Siftome Phase 3L

GSE184616

RNA-seq of HPV-negative Oral Squamous Cell Carcinoma Patients

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: 2021-09-22
Last update: 2021-12-26
Organization: University of Sydney
Department: School of Mathematics and Statistics
Public date: 2021-11-25
Experiment types: Expression profiling by high throughput sequencing
Platforms: GPL24676 Illumina NovaSeq 6000 (Homo sapiens)
Series type: Series
SubSeries: Not available
BioProject: PRJNA765370
Supplementary files: TXT: GSE184616_genesFPKMs.txt.gz; TXT: GSE184616_unnormalisedGeneCounts.txt.gz
Organism: Homo sapiens
Assay: bulk RNA-seq
Samples: 30
Study design: Tumor vs matched normal
Specimen/source: Tissue
Scoring version: intent-aware-scoring-v15
Ranking batch: b69568dd1e4fe1b9ee2d880bf5495d748a7e4c5c11e4107f02528c3be0e76012
Ranking created: 2026-06-05T20:20:27.088676Z
Warning version: intent-aware-warnings-v2

Current Intent Interpretation

Patient tissue tumor-vs-normal

Expectations

Organism: Homo sapiens
Assay: bulk RNA-seq
Specimen/source: patient tissue or biopsy
Controls: matched normal, adjacent normal, paired normal, healthy tissue control, or otherwise normal tissue control

Rules

Default filters: Human only; Bulk RNA-seq only; Tumor-normal only; Tissue or biopsy only; Hide biofluid/model systems
Warning rules: missing or unclear control group, unclear disease context, unclear tissue source, mixed sample types, model-system markers, secondary assay context, missing processed data, or small cohort size
Score caps: non-human datasets stay below the primary recommendation band, missing colorectal/colon/rectal/CRC context stays below the primary recommendation band, biofluid and model-system datasets cannot reach Recommended by default, microarray and secondary assays are capped unless explicitly enabled, or small cohorts are capped below high-confidence recommendations
Downgraded contexts: microarray unless explicitly enabled, biofluid-only datasets, cell-line datasets, organoid datasets, xenograft or PDX datasets, non-colorectal disease contexts, or treatment-only experiments

Study Classification

Tumor vs matched normal Tissue

Tumor samples and matched/adjacent normal controls detected.
Tissue-like source terms detected.
Case metadata contains tumor or disease terms.
Control metadata contains normal or healthy-control terms.

Analysis Readiness

Ready after review

94% 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

7/10 pts

Metadata quality is usable, but still deserves review.

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 50% Organism normalized. Assay type normalized.
comparison suitability 0% Tumor and normal sample groups detected. No excluded sample type flags detected. Matched tumor/normal design boosted for colorectal tumor-vs-normal tissue triage. Patient tissue or biopsy specimens boosted for tissue comparison triage. Non-colorectal cancer context downgraded for colorectal tumor-vs-normal tissue ranking.
metadata quality 70% 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 was not 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 matched normal Study design remains rule-derived: Tumor vs matched normal.
Specimen/source Tissue Specimen/source remains rule-derived: Tissue.
Likely case group tumor sample 15 samples
Likely control group normal tissue 15 samples

Warnings

DISEASE_LABEL_UNCLEAR warning Disease or condition label could not be normalized.
TISSUE_TYPE_MISSING warning Tissue or cell type could not be normalized.

Intent Interpretation

Active intent Patient tissue tumor-vs-normal Ranks human colorectal tissue or biopsy cohorts where tumor samples can be compared with normal controls.
Organism expectation Homo sapiens Dataset organism is interpreted as Homo sapiens.
Assay expectation bulk RNA-seq Dataset assay is interpreted as bulk RNA-seq.
Specimen assumption patient tissue or biopsy Derived specimen/source is Tissue.
Control-group assumption matched normal, adjacent normal, paired normal, healthy tissue control, or otherwise normal tissue control Derived study design is Tumor vs matched normal; likely groups are tumor sample vs normal tissue.
Score caps Applied when matching conditions are present non-human datasets stay below the primary recommendation band, missing colorectal/colon/rectal/CRC context stays below the primary recommendation band, biofluid and model-system datasets cannot reach Recommended by default, microarray and secondary assays are capped unless explicitly enabled, or small cohorts are capped below high-confidence recommendations
Warning rules 2 active warnings missing or unclear control group, unclear disease context, unclear tissue source, mixed sample types, model-system markers, secondary assay context, missing processed data, or small cohort size
Downgrade or exclusion reason Downgraded disease context: 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 matched normal · Tissue · suitability 0%. Contributed to match or upgrade evidence.
Supporting fact Prioritized for patient tissue tumor-vs-normal triage. Contributed to match or upgrade evidence.
Supporting fact Prioritized assay: bulk RNA-seq is the active assay expectation. Contributed to match or upgrade evidence.
Supporting fact Downgraded disease context: not a colorectal/GI cancer cohort. Contributed to match or upgrade evidence.
Supporting fact Processed data is available for downstream review. Contributed to match or upgrade evidence.
Supporting fact 2 warnings require review. Contributed to match or upgrade evidence.
Caution fact Disease or condition label could not be normalized. Contributed to downgrade or manual-review evidence.
Caution fact Tissue or cell type 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: Tissue clarity: Tissue 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: 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

No active manual corrections are applied to this dataset.

Organism · Normalization rules Organism remains rule-derived: Homo sapiens.
Assay · Normalization rules Assay remains rule-derived: bulk RNA-seq.
Study design · Classifier and grouping rules Study design remains rule-derived: Tumor vs matched normal.
Specimen/source · Normalization rules Specimen/source remains rule-derived: Tissue.

Dataset organism

Dataset field · Organism · Global correction

Wrong organism

Current derived value

Homo sapiens

Raw GEO organism

dataset_accession: GSE184616
organism: Homo sapiens
dataset_title: RNA-seq of HPV-negative Oral Squamous Cell Carcinoma Patients

Dataset assay

Dataset field · Assay · Global correction

Wrong assay

Current derived value

bulk RNA-seq

Raw GEO assay metadata

assay_type: bulk RNA-seq
experiment_types: Expression profiling by high throughput sequencing
platforms: GPL24676 Illumina NovaSeq 6000 (Homo sapiens)
dataset_title: RNA-seq of HPV-negative Oral Squamous Cell Carcinoma Patients

Study design

Dataset field · Study design · Global correction

Wrong study design

Current derived value

Tumor vs matched normal

Raw GEO study and sample metadata

dataset_title: RNA-seq of HPV-negative Oral Squamous Cell Carcinoma Patients
experiment_types: Expression profiling by high throughput sequencing
sample_context: GSM5593747: source_name=Tongue; characteristics=patient diagnosis: HPV-negative Oral Squamous Cell Carcinoma; patient id: OSCC_1; tissue: oral mucosa; condition: Adjacent Normal; age: 50; gender: Male; smoking: No
GSM5593748: source_name=Tongue; characteristics=patient diagnosis: HPV-negative Oral Squamous Cell Carcinoma; patient id: OSCC_1; tissue: fresh frozen OSCC; condition: Primary Tumour; age: 50; gender: Male; smoking: No
GSM5593749: source_name=Tongue; characteristics=patient diagnosis: HPV-negative Oral Squamous Cell Carcinoma; patient id: OSCC_2; tissue: oral mucosa; condition: Adjacent Normal; age: 33; gender: Male; smoking: No
GSM5593750: source_name=Tongue; characteristics=patient diagnosis: HPV-negative Oral Squamo
[Correction source preview truncated.]

Specimen/source type

Dataset field · Specimen/source · Global correction

Wrong specimen/source

Current derived value

Tissue

Raw GEO sample source metadata

dataset_title: RNA-seq of HPV-negative Oral Squamous Cell Carcinoma Patients
sample_context: GSM5593747: source_name=Tongue; characteristics=patient diagnosis: HPV-negative Oral Squamous Cell Carcinoma; patient id: OSCC_1; tissue: oral mucosa; condition: Adjacent Normal; age: 50; gender: Male; smoking: No
GSM5593748: source_name=Tongue; characteristics=patient diagnosis: HPV-negative Oral Squamous Cell Carcinoma; patient id: OSCC_1; tissue: fresh frozen OSCC; condition: Primary Tumour; age: 50; gender: Male; smoking: No
GSM5593749: source_name=Tongue; characteristics=patient diagnosis: HPV-negative Oral Squamous Cell Carcinoma; patient id: OSCC_2; tissue: oral mucosa; condition: Adjacent Normal; age: 33; gender: Male; smoking: No
GSM5593750: source_name=Tongue; characteristics=patient diagnosis: HPV-negative Oral Squamous Cell Carcinoma; patient id: OSCC_2; tissue: fresh frozen OSCC; con
[Correction source preview truncated.]

Disease context

Dataset field · Disease context · Global correction

Wrong disease context

Current derived value

No disease context detected

Raw GEO disease context metadata

dataset_title: RNA-seq of HPV-negative Oral Squamous Cell Carcinoma Patients
sample_context: GSM5593747: source_name=Tongue; characteristics=patient diagnosis: HPV-negative Oral Squamous Cell Carcinoma; patient id: OSCC_1; tissue: oral mucosa; condition: Adjacent Normal; age: 50; gender: Male; smoking: No
GSM5593748: source_name=Tongue; characteristics=patient diagnosis: HPV-negative Oral Squamous Cell Carcinoma; patient id: OSCC_1; tissue: fresh frozen OSCC; condition: Primary Tumour; age: 50; gender: Male; smoking: No
GSM5593749: source_name=Tongue; characteristics=patient diagnosis: HPV-negative Oral Squamous Cell Carcinoma; patient id: OSCC_2; tissue: oral mucosa; condition: Adjacent Normal; age: 33; gender: Male; smoking: No
GSM5593750: source_name=Tongue; characteristics=patient diagnosis: HPV-negative Oral Squamous Cell Carcinoma; patient id: OSCC_2; tissue: fresh frozen OSCC; con
[Correction source preview truncated.]

Intent exclusion

Search intent · Intent eligibility · Patient tissue tumor-vs-normal

Exclude from intent

Current derived value

Eligible for Patient tissue tumor-vs-normal as Not suitable

Raw GEO metadata for intent decision

dataset_accession: GSE184616
dataset_title: RNA-seq of HPV-negative Oral Squamous Cell Carcinoma Patients
organism: Homo sapiens
assay_type: bulk RNA-seq
sample_context: GSM5593747: source_name=Tongue; characteristics=patient diagnosis: HPV-negative Oral Squamous Cell Carcinoma; patient id: OSCC_1; tissue: oral mucosa; condition: Adjacent Normal; age: 50; gender: Male; smoking: No
GSM5593748: source_name=Tongue; characteristics=patient diagnosis: HPV-negative Oral Squamous Cell Carcinoma; patient id: OSCC_1; tissue: fresh frozen OSCC; condition: Primary Tumour; age: 50; gender: Male; smoking: No
GSM5593749: source_name=Tongue; characteristics=patient diagnosis: HPV-negative Oral Squamous Cell Carcinoma; patient id: OSCC_2; tissue: oral mucosa; condition: Adjacent Normal; age: 33; gender: Male; smoking: No
GSM5593750: source_name=Tongue; characteristics=patient diagnosis: HPV-negative Ora
[Correction source preview truncated.]

