fca60ae049e068622ef5 medium confidence metastatic sample_accession: GSM4498882 sample_title: CtrlM14 2: Control M14 melanoma source_name: Metastatic melanoma line characteristics: tissue: Metastatic melanoma line CtrlM14 2: Con... controlled vocabulary controlled vocabulary sample type match: metastatic
sample_type tumor sample sample GSM4498883 Runtime Siftome inference GEO:sample:GSM4498883:85c3dd4dc7914203f86c43b1c21e4ec772bbd1cca1e0b8c310bf66dd90c3c40f medium confidence metastatic sample_accession: GSM4498883 sample_title: CtrlM14 3: Control M14 melanoma source_name: Metastatic melanoma line characteristics: tissue: Metastatic melanoma line CtrlM14 3: Con... controlled vocabulary controlled vocabulary sample type match: metastatic
sample_type normal tissue sample GSM4498884 Runtime Siftome inference GEO:sample:GSM4498884:8066ba91df617141799339383856647450138040f03eb5319108eddd904a4192 low confidence normal sample_accession: GSM4498884 sample_title: HEMaLP 1: HEMa-LP normal melanocytes source_name: Normal epidermal melanocytes characteristics: tissue: Normal epidermal melanocytes H... controlled vocabulary controlled vocabulary sample type match: normal
sample_type normal tissue sample GSM4498885 Runtime Siftome inference GEO:sample:GSM4498885:ed5ee836c21b632e8f7510161e031e56f85787c40dd2192bf05de41e7accd72a low confidence normal sample_accession: GSM4498885 sample_title: HEMaLP 2: HEMa-LP normal melanocytes source_name: Normal epidermal melanocytes characteristics: tissue: Normal epidermal melanocytes H... controlled vocabulary controlled vocabulary sample type match: normal
sample_type normal tissue sample GSM4498886 Runtime Siftome inference GEO:sample:GSM4498886:22121affc6f133701ab72471eddc93665cf0ddd2ebf7f26c286cbab920054fee low confidence normal sample_accession: GSM4498886 sample_title: HEMaLP 3: HEMa-LP normal melanocytes source_name: Normal epidermal melanocytes characteristics: tissue: Normal epidermal melanocytes H... controlled vocabulary controlled vocabulary sample type match: normal
tissue skin sample GSM4498884 Runtime Siftome inference GEO:sample:GSM4498884:8066ba91df617141799339383856647450138040f03eb5319108eddd904a4192 medium confidence dermal sample_accession: GSM4498884 sample_title: HEMaLP 1: HEMa-LP normal melanocytes source_name: Normal epidermal melanocytes characteristics: tissue: Normal epidermal melanocytes H... controlled vocabulary controlled vocabulary tissue match: dermal
tissue skin sample GSM4498885 Runtime Siftome inference GEO:sample:GSM4498885:ed5ee836c21b632e8f7510161e031e56f85787c40dd2192bf05de41e7accd72a medium confidence dermal sample_accession: GSM4498885 sample_title: HEMaLP 2: HEMa-LP normal melanocytes source_name: Normal epidermal melanocytes characteristics: tissue: Normal epidermal melanocytes H... controlled vocabulary controlled vocabulary tissue match: dermal
tissue skin sample GSM4498886 Runtime Siftome inference GEO:sample:GSM4498886:22121affc6f133701ab72471eddc93665cf0ddd2ebf7f26c286cbab920054fee medium confidence dermal sample_accession: GSM4498886 sample_title: HEMaLP 3: HEMa-LP normal melanocytes source_name: Normal epidermal melanocytes characteristics: tissue: Normal epidermal melanocytes H... controlled vocabulary controlled vocabulary tissue match: dermal

Sample Group Preview

Possible case samples

Samples currently treated as the comparison case group.

3
  • GSM4498881 CtrlM14 1: Control M14 melanoma tumor sample Case marker detected. Metastatic melanoma line tissue: Metastatic melanoma line
  • GSM4498882 CtrlM14 2: Control M14 melanoma tumor sample Case marker detected. Metastatic melanoma line tissue: Metastatic melanoma line
  • GSM4498883 CtrlM14 3: Control M14 melanoma tumor sample Case marker detected. Metastatic melanoma line tissue: Metastatic melanoma line

Possible control samples

Samples currently treated as controls or baseline.

3
  • GSM4498884 HEMaLP 1: HEMa-LP normal melanocytes normal tissue Control marker detected. Normal epidermal melanocytes tissue: Normal epidermal melanocytes
  • GSM4498885 HEMaLP 2: HEMa-LP normal melanocytes normal tissue Control marker detected. Normal epidermal melanocytes tissue: Normal epidermal melanocytes
  • GSM4498886 HEMaLP 3: HEMa-LP normal melanocytes normal tissue Control marker detected. Normal epidermal melanocytes tissue: Normal epidermal melanocytes

Unassigned samples

Samples with no explicit case or control marker.

3
  • GSM4498887 RAD6BKOM14 1: RAD6B knockout M14 unassigned No explicit case or control marker detected. RAD6B gene disrupted M14 cells tissue: RAD6B gene disrupted M14 cells
  • GSM4498888 RAD6BKOM14 2: RAD6B knockout M14 unassigned No explicit case or control marker detected. RAD6B gene disrupted M14 cells tissue: RAD6B gene disrupted M14 cells
  • GSM4498889 RAD6BKOM14 3: RAD6B knockout M14 unassigned No explicit case or control marker detected. RAD6B gene disrupted M14 cells tissue: RAD6B gene disrupted M14 cells

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

Detected Sample Groups

tumor sample

3 samples
  • GSM4498881 CtrlM14 1: Control M14 melanoma Metastatic melanoma line tissue: Metastatic melanoma line
  • GSM4498882 CtrlM14 2: Control M14 melanoma Metastatic melanoma line tissue: Metastatic melanoma line
  • GSM4498883 CtrlM14 3: Control M14 melanoma Metastatic melanoma line tissue: Metastatic melanoma line

normal tissue

3 samples
  • GSM4498884 HEMaLP 1: HEMa-LP normal melanocytes Normal epidermal melanocytes tissue: Normal epidermal melanocytes
  • GSM4498885 HEMaLP 2: HEMa-LP normal melanocytes Normal epidermal melanocytes tissue: Normal epidermal melanocytes
  • GSM4498886 HEMaLP 3: HEMa-LP normal melanocytes Normal epidermal melanocytes tissue: Normal epidermal melanocytes

unassigned

3 samples
  • GSM4498887 RAD6BKOM14 1: RAD6B knockout M14 RAD6B gene disrupted M14 cells tissue: RAD6B gene disrupted M14 cells
  • GSM4498888 RAD6BKOM14 2: RAD6B knockout M14 RAD6B gene disrupted M14 cells tissue: RAD6B gene disrupted M14 cells
  • GSM4498889 RAD6BKOM14 3: RAD6B knockout M14 RAD6B gene disrupted M14 cells tissue: RAD6B gene disrupted M14 cells

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 fewer than ten samples limit cohort confidence.
  • Overall score capped because tumor/normal grouping is from a non-colorectal cancer context.

Sample Links

9 samples

Review Audit Trail

0 decisions

No review decisions have been stored for this dataset.