Intent-only inclusion

Search intent · Intent eligibility · Patient tissue tumor-vs-normal

Include only for intent

Current derived value

Eligible for Patient tissue tumor-vs-normal as Not suitable

Raw GEO metadata for intent decision

dataset_accession: GSE184616
dataset_title: RNA-seq of HPV-negative Oral Squamous Cell Carcinoma Patients
organism: Homo sapiens
assay_type: bulk RNA-seq
sample_context: GSM5593747: source_name=Tongue; characteristics=patient diagnosis: HPV-negative Oral Squamous Cell Carcinoma; patient id: OSCC_1; tissue: oral mucosa; condition: Adjacent Normal; age: 50; gender: Male; smoking: No
GSM5593748: source_name=Tongue; characteristics=patient diagnosis: HPV-negative Oral Squamous Cell Carcinoma; patient id: OSCC_1; tissue: fresh frozen OSCC; condition: Primary Tumour; age: 50; gender: Male; smoking: No
GSM5593749: source_name=Tongue; characteristics=patient diagnosis: HPV-negative Oral Squamous Cell Carcinoma; patient id: OSCC_2; tissue: oral mucosa; condition: Adjacent Normal; age: 33; gender: Male; smoking: No
GSM5593750: source_name=Tongue; characteristics=patient diagnosis: HPV-negative Ora
[Correction source preview truncated.]

GSM5593747 grouping

Sample field · Grouping · Global correction · GSM5593747

Wrong grouping

Current derived value

normal tissue (control)

Raw GEO sample metadata

sample_accession: GSM5593747
sample_title: OSCC_1-N
source_name: Tongue
characteristics: patient diagnosis: HPV-negative Oral Squamous Cell Carcinoma; patient id: OSCC_1; tissue: oral mucosa; condition: Adjacent Normal; age: 50; gender: Male; smoking: No

GSM5593747 exclusion decision

Sample field · Sample exclusion · Global correction · GSM5593747

Wrong sample exclusion

Current derived value

Included in derived sample grouping as normal tissue

Raw GEO sample metadata

sample_accession: GSM5593747
sample_title: OSCC_1-N
source_name: Tongue
characteristics: patient diagnosis: HPV-negative Oral Squamous Cell Carcinoma; patient id: OSCC_1; tissue: oral mucosa; condition: Adjacent Normal; age: 50; gender: Male; smoking: No

GSM5593748 grouping

Sample field · Grouping · Global correction · GSM5593748

Wrong grouping

Current derived value

tumor sample (case)

Raw GEO sample metadata

sample_accession: GSM5593748
sample_title: OSCC_1-P
source_name: Tongue
characteristics: patient diagnosis: HPV-negative Oral Squamous Cell Carcinoma; patient id: OSCC_1; tissue: fresh frozen OSCC; condition: Primary Tumour; age: 50; gender: Male; smoking: No

GSM5593748 exclusion decision

Sample field · Sample exclusion · Global correction · GSM5593748

Wrong sample exclusion

Current derived value

Included in derived sample grouping as tumor sample

Raw GEO sample metadata

sample_accession: GSM5593748
sample_title: OSCC_1-P
source_name: Tongue
characteristics: patient diagnosis: HPV-negative Oral Squamous Cell Carcinoma; patient id: OSCC_1; tissue: fresh frozen OSCC; condition: Primary Tumour; age: 50; gender: Male; smoking: No

GSM5593749 grouping

Sample field · Grouping · Global correction · GSM5593749

Wrong grouping

Current derived value

normal tissue (control)

Raw GEO sample metadata

sample_accession: GSM5593749
sample_title: OSCC_2-N
source_name: Tongue
characteristics: patient diagnosis: HPV-negative Oral Squamous Cell Carcinoma; patient id: OSCC_2; tissue: oral mucosa; condition: Adjacent Normal; age: 33; gender: Male; smoking: No

GSM5593749 exclusion decision

Sample field · Sample exclusion · Global correction · GSM5593749

Wrong sample exclusion

Current derived value

Included in derived sample grouping as normal tissue

Raw GEO sample metadata

sample_accession: GSM5593749
sample_title: OSCC_2-N
source_name: Tongue
characteristics: patient diagnosis: HPV-negative Oral Squamous Cell Carcinoma; patient id: OSCC_2; tissue: oral mucosa; condition: Adjacent Normal; age: 33; gender: Male; smoking: No

GSM5593750 grouping

Sample field · Grouping · Global correction · GSM5593750

Wrong grouping

Current derived value

tumor sample (case)

Raw GEO sample metadata

sample_accession: GSM5593750
sample_title: OSCC_2-P
source_name: Tongue
characteristics: patient diagnosis: HPV-negative Oral Squamous Cell Carcinoma; patient id: OSCC_2; tissue: fresh frozen OSCC; condition: Primary Tumour; age: 33; gender: Male; smoking: No

GSM5593750 exclusion decision

Sample field · Sample exclusion · Global correction · GSM5593750

Wrong sample exclusion

Current derived value

Included in derived sample grouping as tumor sample

Raw GEO sample metadata

sample_accession: GSM5593750
sample_title: OSCC_2-P
source_name: Tongue
characteristics: patient diagnosis: HPV-negative Oral Squamous Cell Carcinoma; patient id: OSCC_2; tissue: fresh frozen OSCC; condition: Primary Tumour; age: 33; gender: Male; smoking: No

GSM5593751 grouping

Sample field · Grouping · Global correction · GSM5593751

Wrong grouping

Current derived value

normal tissue (control)

Raw GEO sample metadata

sample_accession: GSM5593751
sample_title: OSCC_3-N
source_name: Gingivolingual sulcus
characteristics: patient diagnosis: HPV-negative Oral Squamous Cell Carcinoma; patient id: OSCC_3; tissue: oral mucosa; condition: Adjacent Normal; age: 45; gender: Male; smoking: Yes

GSM5593751 exclusion decision

Sample field · Sample exclusion · Global correction · GSM5593751

Wrong sample exclusion

Current derived value

Included in derived sample grouping as normal tissue

Raw GEO sample metadata

sample_accession: GSM5593751
sample_title: OSCC_3-N
source_name: Gingivolingual sulcus
characteristics: patient diagnosis: HPV-negative Oral Squamous Cell Carcinoma; patient id: OSCC_3; tissue: oral mucosa; condition: Adjacent Normal; age: 45; gender: Male; smoking: Yes

GSM5593752 grouping

Sample field · Grouping · Global correction · GSM5593752

Wrong grouping

Current derived value

tumor sample (case)

Raw GEO sample metadata

sample_accession: GSM5593752
sample_title: OSCC_3-P
source_name: Gingivolingual sulcus
characteristics: patient diagnosis: HPV-negative Oral Squamous Cell Carcinoma; patient id: OSCC_3; tissue: fresh frozen OSCC; condition: Primary Tumour; age: 45; gender: Male; smoking: Yes

GSM5593752 exclusion decision

Sample field · Sample exclusion · Global correction · GSM5593752

Wrong sample exclusion

Current derived value

Included in derived sample grouping as tumor sample

Raw GEO sample metadata

sample_accession: GSM5593752
sample_title: OSCC_3-P
source_name: Gingivolingual sulcus
characteristics: patient diagnosis: HPV-negative Oral Squamous Cell Carcinoma; patient id: OSCC_3; tissue: fresh frozen OSCC; condition: Primary Tumour; age: 45; gender: Male; smoking: Yes

GSM5593753 grouping

Sample field · Grouping · Global correction · GSM5593753

Wrong grouping

Current derived value

normal tissue (control)

Raw GEO sample metadata

sample_accession: GSM5593753
sample_title: OSCC_4-N
source_name: Floor of mouth
characteristics: patient diagnosis: HPV-negative Oral Squamous Cell Carcinoma; patient id: OSCC_4; tissue: oral mucosa; condition: Adjacent Normal; age: 48; gender: Male; smoking: Yes

GSM5593753 exclusion decision

Sample field · Sample exclusion · Global correction · GSM5593753

Wrong sample exclusion

Current derived value

Included in derived sample grouping as normal tissue

Raw GEO sample metadata

sample_accession: GSM5593753
sample_title: OSCC_4-N
source_name: Floor of mouth
characteristics: patient diagnosis: HPV-negative Oral Squamous Cell Carcinoma; patient id: OSCC_4; tissue: oral mucosa; condition: Adjacent Normal; age: 48; gender: Male; smoking: Yes

GSM5593754 grouping

Sample field · Grouping · Global correction · GSM5593754

Wrong grouping

Current derived value

tumor sample (case)

Raw GEO sample metadata

sample_accession: GSM5593754
sample_title: OSCC_4-P
source_name: Floor of mouth
characteristics: patient diagnosis: HPV-negative Oral Squamous Cell Carcinoma; patient id: OSCC_4; tissue: fresh frozen OSCC; condition: Primary Tumour; age: 48; gender: Male; smoking: Yes

GSM5593754 exclusion decision

Sample field · Sample exclusion · Global correction · GSM5593754

Wrong sample exclusion

Current derived value

Included in derived sample grouping as tumor sample

Raw GEO sample metadata

sample_accession: GSM5593754
sample_title: OSCC_4-P
source_name: Floor of mouth
characteristics: patient diagnosis: HPV-negative Oral Squamous Cell Carcinoma; patient id: OSCC_4; tissue: fresh frozen OSCC; condition: Primary Tumour; age: 48; gender: Male; smoking: Yes

GSM5593755 grouping

Sample field · Grouping · Global correction · GSM5593755

Wrong grouping

Current derived value

normal tissue (control)

Raw GEO sample metadata

sample_accession: GSM5593755
sample_title: OSCC_5-N
source_name: Tongue
characteristics: patient diagnosis: HPV-negative Oral Squamous Cell Carcinoma; patient id: OSCC_5; tissue: oral mucosa; condition: Adjacent Normal; age: 22; gender: Male; smoking: Yes

GSM5593755 exclusion decision

Sample field · Sample exclusion · Global correction · GSM5593755

Wrong sample exclusion

Current derived value

Included in derived sample grouping as normal tissue

Raw GEO sample metadata

sample_accession: GSM5593755
sample_title: OSCC_5-N
source_name: Tongue
characteristics: patient diagnosis: HPV-negative Oral Squamous Cell Carcinoma; patient id: OSCC_5; tissue: oral mucosa; condition: Adjacent Normal; age: 22; gender: Male; smoking: Yes

GSM5593756 grouping

Sample field · Grouping · Global correction · GSM5593756

Wrong grouping

Current derived value

tumor sample (case)

Raw GEO sample metadata

sample_accession: GSM5593756
sample_title: OSCC_5-P
source_name: Tongue
characteristics: patient diagnosis: HPV-negative Oral Squamous Cell Carcinoma; patient id: OSCC_5; tissue: fresh frozen OSCC; condition: Primary Tumour; age: 22; gender: Male; smoking: Yes

GSM5593756 exclusion decision

Sample field · Sample exclusion · Global correction · GSM5593756

Wrong sample exclusion

Current derived value

Included in derived sample grouping as tumor sample

Raw GEO sample metadata

sample_accession: GSM5593756
sample_title: OSCC_5-P
source_name: Tongue
characteristics: patient diagnosis: HPV-negative Oral Squamous Cell Carcinoma; patient id: OSCC_5; tissue: fresh frozen OSCC; condition: Primary Tumour; age: 22; gender: Male; smoking: Yes

GSM5593757 grouping

Sample field · Grouping · Global correction · GSM5593757

Wrong grouping

Current derived value

normal tissue (control)

Raw GEO sample metadata

sample_accession: GSM5593757
sample_title: OSCC_6-N
source_name: Tongue
characteristics: patient diagnosis: HPV-negative Oral Squamous Cell Carcinoma; patient id: OSCC_6; tissue: oral mucosa; condition: Adjacent Normal; age: 48; gender: Female; smoking: No

GSM5593757 exclusion decision

Sample field · Sample exclusion · Global correction · GSM5593757

Wrong sample exclusion

Current derived value

Included in derived sample grouping as normal tissue

Raw GEO sample metadata

sample_accession: GSM5593757
sample_title: OSCC_6-N
source_name: Tongue
characteristics: patient diagnosis: HPV-negative Oral Squamous Cell Carcinoma; patient id: OSCC_6; tissue: oral mucosa; condition: Adjacent Normal; age: 48; gender: Female; smoking: No

GSM5593758 grouping

Sample field · Grouping · Global correction · GSM5593758

Wrong grouping

Current derived value

tumor sample (case)

Raw GEO sample metadata

sample_accession: GSM5593758
sample_title: OSCC_6-P
source_name: Tongue
characteristics: patient diagnosis: HPV-negative Oral Squamous Cell Carcinoma; patient id: OSCC_6; tissue: fresh frozen OSCC; condition: Primary Tumour; age: 48; gender: Female; smoking: No

GSM5593758 exclusion decision

Sample field · Sample exclusion · Global correction · GSM5593758

Wrong sample exclusion

Current derived value

Included in derived sample grouping as tumor sample

Raw GEO sample metadata

sample_accession: GSM5593758
sample_title: OSCC_6-P
source_name: Tongue
characteristics: patient diagnosis: HPV-negative Oral Squamous Cell Carcinoma; patient id: OSCC_6; tissue: fresh frozen OSCC; condition: Primary Tumour; age: 48; gender: Female; smoking: No

GSM5593759 grouping

Sample field · Grouping · Global correction · GSM5593759

Wrong grouping

Current derived value

normal tissue (control)

Raw GEO sample metadata

sample_accession: GSM5593759
sample_title: OSCC_7-N
source_name: Palatal mucosa to maxilla
characteristics: patient diagnosis: HPV-negative Oral Squamous Cell Carcinoma; patient id: OSCC_7; tissue: oral mucosa; condition: Adjacent Normal; age: 49; gender: Male; smoking: Yes

GSM5593759 exclusion decision

Sample field · Sample exclusion · Global correction · GSM5593759

Wrong sample exclusion

Current derived value

Included in derived sample grouping as normal tissue

Raw GEO sample metadata

sample_accession: GSM5593759
sample_title: OSCC_7-N
source_name: Palatal mucosa to maxilla
characteristics: patient diagnosis: HPV-negative Oral Squamous Cell Carcinoma; patient id: OSCC_7; tissue: oral mucosa; condition: Adjacent Normal; age: 49; gender: Male; smoking: Yes

GSM5593760 grouping

Sample field · Grouping · Global correction · GSM5593760

Wrong grouping

Current derived value

tumor sample (case)

Raw GEO sample metadata

sample_accession: GSM5593760
sample_title: OSCC_7-P
source_name: Palatal mucosa to maxilla
characteristics: patient diagnosis: Oral Squamous Cell Carcinoma; patient id: OSCC_7; tissue: fresh frozen OSCC; condition: Primary Tumour; age: 49; gender: Male; smoking: Yes

GSM5593760 exclusion decision

Sample field · Sample exclusion · Global correction · GSM5593760

Wrong sample exclusion

Current derived value

Included in derived sample grouping as tumor sample

Raw GEO sample metadata

sample_accession: GSM5593760
sample_title: OSCC_7-P
source_name: Palatal mucosa to maxilla
characteristics: patient diagnosis: Oral Squamous Cell Carcinoma; patient id: OSCC_7; tissue: fresh frozen OSCC; condition: Primary Tumour; age: 49; gender: Male; smoking: Yes

GSM5593761 grouping

Sample field · Grouping · Global correction · GSM5593761

Wrong grouping

Current derived value

normal tissue (control)

Raw GEO sample metadata

sample_accession: GSM5593761
sample_title: OSCC_8-N
source_name: Tongue
characteristics: patient diagnosis: HPV-negative Oral Squamous Cell Carcinoma; patient id: OSCC_8; tissue: oral mucosa; condition: Adjacent Normal; age: 37; gender: Female; smoking: No

GSM5593761 exclusion decision

Sample field · Sample exclusion · Global correction · GSM5593761

Wrong sample exclusion

Current derived value

Included in derived sample grouping as normal tissue

Raw GEO sample metadata

sample_accession: GSM5593761
sample_title: OSCC_8-N
source_name: Tongue
characteristics: patient diagnosis: HPV-negative Oral Squamous Cell Carcinoma; patient id: OSCC_8; tissue: oral mucosa; condition: Adjacent Normal; age: 37; gender: Female; smoking: No

GSM5593762 grouping

Sample field · Grouping · Global correction · GSM5593762

Wrong grouping

Current derived value

tumor sample (case)

Raw GEO sample metadata

sample_accession: GSM5593762
sample_title: OSCC_8-P
source_name: Tongue
characteristics: patient diagnosis: HPV-negative Oral Squamous Cell Carcinoma; patient id: OSCC_8; tissue: fresh frozen OSCC; condition: Primary Tumour; age: 37; gender: Female; smoking: No

GSM5593762 exclusion decision

Sample field · Sample exclusion · Global correction · GSM5593762

Wrong sample exclusion

Current derived value

Included in derived sample grouping as tumor sample

Raw GEO sample metadata

sample_accession: GSM5593762
sample_title: OSCC_8-P
source_name: Tongue
characteristics: patient diagnosis: HPV-negative Oral Squamous Cell Carcinoma; patient id: OSCC_8; tissue: fresh frozen OSCC; condition: Primary Tumour; age: 37; gender: Female; smoking: No

GSM5593763 grouping

Sample field · Grouping · Global correction · GSM5593763

Wrong grouping

Current derived value

normal tissue (control)

Raw GEO sample metadata

sample_accession: GSM5593763
sample_title: OSCC_9-N
source_name: Tongue
characteristics: patient diagnosis: HPV-negative Oral Squamous Cell Carcinoma; patient id: OSCC_9; tissue: oral mucosa; condition: Adjacent Normal; age: 21; gender: Female; smoking: No

GSM5593763 exclusion decision

Sample field · Sample exclusion · Global correction · GSM5593763

Wrong sample exclusion

Current derived value

Included in derived sample grouping as normal tissue

Raw GEO sample metadata

sample_accession: GSM5593763
sample_title: OSCC_9-N
source_name: Tongue
characteristics: patient diagnosis: HPV-negative Oral Squamous Cell Carcinoma; patient id: OSCC_9; tissue: oral mucosa; condition: Adjacent Normal; age: 21; gender: Female; smoking: No

GSM5593764 grouping

Sample field · Grouping · Global correction · GSM5593764

Wrong grouping

Current derived value

tumor sample (case)

Raw GEO sample metadata

sample_accession: GSM5593764
sample_title: OSCC_9-P
source_name: Tongue
characteristics: patient diagnosis: HPV-negative Oral Squamous Cell Carcinoma; patient id: OSCC_9; tissue: fresh frozen OSCC; condition: Primary Tumour; age: 21; gender: Female; smoking: No

GSM5593764 exclusion decision

Sample field · Sample exclusion · Global correction · GSM5593764

Wrong sample exclusion

Current derived value

Included in derived sample grouping as tumor sample

Raw GEO sample metadata

sample_accession: GSM5593764
sample_title: OSCC_9-P
source_name: Tongue
characteristics: patient diagnosis: HPV-negative Oral Squamous Cell Carcinoma; patient id: OSCC_9; tissue: fresh frozen OSCC; condition: Primary Tumour; age: 21; gender: Female; smoking: No

GSM5593765 grouping

Sample field · Grouping · Global correction · GSM5593765

Wrong grouping

Current derived value

normal tissue (control)

Raw GEO sample metadata

sample_accession: GSM5593765
sample_title: OSCC_10-N
source_name: Tongue
characteristics: patient diagnosis: HPV-negative Oral Squamous Cell Carcinoma; patient id: OSCC_10; tissue: oral mucosa; condition: Adjacent Normal; age: 46; gender: Male; smoking: No

GSM5593765 exclusion decision

Sample field · Sample exclusion · Global correction · GSM5593765

Wrong sample exclusion

Current derived value

Included in derived sample grouping as normal tissue

Raw GEO sample metadata

sample_accession: GSM5593765
sample_title: OSCC_10-N
source_name: Tongue
characteristics: patient diagnosis: HPV-negative Oral Squamous Cell Carcinoma; patient id: OSCC_10; tissue: oral mucosa; condition: Adjacent Normal; age: 46; gender: Male; smoking: No

GSM5593766 grouping

Sample field · Grouping · Global correction · GSM5593766

Wrong grouping

Current derived value

tumor sample (case)

Raw GEO sample metadata

sample_accession: GSM5593766
sample_title: OSCC_10-P
source_name: Tongue
characteristics: patient diagnosis: HPV-negative Oral Squamous Cell Carcinoma; patient id: OSCC_10; tissue: fresh frozen OSCC; condition: Primary Tumour; age: 46; gender: Male; smoking: No

GSM5593766 exclusion decision

Sample field · Sample exclusion · Global correction · GSM5593766

Wrong sample exclusion

Current derived value

Included in derived sample grouping as tumor sample

Raw GEO sample metadata

sample_accession: GSM5593766
sample_title: OSCC_10-P
source_name: Tongue
characteristics: patient diagnosis: HPV-negative Oral Squamous Cell Carcinoma; patient id: OSCC_10; tissue: fresh frozen OSCC; condition: Primary Tumour; age: 46; gender: Male; smoking: No

GSM5593767 grouping

Sample field · Grouping · Global correction · GSM5593767

Wrong grouping

Current derived value

normal tissue (control)

Raw GEO sample metadata

sample_accession: GSM5593767
sample_title: OSCC_11-N
source_name: Floor of mouth
characteristics: patient diagnosis: HPV-negative Oral Squamous Cell Carcinoma; patient id: OSCC_11; tissue: oral mucosa; condition: Adjacent Normal; age: 50; gender: Female; smoking: No

GSM5593767 exclusion decision

Sample field · Sample exclusion · Global correction · GSM5593767

Wrong sample exclusion

Current derived value

Included in derived sample grouping as normal tissue

Raw GEO sample metadata

sample_accession: GSM5593767
sample_title: OSCC_11-N
source_name: Floor of mouth
characteristics: patient diagnosis: HPV-negative Oral Squamous Cell Carcinoma; patient id: OSCC_11; tissue: oral mucosa; condition: Adjacent Normal; age: 50; gender: Female; smoking: No

GSM5593768 grouping

Sample field · Grouping · Global correction · GSM5593768

Wrong grouping

Current derived value

tumor sample (case)

Raw GEO sample metadata

sample_accession: GSM5593768
sample_title: OSCC_11-P
source_name: Floor of mouth
characteristics: patient diagnosis: HPV-negative Oral Squamous Cell Carcinoma; patient id: OSCC_11; tissue: fresh frozen OSCC; condition: Primary Tumour; age: 50; gender: Female; smoking: No

GSM5593768 exclusion decision

Sample field · Sample exclusion · Global correction · GSM5593768

Wrong sample exclusion

Current derived value

Included in derived sample grouping as tumor sample

Raw GEO sample metadata

sample_accession: GSM5593768
sample_title: OSCC_11-P
source_name: Floor of mouth
characteristics: patient diagnosis: HPV-negative Oral Squamous Cell Carcinoma; patient id: OSCC_11; tissue: fresh frozen OSCC; condition: Primary Tumour; age: 50; gender: Female; smoking: No

GSM5593769 grouping

Sample field · Grouping · Global correction · GSM5593769

Wrong grouping

Current derived value

normal tissue (control)

Raw GEO sample metadata

sample_accession: GSM5593769
sample_title: OSCC_12-N
source_name: Tongue
characteristics: patient diagnosis: HPV-negative Oral Squamous Cell Carcinoma; patient id: OSCC_12; tissue: oral mucosa; condition: Adjacent Normal; age: 34; gender: Female; smoking: No

GSM5593769 exclusion decision

Sample field · Sample exclusion · Global correction · GSM5593769

Wrong sample exclusion

Current derived value

Included in derived sample grouping as normal tissue

Raw GEO sample metadata

sample_accession: GSM5593769
sample_title: OSCC_12-N
source_name: Tongue
characteristics: patient diagnosis: HPV-negative Oral Squamous Cell Carcinoma; patient id: OSCC_12; tissue: oral mucosa; condition: Adjacent Normal; age: 34; gender: Female; smoking: No

GSM5593770 grouping

Sample field · Grouping · Global correction · GSM5593770

Wrong grouping

Current derived value

tumor sample (case)

Raw GEO sample metadata

sample_accession: GSM5593770
sample_title: OSCC_12-P
source_name: Tongue
characteristics: patient diagnosis: HPV-negative Oral Squamous Cell Carcinoma; patient id: OSCC_12; tissue: fresh frozen OSCC; condition: Primary Tumour; age: 34; gender: Female; smoking: No

GSM5593770 exclusion decision

Sample field · Sample exclusion · Global correction · GSM5593770

Wrong sample exclusion

Current derived value

Included in derived sample grouping as tumor sample

Raw GEO sample metadata

sample_accession: GSM5593770
sample_title: OSCC_12-P
source_name: Tongue
characteristics: patient diagnosis: HPV-negative Oral Squamous Cell Carcinoma; patient id: OSCC_12; tissue: fresh frozen OSCC; condition: Primary Tumour; age: 34; gender: Female; smoking: No

GSM5593771 grouping

Sample field · Grouping · Global correction · GSM5593771

Wrong grouping

Current derived value

normal tissue (control)

Raw GEO sample metadata

sample_accession: GSM5593771
sample_title: OSCC_13-N
source_name: Tongue
characteristics: patient diagnosis: HPV-negative Oral Squamous Cell Carcinoma; patient id: OSCC_13; tissue: oral mucosa; condition: Adjacent Normal; age: 37; gender: Male; smoking: Yes

GSM5593771 exclusion decision

Sample field · Sample exclusion · Global correction · GSM5593771

Wrong sample exclusion

Current derived value

Included in derived sample grouping as normal tissue

Raw GEO sample metadata

sample_accession: GSM5593771
sample_title: OSCC_13-N
source_name: Tongue
characteristics: patient diagnosis: HPV-negative Oral Squamous Cell Carcinoma; patient id: OSCC_13; tissue: oral mucosa; condition: Adjacent Normal; age: 37; gender: Male; smoking: Yes

GSM5593772 grouping

Sample field · Grouping · Global correction · GSM5593772

Wrong grouping

Current derived value

tumor sample (case)

Raw GEO sample metadata

sample_accession: GSM5593772
sample_title: OSCC_13-P
source_name: Tongue
characteristics: patient diagnosis: HPV-negative Oral Squamous Cell Carcinoma; patient id: OSCC_13; tissue: fresh frozen OSCC; condition: Primary Tumour; age: 37; gender: Male; smoking: Yes

GSM5593772 exclusion decision

Sample field · Sample exclusion · Global correction · GSM5593772

Wrong sample exclusion

Current derived value

Included in derived sample grouping as tumor sample

Raw GEO sample metadata

sample_accession: GSM5593772
sample_title: OSCC_13-P
source_name: Tongue
characteristics: patient diagnosis: HPV-negative Oral Squamous Cell Carcinoma; patient id: OSCC_13; tissue: fresh frozen OSCC; condition: Primary Tumour; age: 37; gender: Male; smoking: Yes

GSM5593773 grouping

Sample field · Grouping · Global correction · GSM5593773

Wrong grouping

Current derived value

normal tissue (control)

Raw GEO sample metadata

sample_accession: GSM5593773
sample_title: OSCC_14-N
source_name: Tongue
characteristics: patient diagnosis: HPV-negative Oral Squamous Cell Carcinoma; patient id: OSCC_14; tissue: oral mucosa; condition: Adjacent Normal; age: 36; gender: Female; smoking: No

GSM5593773 exclusion decision

Sample field · Sample exclusion · Global correction · GSM5593773

Wrong sample exclusion

Current derived value

Included in derived sample grouping as normal tissue

Raw GEO sample metadata

sample_accession: GSM5593773
sample_title: OSCC_14-N
source_name: Tongue
characteristics: patient diagnosis: HPV-negative Oral Squamous Cell Carcinoma; patient id: OSCC_14; tissue: oral mucosa; condition: Adjacent Normal; age: 36; gender: Female; smoking: No

GSM5593774 grouping

Sample field · Grouping · Global correction · GSM5593774

Wrong grouping

Current derived value

tumor sample (case)

Raw GEO sample metadata

sample_accession: GSM5593774
sample_title: OSCC_14-P
source_name: Tongue
characteristics: patient diagnosis: HPV-negative Oral Squamous Cell Carcinoma; patient id: OSCC_14; tissue: fresh frozen OSCC; condition: Primary Tumour; age: 36; gender: Female; smoking: No

GSM5593774 exclusion decision

Sample field · Sample exclusion · Global correction · GSM5593774

Wrong sample exclusion

Current derived value

Included in derived sample grouping as tumor sample

Raw GEO sample metadata

sample_accession: GSM5593774
sample_title: OSCC_14-P
source_name: Tongue
characteristics: patient diagnosis: HPV-negative Oral Squamous Cell Carcinoma; patient id: OSCC_14; tissue: fresh frozen OSCC; condition: Primary Tumour; age: 36; gender: Female; smoking: No

GSM5593775 grouping

Sample field · Grouping · Global correction · GSM5593775

Wrong grouping

Current derived value

normal tissue (control)

Raw GEO sample metadata

sample_accession: GSM5593775
sample_title: OSCC_16-N
source_name: Tongue
characteristics: patient diagnosis: HPV-negative Oral Squamous Cell Carcinoma; patient id: OSCC_16; tissue: oral mucosa; condition: Adjacent Normal; age: 42; gender: Male; smoking: Yes

GSM5593775 exclusion decision

Sample field · Sample exclusion · Global correction · GSM5593775

Wrong sample exclusion

Current derived value

Included in derived sample grouping as normal tissue

Raw GEO sample metadata

sample_accession: GSM5593775
sample_title: OSCC_16-N
source_name: Tongue
characteristics: patient diagnosis: HPV-negative Oral Squamous Cell Carcinoma; patient id: OSCC_16; tissue: oral mucosa; condition: Adjacent Normal; age: 42; gender: Male; smoking: Yes

GSM5593776 grouping

Sample field · Grouping · Global correction · GSM5593776

Wrong grouping

Current derived value

tumor sample (case)

Raw GEO sample metadata

sample_accession: GSM5593776
sample_title: OSCC_16-P
source_name: Tongue
characteristics: patient diagnosis: HPV-negative Oral Squamous Cell Carcinoma; patient id: OSCC_16; tissue: fresh frozen OSCC; condition: Primary Tumour; age: 42; gender: Male; smoking: Yes

GSM5593776 exclusion decision

Sample field · Sample exclusion · Global correction · GSM5593776

Wrong sample exclusion

Current derived value

Included in derived sample grouping as tumor sample

Raw GEO sample metadata

sample_accession: GSM5593776
sample_title: OSCC_16-P
source_name: Tongue
characteristics: patient diagnosis: HPV-negative Oral Squamous Cell Carcinoma; patient id: OSCC_16; tissue: fresh frozen OSCC; condition: Primary Tumour; age: 42; gender: Male; smoking: Yes

Source Evidence

4 sources

GEO

Primary source

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

Dataset accession: GSE184616
Sample records: 30 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: GSE184616

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.

Expression Atlas

Not imported

Planned source for curated expression experiment links.

GEO accession: GSE184616

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.

PubMed

Unavailable

Publication context when PubMed identifiers are already known.

GEO accession: GSE184616

No PubMed identifier is present in the current runtime metadata.
No live PubMed search is performed from the dataset detail page.

Dataset Feedback

0 stored

No project feedback stored for this dataset.

Original GEO Metadata

dataset_accession: GSE184616
dataset_title: RNA-seq of HPV-negative Oral Squamous Cell Carcinoma Patients
organism: Homo sapiens
assay_type: bulk RNA-seq
processed_data_available: true
raw_data_available: true
submission_date: 2021-09-22
last_update_date: 2021-12-26
organization_name: University of Sydney
department: School of Mathematics and Statistics
public_date: 2021-11-25
experiment_types: Expression profiling by high throughput sequencing
platforms: GPL24676 Illumina NovaSeq 6000 (Homo sapiens)
sub_series: Not available
bioproject: PRJNA765370
supplementary_files: TXT: GSE184616_genesFPKMs.txt.gz; TXT: GSE184616_unnormalisedGeneCounts.txt.gz
series_type: Series

Why It Matched

Tumor vs matched normal · Tissue · suitability 0%.
Prioritized for patient tissue tumor-vs-normal triage.
Prioritized assay: bulk RNA-seq is the active assay expectation.
Downgraded disease context: not a colorectal/GI cancer cohort.
Processed data is available for downstream review.
2 warnings require review.

Why It May Not Be Suitable

Disease or condition label could not be normalized.
Tissue or cell type 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: Tissue clarity: Tissue 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: not a colorectal/GI cancer cohort.
Comparison suitability score is below the Phase 1 recommended threshold.

Warnings

warning DISEASE_LABEL_UNCLEAR Disease or condition label could not be normalized.
warning TISSUE_TYPE_MISSING Tissue or cell type could not be normalized.

Normalized Fields

77 fields

Field Value Source Origin Confidence Evidence Reason

assay_type bulk RNA-seq dataset GSE184616 Runtime Siftome inference GEO:dataset:GSE184616:f08a76bda253d40675a043979f1782392e4c053891292e82533190100c32e44f high confidence bulk rna-seq dataset_accession: GSE184616 dataset_title: RNA-seq of HPV-negative Oral Squamous Cell Carcinoma Patients organism: Homo sapiens assay_type: bulk RNA-seq processed_data_availabl... keyword match keyword match: bulk rna-seq

normal_tissue_type adjacent normal sample GSM5593747 Runtime Siftome inference GEO:sample:GSM5593747:21901b5ed971f48e67a6993a192feefdb900ba6b394bceb530f3e6aa3a92cad0 high confidence adjacent normal sample_accession: GSM5593747 sample_title: OSCC_1-N source_name: Tongue characteristics: patient diagnosis: HPV-negative Oral Squamous Cell Carcinoma; patient id: OSCC_1; tissue... controlled vocabulary controlled vocabulary normal tissue type match: adjacent normal

normal_tissue_type adjacent normal sample GSM5593749 Runtime Siftome inference GEO:sample:GSM5593749:66454232d0a0febdd281566b03c8ea1f58b27f0e79e6f29481f264f3a1557131 high confidence adjacent normal sample_accession: GSM5593749 sample_title: OSCC_2-N source_name: Tongue characteristics: patient diagnosis: HPV-negative Oral Squamous Cell Carcinoma; patient id: OSCC_2; tissue... controlled vocabulary controlled vocabulary normal tissue type match: adjacent normal

normal_tissue_type adjacent normal sample GSM5593751 Runtime Siftome inference GEO:sample:GSM5593751:0eda12557a2fe4c67eb12a91c21efb037f3953c063d3ad640ce01ec769c7e054 high confidence adjacent normal sample_accession: GSM5593751 sample_title: OSCC_3-N source_name: Gingivolingual sulcus characteristics: patient diagnosis: HPV-negative Oral Squamous Cell Carcinoma; patient id:... controlled vocabulary controlled vocabulary normal tissue type match: adjacent normal

normal_tissue_type adjacent normal sample GSM5593753 Runtime Siftome inference GEO:sample:GSM5593753:9da2895a88a9b3b6ec99d248f4fb49f7adc10f4c9e8965b7567febc1f0e82ff1 high confidence adjacent normal sample_accession: GSM5593753 sample_title: OSCC_4-N source_name: Floor of mouth characteristics: patient diagnosis: HPV-negative Oral Squamous Cell Carcinoma; patient id: OSCC_4... controlled vocabulary controlled vocabulary normal tissue type match: adjacent normal

normal_tissue_type adjacent normal sample GSM5593755 Runtime Siftome inference GEO:sample:GSM5593755:7829226c510deaeaee9e1a1747632bfa2d54dd429e83b49cc658d7c3e6bb7576 high confidence adjacent normal sample_accession: GSM5593755 sample_title: OSCC_5-N source_name: Tongue characteristics: patient diagnosis: HPV-negative Oral Squamous Cell Carcinoma; patient id: OSCC_5; tissue... controlled vocabulary controlled vocabulary normal tissue type match: adjacent normal

normal_tissue_type adjacent normal sample GSM5593757 Runtime Siftome inference GEO:sample:GSM5593757:d13b7e7f1472b63864b647be0a18999860ee49d03e67ae67189553a50f334dc0 high confidence adjacent normal sample_accession: GSM5593757 sample_title: OSCC_6-N source_name: Tongue characteristics: patient diagnosis: HPV-negative Oral Squamous Cell Carcinoma; patient id: OSCC_6; tissue... controlled vocabulary controlled vocabulary normal tissue type match: adjacent normal

normal_tissue_type adjacent normal sample GSM5593759 Runtime Siftome inference GEO:sample:GSM5593759:fbb7968ebf9bd68b4468c6d8cfc56f4acf5cd58541e1f2d65c556803700a83d4 high confidence adjacent normal sample_accession: GSM5593759 sample_title: OSCC_7-N source_name: Palatal mucosa to maxilla characteristics: patient diagnosis: HPV-negative Oral Squamous Cell Carcinoma; patient... controlled vocabulary controlled vocabulary normal tissue type match: adjacent normal

normal_tissue_type adjacent normal sample GSM5593761 Runtime Siftome inference GEO:sample:GSM5593761:b2dcde3f2e29a4b2ee21bbfda75f36ff3a9529568b90398125ba0c35c226fc44 high confidence adjacent normal sample_accession: GSM5593761 sample_title: OSCC_8-N source_name: Tongue characteristics: patient diagnosis: HPV-negative Oral Squamous Cell Carcinoma; patient id: OSCC_8; tissue... controlled vocabulary controlled vocabulary normal tissue type match: adjacent normal

normal_tissue_type adjacent normal sample GSM5593763 Runtime Siftome inference GEO:sample:GSM5593763:2b824f0240385cba33b28b5f6028561f79fe236c1623d6b056e38d544243c662 high confidence adjacent normal sample_accession: GSM5593763 sample_title: OSCC_9-N source_name: Tongue characteristics: patient diagnosis: HPV-negative Oral Squamous Cell Carcinoma; patient id: OSCC_9; tissue... controlled vocabulary controlled vocabulary normal tissue type match: adjacent normal

normal_tissue_type adjacent normal sample GSM5593765 Runtime Siftome inference GEO:sample:GSM5593765:fc06fc86df3af026b96339c38893853cdc912ab0cfa4deec6c50b55b50d7d2a1 high confidence adjacent normal sample_accession: GSM5593765 sample_title: OSCC_10-N source_name: Tongue characteristics: patient diagnosis: HPV-negative Oral Squamous Cell Carcinoma; patient id: OSCC_10; tiss... controlled vocabulary controlled vocabulary normal tissue type match: adjacent normal

normal_tissue_type adjacent normal sample GSM5593767 Runtime Siftome inference GEO:sample:GSM5593767:71f070ab8e01c54f6544d763cd73cbbac46c1e4a2728e109c22c0544c4ae6607 high confidence adjacent normal sample_accession: GSM5593767 sample_title: OSCC_11-N source_name: Floor of mouth characteristics: patient diagnosis: HPV-negative Oral Squamous Cell Carcinoma; patient id: OSCC_... controlled vocabulary controlled vocabulary normal tissue type match: adjacent normal

normal_tissue_type adjacent normal sample GSM5593769 Runtime Siftome inference GEO:sample:GSM5593769:ced057cf35206801f11aeff7be9a10b49e7156847587044fb4f8733dafe12b1e high confidence adjacent normal sample_accession: GSM5593769 sample_title: OSCC_12-N source_name: Tongue characteristics: patient diagnosis: HPV-negative Oral Squamous Cell Carcinoma; patient id: OSCC_12; tiss... controlled vocabulary controlled vocabulary normal tissue type match: adjacent normal

normal_tissue_type adjacent normal sample GSM5593771 Runtime Siftome inference GEO:sample:GSM5593771:7f0b482d926f3ecb354e857337ac87d0ef351c4ec7cd9153220436d5f3c40c2e high confidence adjacent normal sample_accession: GSM5593771 sample_title: OSCC_13-N source_name: Tongue characteristics: patient diagnosis: HPV-negative Oral Squamous Cell Carcinoma; patient id: OSCC_13; tiss... controlled vocabulary controlled vocabulary normal tissue type match: adjacent normal

normal_tissue_type adjacent normal sample GSM5593773 Runtime Siftome inference GEO:sample:GSM5593773:933900b75a9e83244c53371d74db248238f0168a70ca0b0d2e07b07a884e4605 high confidence adjacent normal sample_accession: GSM5593773 sample_title: OSCC_14-N source_name: Tongue characteristics: patient diagnosis: HPV-negative Oral Squamous Cell Carcinoma; patient id: OSCC_14; tiss... controlled vocabulary controlled vocabulary normal tissue type match: adjacent normal

normal_tissue_type adjacent normal sample GSM5593775 Runtime Siftome inference GEO:sample:GSM5593775:8535dcc98b3b923b0d0ce48346f539233c25cd54c0e550b74e3ad98624ddeb4f high confidence adjacent normal sample_accession: GSM5593775 sample_title: OSCC_16-N source_name: Tongue characteristics: patient diagnosis: HPV-negative Oral Squamous Cell Carcinoma; patient id: OSCC_16; tiss... controlled vocabulary controlled vocabulary normal tissue type match: adjacent normal

organism Homo sapiens dataset GSE184616 Runtime Siftome inference GEO:dataset:GSE184616:f08a76bda253d40675a043979f1782392e4c053891292e82533190100c32e44f high confidence homo sapiens dataset_accession: GSE184616 dataset_title: RNA-seq of HPV-negative Oral Squamous Cell Carcinoma Patients organism: Homo sapiens assay_type: bulk RNA-seq processed_data_availabl... keyword match keyword match: homo sapiens

sample_type normal tissue sample GSM5593747 Runtime Siftome inference GEO:sample:GSM5593747:21901b5ed971f48e67a6993a192feefdb900ba6b394bceb530f3e6aa3a92cad0 high confidence adjacent normal sample_accession: GSM5593747 sample_title: OSCC_1-N source_name: Tongue characteristics: patient diagnosis: HPV-negative Oral Squamous Cell Carcinoma; patient id: OSCC_1; tissue... controlled vocabulary controlled vocabulary sample type match: adjacent normal

sample_type tumor sample sample GSM5593747 Runtime Siftome inference GEO:sample:GSM5593747:21901b5ed971f48e67a6993a192feefdb900ba6b394bceb530f3e6aa3a92cad0 medium confidence carcinoma sample_accession: GSM5593747 sample_title: OSCC_1-N source_name: Tongue characteristics: patient diagnosis: HPV-negative Oral Squamous Cell Carcinoma; patient id: OSCC_1; tissue... controlled vocabulary controlled vocabulary sample type match: carcinoma

sample_type tumor sample sample GSM5593748 Runtime Siftome inference GEO:sample:GSM5593748:dbdf0f1744949b8e8be253a10ff3425fdc1dc787d64322d1a7af5e1677ad94ed low confidence tumour sample_accession: GSM5593748 sample_title: OSCC_1-P source_name: Tongue characteristics: patient diagnosis: HPV-negative Oral Squamous Cell Carcinoma; patient id: OSCC_1; tissue... controlled vocabulary controlled vocabulary sample type match: tumour

sample_type normal tissue sample GSM5593749 Runtime Siftome inference GEO:sample:GSM5593749:66454232d0a0febdd281566b03c8ea1f58b27f0e79e6f29481f264f3a1557131 high confidence adjacent normal sample_accession: GSM5593749 sample_title: OSCC_2-N source_name: Tongue characteristics: patient diagnosis: HPV-negative Oral Squamous Cell Carcinoma; patient id: OSCC_2; tissue... controlled vocabulary controlled vocabulary sample type match: adjacent normal

sample_type tumor sample sample GSM5593749 Runtime Siftome inference GEO:sample:GSM5593749:66454232d0a0febdd281566b03c8ea1f58b27f0e79e6f29481f264f3a1557131 medium confidence carcinoma sample_accession: GSM5593749 sample_title: OSCC_2-N source_name: Tongue characteristics: patient diagnosis: HPV-negative Oral Squamous Cell Carcinoma; patient id: OSCC_2; tissue... controlled vocabulary controlled vocabulary sample type match: carcinoma

sample_type tumor sample sample GSM5593750 Runtime Siftome inference GEO:sample:GSM5593750:5e093832a2649d3569f9f6e8c8f2ba41e1fb365e14e24cf45738c37364c07fcd low confidence tumour sample_accession: GSM5593750 sample_title: OSCC_2-P source_name: Tongue characteristics: patient diagnosis: HPV-negative Oral Squamous Cell Carcinoma; patient id: OSCC_2; tissue... controlled vocabulary controlled vocabulary sample type match: tumour

sample_type normal tissue sample GSM5593751 Runtime Siftome inference GEO:sample:GSM5593751:0eda12557a2fe4c67eb12a91c21efb037f3953c063d3ad640ce01ec769c7e054 high confidence adjacent normal sample_accession: GSM5593751 sample_title: OSCC_3-N source_name: Gingivolingual sulcus characteristics: patient diagnosis: HPV-negative Oral Squamous Cell Carcinoma; patient id:... controlled vocabulary controlled vocabulary sample type match: adjacent normal

sample_type tumor sample sample GSM5593751 Runtime Siftome inference GEO:sample:GSM5593751:0eda12557a2fe4c67eb12a91c21efb037f3953c063d3ad640ce01ec769c7e054 medium confidence carcinoma sample_accession: GSM5593751 sample_title: OSCC_3-N source_name: Gingivolingual sulcus characteristics: patient diagnosis: HPV-negative Oral Squamous Cell Carcinoma; patient id:... controlled vocabulary controlled vocabulary sample type match: carcinoma

sample_type tumor sample sample GSM5593752 Runtime Siftome inference GEO:sample:GSM5593752:c7afe7bcb990756d6bca03c708ae06be4dc9f92a1789f83f0f55add64482cb56 low confidence tumour sample_accession: GSM5593752 sample_title: OSCC_3-P source_name: Gingivolingual sulcus characteristics: patient diagnosis: HPV-negative Oral Squamous Cell Carcinoma; patient id:... controlled vocabulary controlled vocabulary sample type match: tumour

sample_type normal tissue sample GSM5593753 Runtime Siftome inference GEO:sample:GSM5593753:9da2895a88a9b3b6ec99d248f4fb49f7adc10f4c9e8965b7567febc1f0e82ff1 high confidence adjacent normal sample_accession: GSM5593753 sample_title: OSCC_4-N source_name: Floor of mouth characteristics: patient diagnosis: HPV-negative Oral Squamous Cell Carcinoma; patient id: OSCC_4... controlled vocabulary controlled vocabulary sample type match: adjacent normal

sample_type tumor sample sample GSM5593753 Runtime Siftome inference GEO:sample:GSM5593753:9da2895a88a9b3b6ec99d248f4fb49f7adc10f4c9e8965b7567febc1f0e82ff1 medium confidence carcinoma sample_accession: GSM5593753 sample_title: OSCC_4-N source_name: Floor of mouth characteristics: patient diagnosis: HPV-negative Oral Squamous Cell Carcinoma; patient id: OSCC_4... controlled vocabulary controlled vocabulary sample type match: carcinoma

sample_type tumor sample sample GSM5593754 Runtime Siftome inference GEO:sample:GSM5593754:c891cea7ec2ae5bc0c7e54bcd266e25013b32dd4c29c2eb14fd551bd1d495e6e low confidence tumour sample_accession: GSM5593754 sample_title: OSCC_4-P source_name: Floor of mouth characteristics: patient diagnosis: HPV-negative Oral Squamous Cell Carcinoma; patient id: OSCC_4... controlled vocabulary controlled vocabulary sample type match: tumour

sample_type normal tissue sample GSM5593755 Runtime Siftome inference GEO:sample:GSM5593755:7829226c510deaeaee9e1a1747632bfa2d54dd429e83b49cc658d7c3e6bb7576 high confidence adjacent normal sample_accession: GSM5593755 sample_title: OSCC_5-N source_name: Tongue characteristics: patient diagnosis: HPV-negative Oral Squamous Cell Carcinoma; patient id: OSCC_5; tissue... controlled vocabulary controlled vocabulary sample type match: adjacent normal

sample_type tumor sample sample GSM5593755 Runtime Siftome inference GEO:sample:GSM5593755:7829226c510deaeaee9e1a1747632bfa2d54dd429e83b49cc658d7c3e6bb7576 medium confidence carcinoma sample_accession: GSM5593755 sample_title: OSCC_5-N source_name: Tongue characteristics: patient diagnosis: HPV-negative Oral Squamous Cell Carcinoma; patient id: OSCC_5; tissue... controlled vocabulary controlled vocabulary sample type match: carcinoma

sample_type tumor sample sample GSM5593756 Runtime Siftome inference GEO:sample:GSM5593756:a89e95087018eb29b863b330cff27d254e86d52af74c3ba9242ddd5480e3f1ec low confidence tumour sample_accession: GSM5593756 sample_title: OSCC_5-P source_name: Tongue characteristics: patient diagnosis: HPV-negative Oral Squamous Cell Carcinoma; patient id: OSCC_5; tissue... controlled vocabulary controlled vocabulary sample type match: tumour

sample_type normal tissue sample GSM5593757 Runtime Siftome inference GEO:sample:GSM5593757:d13b7e7f1472b63864b647be0a18999860ee49d03e67ae67189553a50f334dc0 high confidence adjacent normal sample_accession: GSM5593757 sample_title: OSCC_6-N source_name: Tongue characteristics: patient diagnosis: HPV-negative Oral Squamous Cell Carcinoma; patient id: OSCC_6; tissue... controlled vocabulary controlled vocabulary sample type match: adjacent normal

sample_type tumor sample sample GSM5593757 Runtime Siftome inference GEO:sample:GSM5593757:d13b7e7f1472b63864b647be0a18999860ee49d03e67ae67189553a50f334dc0 medium confidence carcinoma sample_accession: GSM5593757 sample_title: OSCC_6-N source_name: Tongue characteristics: patient diagnosis: HPV-negative Oral Squamous Cell Carcinoma; patient id: OSCC_6; tissue... controlled vocabulary controlled vocabulary sample type match: carcinoma

sample_type tumor sample sample GSM5593758 Runtime Siftome inference GEO:sample:GSM5593758:b78e7eb347547dcc8f71cf0260d91481f9c2eb8d5f7bed83c07a86f448c479aa low confidence tumour sample_accession: GSM5593758 sample_title: OSCC_6-P source_name: Tongue characteristics: patient diagnosis: HPV-negative Oral Squamous Cell Carcinoma; patient id: OSCC_6; tissue... controlled vocabulary controlled vocabulary sample type match: tumour

sample_type normal tissue sample GSM5593759 Runtime Siftome inference GEO:sample:GSM5593759:fbb7968ebf9bd68b4468c6d8cfc56f4acf5cd58541e1f2d65c556803700a83d4 high confidence adjacent normal sample_accession: GSM5593759 sample_title: OSCC_7-N source_name: Palatal mucosa to maxilla characteristics: patient diagnosis: HPV-negative Oral Squamous Cell Carcinoma; patient... controlled vocabulary controlled vocabulary sample type match: adjacent normal

sample_type tumor sample sample GSM5593759 Runtime Siftome inference GEO:sample:GSM5593759:fbb7968ebf9bd68b4468c6d8cfc56f4acf5cd58541e1f2d65c556803700a83d4 medium confidence carcinoma sample_accession: GSM5593759 sample_title: OSCC_7-N source_name: Palatal mucosa to maxilla characteristics: patient diagnosis: HPV-negative Oral Squamous Cell Carcinoma; patient... controlled vocabulary controlled vocabulary sample type match: carcinoma

sample_type tumor sample sample GSM5593760 Runtime Siftome inference GEO:sample:GSM5593760:93ac35ca87cc150167fd4f3531fc2837aa166d7b09fd2c78e8d83ab6715c3b84 low confidence tumour sample_accession: GSM5593760 sample_title: OSCC_7-P source_name: Palatal mucosa to maxilla characteristics: patient diagnosis: Oral Squamous Cell Carcinoma; patient id: OSCC_7; ... controlled vocabulary controlled vocabulary sample type match: tumour

sample_type normal tissue sample GSM5593761 Runtime Siftome inference GEO:sample:GSM5593761:b2dcde3f2e29a4b2ee21bbfda75f36ff3a9529568b90398125ba0c35c226fc44 high confidence adjacent normal sample_accession: GSM5593761 sample_title: OSCC_8-N source_name: Tongue characteristics: patient diagnosis: HPV-negative Oral Squamous Cell Carcinoma; patient id: OSCC_8; tissue... controlled vocabulary controlled vocabulary sample type match: adjacent normal

sample_type tumor sample sample GSM5593761 Runtime Siftome inference GEO:sample:GSM5593761:b2dcde3f2e29a4b2ee21bbfda75f36ff3a9529568b90398125ba0c35c226fc44 medium confidence carcinoma sample_accession: GSM5593761 sample_title: OSCC_8-N source_name: Tongue characteristics: patient diagnosis: HPV-negative Oral Squamous Cell Carcinoma; patient id: OSCC_8; tissue... controlled vocabulary controlled vocabulary sample type match: carcinoma

sample_type tumor sample sample GSM5593762 Runtime Siftome inference GEO:sample:GSM5593762:9be3079c6681b2edab88b18faf43e853b74a5dc12793647c3eb931a53e22b122 low confidence tumour sample_accession: GSM5593762 sample_title: OSCC_8-P source_name: Tongue characteristics: patient diagnosis: HPV-negative Oral Squamous Cell Carcinoma; patient id: OSCC_8; tissue... controlled vocabulary controlled vocabulary sample type match: tumour

sample_type normal tissue sample GSM5593763 Runtime Siftome inference GEO:sample:GSM5593763:2b824f0240385cba33b28b5f6028561f79fe236c1623d6b056e38d544243c662 high confidence adjacent normal sample_accession: GSM5593763 sample_title: OSCC_9-N source_name: Tongue characteristics: patient diagnosis: HPV-negative Oral Squamous Cell Carcinoma; patient id: OSCC_9; tissue... controlled vocabulary controlled vocabulary sample type match: adjacent normal

sample_type tumor sample sample GSM5593763 Runtime Siftome inference GEO:sample:GSM5593763:2b824f0240385cba33b28b5f6028561f79fe236c1623d6b056e38d544243c662 medium confidence carcinoma sample_accession: GSM5593763 sample_title: OSCC_9-N source_name: Tongue characteristics: patient diagnosis: HPV-negative Oral Squamous Cell Carcinoma; patient id: OSCC_9; tissue... controlled vocabulary controlled vocabulary sample type match: carcinoma

sample_type tumor sample sample GSM5593764 Runtime Siftome inference GEO:sample:GSM5593764:7608cfb16aa9960d5cd05ad2b78843d0dca69cec50293a93a79498851b461db4 low confidence tumour sample_accession: GSM5593764 sample_title: OSCC_9-P source_name: Tongue characteristics: patient diagnosis: HPV-negative Oral Squamous Cell Carcinoma; patient id: OSCC_9; tissue... controlled vocabulary controlled vocabulary sample type match: tumour

sample_type normal tissue sample GSM5593765 Runtime Siftome inference GEO:sample:GSM5593765:fc06fc86df3af026b96339c38893853cdc912ab0cfa4deec6c50b55b50d7d2a1 high confidence adjacent normal sample_accession: GSM5593765 sample_title: OSCC_10-N source_name: Tongue characteristics: patient diagnosis: HPV-negative Oral Squamous Cell Carcinoma; patient id: OSCC_10; tiss... controlled vocabulary controlled vocabulary sample type match: adjacent normal

sample_type tumor sample sample GSM5593765 Runtime Siftome inference GEO:sample:GSM5593765:fc06fc86df3af026b96339c38893853cdc912ab0cfa4deec6c50b55b50d7d2a1 medium confidence carcinoma sample_accession: GSM5593765 sample_title: OSCC_10-N source_name: Tongue characteristics: patient diagnosis: HPV-negative Oral Squamous Cell Carcinoma; patient id: OSCC_10; tiss... controlled vocabulary controlled vocabulary sample type match: carcinoma

sample_type tumor sample sample GSM5593766 Runtime Siftome inference GEO:sample:GSM5593766:1c4354121edcfabb7d53c2d0be767bcc34a5880e8f33a23f2875c8d66efc05eb low confidence tumour sample_accession: GSM5593766 sample_title: OSCC_10-P source_name: Tongue characteristics: patient diagnosis: HPV-negative Oral Squamous Cell Carcinoma; patient id: OSCC_10; tiss... controlled vocabulary controlled vocabulary sample type match: tumour

sample_type normal tissue sample GSM5593767 Runtime Siftome inference GEO:sample:GSM5593767:71f070ab8e01c54f6544d763cd73cbbac46c1e4a2728e109c22c0544c4ae6607 high confidence adjacent normal sample_accession: GSM5593767 sample_title: OSCC_11-N source_name: Floor of mouth characteristics: patient diagnosis: HPV-negative Oral Squamous Cell Carcinoma; patient id: OSCC_... controlled vocabulary controlled vocabulary sample type match: adjacent normal

sample_type tumor sample sample GSM5593767 Runtime Siftome inference GEO:sample:GSM5593767:71f070ab8e01c54f6544d763cd73cbbac46c1e4a2728e109c22c0544c4ae6607 medium confidence carcinoma sample_accession: GSM5593767 sample_title: OSCC_11-N source_name: Floor of mouth characteristics: patient diagnosis: HPV-negative Oral Squamous Cell Carcinoma; patient id: OSCC_... controlled vocabulary controlled vocabulary sample type match: carcinoma

sample_type tumor sample sample GSM5593768 Runtime Siftome inference GEO:sample:GSM5593768:ec6d0d1e01609570d7cc3150b19269999647c1ad4720e49446f29a5af370e237 low confidence tumour sample_accession: GSM5593768 sample_title: OSCC_11-P source_name: Floor of mouth characteristics: patient diagnosis: HPV-negative Oral Squamous Cell Carcinoma; patient id: OSCC_... controlled vocabulary controlled vocabulary sample type match: tumour

sample_type normal tissue sample GSM5593769 Runtime Siftome inference GEO:sample:GSM5593769:ced057cf35206801f11aeff7be9a10b49e7156847587044fb4f8733dafe12b1e high confidence adjacent normal sample_accession: GSM5593769 sample_title: OSCC_12-N source_name: Tongue characteristics: patient diagnosis: HPV-negative Oral Squamous Cell Carcinoma; patient id: OSCC_12; tiss... controlled vocabulary controlled vocabulary sample type match: adjacent normal

sample_type tumor sample sample GSM5593769 Runtime Siftome inference GEO:sample:GSM5593769:ced057cf35206801f11aeff7be9a10b49e7156847587044fb4f8733dafe12b1e medium confidence carcinoma sample_accession: GSM5593769 sample_title: OSCC_12-N source_name: Tongue characteristics: patient diagnosis: HPV-negative Oral Squamous Cell Carcinoma; patient id: OSCC_12; tiss... controlled vocabulary controlled vocabulary sample type match: carcinoma

sample_type tumor sample sample GSM5593770 Runtime Siftome inference GEO:sample:GSM5593770:fe41a2250ad1e9e00bfeeb26ffb74f08310948a29b1e8af21af1222b7f2dd3db low confidence tumour sample_accession: GSM5593770 sample_title: OSCC_12-P source_name: Tongue characteristics: patient diagnosis: HPV-negative Oral Squamous Cell Carcinoma; patient id: OSCC_12; tiss... controlled vocabulary controlled vocabulary sample type match: tumour

sample_type normal tissue sample GSM5593771 Runtime Siftome inference GEO:sample:GSM5593771:7f0b482d926f3ecb354e857337ac87d0ef351c4ec7cd9153220436d5f3c40c2e high confidence adjacent normal sample_accession: GSM5593771 sample_title: OSCC_13-N source_name: Tongue characteristics: patient diagnosis: HPV-negative Oral Squamous Cell Carcinoma; patient id: OSCC_13; tiss... controlled vocabulary controlled vocabulary sample type match: adjacent normal

sample_type tumor sample sample GSM5593771 Runtime Siftome inference GEO:sample:GSM5593771:7f0b482d926f3ecb354e857337ac87d0ef351c4ec7cd9153220436d5f3c40c2e medium confidence carcinoma sample_accession: GSM5593771 sample_title: OSCC_13-N source_name: Tongue characteristics: patient diagnosis: HPV-negative Oral Squamous Cell Carcinoma; patient id: OSCC_13; tiss... controlled vocabulary controlled vocabulary sample type match: carcinoma

sample_type tumor sample sample GSM5593772 Runtime Siftome inference GEO:sample:GSM5593772:4b3e386faf1e914e07da3bebac9c5cb2997854af34fb081aec3c7f22a1d5bf4b low confidence tumour sample_accession: GSM5593772 sample_title: OSCC_13-P source_name: Tongue characteristics: patient diagnosis: HPV-negative Oral Squamous Cell Carcinoma; patient id: OSCC_13; tiss... controlled vocabulary controlled vocabulary sample type match: tumour

sample_type normal tissue sample GSM5593773 Runtime Siftome inference GEO:sample:GSM5593773:933900b75a9e83244c53371d74db248238f0168a70ca0b0d2e07b07a884e4605 high confidence adjacent normal sample_accession: GSM5593773 sample_title: OSCC_14-N source_name: Tongue characteristics: patient diagnosis: HPV-negative Oral Squamous Cell Carcinoma; patient id: OSCC_14; tiss... controlled vocabulary controlled vocabulary sample type match: adjacent normal

sample_type tumor sample sample GSM5593773 Runtime Siftome inference GEO:sample:GSM5593773:933900b75a9e83244c53371d74db248238f0168a70ca0b0d2e07b07a884e4605 medium confidence carcinoma sample_accession: GSM5593773 sample_title: OSCC_14-N source_name: Tongue characteristics: patient diagnosis: HPV-negative Oral Squamous Cell Carcinoma; patient id: OSCC_14; tiss... controlled vocabulary controlled vocabulary sample type match: carcinoma

sample_type tumor sample sample GSM5593774 Runtime Siftome inference GEO:sample:GSM5593774:76d2e00566598945bc6b1f7cf01e88c216441ab7088960fbdc6ffb4dba8a3e86 low confidence tumour sample_accession: GSM5593774 sample_title: OSCC_14-P source_name: Tongue characteristics: patient diagnosis: HPV-negative Oral Squamous Cell Carcinoma; patient id: OSCC_14; tiss... controlled vocabulary controlled vocabulary sample type match: tumour

sample_type normal tissue sample GSM5593775 Runtime Siftome inference GEO:sample:GSM5593775:8535dcc98b3b923b0d0ce48346f539233c25cd54c0e550b74e3ad98624ddeb4f high confidence adjacent normal sample_accession: GSM5593775 sample_title: OSCC_16-N source_name: Tongue characteristics: patient diagnosis: HPV-negative Oral Squamous Cell Carcinoma; patient id: OSCC_16; tiss... controlled vocabulary controlled vocabulary sample type match: adjacent normal

sample_type tumor sample sample GSM5593775 Runtime Siftome inference GEO:sample:GSM5593775:8535dcc98b3b923b0d0ce48346f539233c25cd54c0e550b74e3ad98624ddeb4f medium confidence carcinoma sample_accession: GSM5593775 sample_title: OSCC_16-N source_name: Tongue characteristics: patient diagnosis: HPV-negative Oral Squamous Cell Carcinoma; patient id: OSCC_16; tiss... controlled vocabulary controlled vocabulary sample type match: carcinoma

sample_type tumor sample sample GSM5593776 Runtime Siftome inference GEO:sample:GSM5593776:e7c2142d7d8e89e82e742eb0021859040c13c8ec75c10f9d5c2b62ee1b1c9c65 low confidence tumour sample_accession: GSM5593776 sample_title: OSCC_16-P source_name: Tongue characteristics: patient diagnosis: HPV-negative Oral Squamous Cell Carcinoma; patient id: OSCC_16; tiss... controlled vocabulary controlled vocabulary sample type match: tumour

tumor_type primary tumor sample GSM5593748 Runtime Siftome inference GEO:sample:GSM5593748:dbdf0f1744949b8e8be253a10ff3425fdc1dc787d64322d1a7af5e1677ad94ed high confidence primary tumour sample_accession: GSM5593748 sample_title: OSCC_1-P source_name: Tongue characteristics: patient diagnosis: HPV-negative Oral Squamous Cell Carcinoma; patient id: OSCC_1; tissue... controlled vocabulary controlled vocabulary tumor type match: primary tumour

tumor_type primary tumor sample GSM5593750 Runtime Siftome inference GEO:sample:GSM5593750:5e093832a2649d3569f9f6e8c8f2ba41e1fb365e14e24cf45738c37364c07fcd high confidence primary tumour sample_accession: GSM5593750 sample_title: OSCC_2-P source_name: Tongue characteristics: patient diagnosis: HPV-negative Oral Squamous Cell Carcinoma; patient id: OSCC_2; tissue... controlled vocabulary controlled vocabulary tumor type match: primary tumour

tumor_type primary tumor sample GSM5593752 Runtime Siftome inference GEO:sample:GSM5593752:c7afe7bcb990756d6bca03c708ae06be4dc9f92a1789f83f0f55add64482cb56 high confidence primary tumour sample_accession: GSM5593752 sample_title: OSCC_3-P source_name: Gingivolingual sulcus characteristics: patient diagnosis: HPV-negative Oral Squamous Cell Carcinoma; patient id:... controlled vocabulary controlled vocabulary tumor type match: primary tumour

tumor_type primary tumor sample GSM5593754 Runtime Siftome inference GEO:sample:GSM5593754:c891cea7ec2ae5bc0c7e54bcd266e25013b32dd4c29c2eb14fd551bd1d495e6e high confidence primary tumour sample_accession: GSM5593754 sample_title: OSCC_4-P source_name: Floor of mouth characteristics: patient diagnosis: HPV-negative Oral Squamous Cell Carcinoma; patient id: OSCC_4... controlled vocabulary controlled vocabulary tumor type match: primary tumour

tumor_type primary tumor sample GSM5593756 Runtime Siftome inference GEO:sample:GSM5593756:a89e95087018eb29b863b330cff27d254e86d52af74c3ba9242ddd5480e3f1ec high confidence primary tumour sample_accession: GSM5593756 sample_title: OSCC_5-P source_name: Tongue characteristics: patient diagnosis: HPV-negative Oral Squamous Cell Carcinoma; patient id: OSCC_5; tissue... controlled vocabulary controlled vocabulary tumor type match: primary tumour

tumor_type primary tumor sample GSM5593758 Runtime Siftome inference GEO:sample:GSM5593758:b78e7eb347547dcc8f71cf0260d91481f9c2eb8d5f7bed83c07a86f448c479aa high confidence primary tumour sample_accession: GSM5593758 sample_title: OSCC_6-P source_name: Tongue characteristics: patient diagnosis: HPV-negative Oral Squamous Cell Carcinoma; patient id: OSCC_6; tissue... controlled vocabulary controlled vocabulary tumor type match: primary tumour

tumor_type primary tumor sample GSM5593760 Runtime Siftome inference GEO:sample:GSM5593760:93ac35ca87cc150167fd4f3531fc2837aa166d7b09fd2c78e8d83ab6715c3b84 high confidence primary tumour sample_accession: GSM5593760 sample_title: OSCC_7-P source_name: Palatal mucosa to maxilla characteristics: patient diagnosis: Oral Squamous Cell Carcinoma; patient id: OSCC_7; ... controlled vocabulary controlled vocabulary tumor type match: primary tumour

tumor_type primary tumor sample GSM5593762 Runtime Siftome inference GEO:sample:GSM5593762:9be3079c6681b2edab88b18faf43e853b74a5dc12793647c3eb931a53e22b122 high confidence primary tumour sample_accession: GSM5593762 sample_title: OSCC_8-P source_name: Tongue characteristics: patient diagnosis: HPV-negative Oral Squamous Cell Carcinoma; patient id: OSCC_8; tissue... controlled vocabulary controlled vocabulary tumor type match: primary tumour

tumor_type primary tumor sample GSM5593764 Runtime Siftome inference GEO:sample:GSM5593764:7608cfb16aa9960d5cd05ad2b78843d0dca69cec50293a93a79498851b461db4 high confidence primary tumour sample_accession: GSM5593764 sample_title: OSCC_9-P source_name: Tongue characteristics: patient diagnosis: HPV-negative Oral Squamous Cell Carcinoma; patient id: OSCC_9; tissue... controlled vocabulary controlled vocabulary tumor type match: primary tumour

tumor_type primary tumor sample GSM5593766 Runtime Siftome inference GEO:sample:GSM5593766:1c4354121edcfabb7d53c2d0be767bcc34a5880e8f33a23f2875c8d66efc05eb high confidence primary tumour sample_accession: GSM5593766 sample_title: OSCC_10-P source_name: Tongue characteristics: patient diagnosis: HPV-negative Oral Squamous Cell Carcinoma; patient id: OSCC_10; tiss... controlled vocabulary controlled vocabulary tumor type match: primary tumour

tumor_type primary tumor sample GSM5593768 Runtime Siftome inference GEO:sample:GSM5593768:ec6d0d1e01609570d7cc3150b19269999647c1ad4720e49446f29a5af370e237 high confidence primary tumour sample_accession: GSM5593768 sample_title: OSCC_11-P source_name: Floor of mouth characteristics: patient diagnosis: HPV-negative Oral Squamous Cell Carcinoma; patient id: OSCC_... controlled vocabulary controlled vocabulary tumor type match: primary tumour

tumor_type primary tumor sample GSM5593770 Runtime Siftome inference GEO:sample:GSM5593770:fe41a2250ad1e9e00bfeeb26ffb74f08310948a29b1e8af21af1222b7f2dd3db high confidence primary tumour sample_accession: GSM5593770 sample_title: OSCC_12-P source_name: Tongue characteristics: patient diagnosis: HPV-negative Oral Squamous Cell Carcinoma; patient id: OSCC_12; tiss... controlled vocabulary controlled vocabulary tumor type match: primary tumour

tumor_type primary tumor sample GSM5593772 Runtime Siftome inference GEO:sample:GSM5593772:4b3e386faf1e914e07da3bebac9c5cb2997854af34fb081aec3c7f22a1d5bf4b high confidence primary tumour sample_accession: GSM5593772 sample_title: OSCC_13-P source_name: Tongue characteristics: patient diagnosis: HPV-negative Oral Squamous Cell Carcinoma; patient id: OSCC_13; tiss... controlled vocabulary controlled vocabulary tumor type match: primary tumour

tumor_type primary tumor sample GSM5593774 Runtime Siftome inference GEO:sample:GSM5593774:76d2e00566598945bc6b1f7cf01e88c216441ab7088960fbdc6ffb4dba8a3e86 high confidence primary tumour sample_accession: GSM5593774 sample_title: OSCC_14-P source_name: Tongue characteristics: patient diagnosis: HPV-negative Oral Squamous Cell Carcinoma; patient id: OSCC_14; tiss... controlled vocabulary controlled vocabulary tumor type match: primary tumour

tumor_type primary tumor sample GSM5593776 Runtime Siftome inference GEO:sample:GSM5593776:e7c2142d7d8e89e82e742eb0021859040c13c8ec75c10f9d5c2b62ee1b1c9c65 high confidence primary tumour sample_accession: GSM5593776 sample_title: OSCC_16-P source_name: Tongue characteristics: patient diagnosis: HPV-negative Oral Squamous Cell Carcinoma; patient id: OSCC_16; tiss... controlled vocabulary controlled vocabulary tumor type match: primary tumour

Sample Group Preview

Possible case samples

Samples currently treated as the comparison case group.

15

GSM5593748 OSCC_1-P tumor sample Case marker detected. Tongue patient diagnosis: HPV-negative Oral Squamous Cell Carcinoma; patient id: OSCC_1; tissue: fresh frozen OSCC; condition: Primary Tumour; age: 50; gender: Male; smoking: No
GSM5593750 OSCC_2-P tumor sample Case marker detected. Tongue patient diagnosis: HPV-negative Oral Squamous Cell Carcinoma; patient id: OSCC_2; tissue: fresh frozen OSCC; condition: Primary Tumour; age: 33; gender: Male; smoking: No
GSM5593752 OSCC_3-P tumor sample Case marker detected. Gingivolingual sulcus patient diagnosis: HPV-negative Oral Squamous Cell Carcinoma; patient id: OSCC_3; tissue: fresh frozen OSCC; condition: Primary Tumour; age: 45; gender: Male; smoking: Yes
GSM5593754 OSCC_4-P tumor sample Case marker detected. Floor of mouth patient diagnosis: HPV-negative Oral Squamous Cell Carcinoma; patient id: OSCC_4; tissue: fresh frozen OSCC; condition: Primary Tumour; age: 48; gender: Male; smoking: Yes
GSM5593756 OSCC_5-P tumor sample Case marker detected. Tongue patient diagnosis: HPV-negative Oral Squamous Cell Carcinoma; patient id: OSCC_5; tissue: fresh frozen OSCC; condition: Primary Tumour; age: 22; gender: Male; smoking: Yes
GSM5593758 OSCC_6-P tumor sample Case marker detected. Tongue patient diagnosis: HPV-negative Oral Squamous Cell Carcinoma; patient id: OSCC_6; tissue: fresh frozen OSCC; condition: Primary Tumour; age: 48; gender: Female; smoking: No
GSM5593760 OSCC_7-P tumor sample Case marker detected. Palatal mucosa to maxilla patient diagnosis: Oral Squamous Cell Carcinoma; patient id: OSCC_7; tissue: fresh frozen OSCC; condition: Primary Tumour; age: 49; gender: Male; smoking: Yes
GSM5593762 OSCC_8-P tumor sample Case marker detected. Tongue patient diagnosis: HPV-negative Oral Squamous Cell Carcinoma; patient id: OSCC_8; tissue: fresh frozen OSCC; condition: Primary Tumour; age: 37; gender: Female; smoking: No
GSM5593764 OSCC_9-P tumor sample Case marker detected. Tongue patient diagnosis: HPV-negative Oral Squamous Cell Carcinoma; patient id: OSCC_9; tissue: fresh frozen OSCC; condition: Primary Tumour; age: 21; gender: Female; smoking: No
GSM5593766 OSCC_10-P tumor sample Case marker detected. Tongue patient diagnosis: HPV-negative Oral Squamous Cell Carcinoma; patient id: OSCC_10; tissue: fresh frozen OSCC; condition: Primary Tumour; age: 46; gender: Male; smoking: No
GSM5593768 OSCC_11-P tumor sample Case marker detected. Floor of mouth patient diagnosis: HPV-negative Oral Squamous Cell Carcinoma; patient id: OSCC_11; tissue: fresh frozen OSCC; condition: Primary Tumour; age: 50; gender: Female; smoking: No
GSM5593770 OSCC_12-P tumor sample Case marker detected. Tongue patient diagnosis: HPV-negative Oral Squamous Cell Carcinoma; patient id: OSCC_12; tissue: fresh frozen OSCC; condition: Primary Tumour; age: 34; gender: Female; smoking: No
GSM5593772 OSCC_13-P tumor sample Case marker detected. Tongue patient diagnosis: HPV-negative Oral Squamous Cell Carcinoma; patient id: OSCC_13; tissue: fresh frozen OSCC; condition: Primary Tumour; age: 37; gender: Male; smoking: Yes
GSM5593774 OSCC_14-P tumor sample Case marker detected. Tongue patient diagnosis: HPV-negative Oral Squamous Cell Carcinoma; patient id: OSCC_14; tissue: fresh frozen OSCC; condition: Primary Tumour; age: 36; gender: Female; smoking: No
GSM5593776 OSCC_16-P tumor sample Case marker detected. Tongue patient diagnosis: HPV-negative Oral Squamous Cell Carcinoma; patient id: OSCC_16; tissue: fresh frozen OSCC; condition: Primary Tumour; age: 42; gender: Male; smoking: Yes

Possible control samples

Samples currently treated as controls or baseline.

15

GSM5593747 OSCC_1-N normal tissue Control marker detected. Tongue patient diagnosis: HPV-negative Oral Squamous Cell Carcinoma; patient id: OSCC_1; tissue: oral mucosa; condition: Adjacent Normal; age: 50; gender: Male; smoking: No
GSM5593749 OSCC_2-N normal tissue Control marker detected. Tongue patient diagnosis: HPV-negative Oral Squamous Cell Carcinoma; patient id: OSCC_2; tissue: oral mucosa; condition: Adjacent Normal; age: 33; gender: Male; smoking: No
GSM5593751 OSCC_3-N normal tissue Control marker detected. Gingivolingual sulcus patient diagnosis: HPV-negative Oral Squamous Cell Carcinoma; patient id: OSCC_3; tissue: oral mucosa; condition: Adjacent Normal; age: 45; gender: Male; smoking: Yes
GSM5593753 OSCC_4-N normal tissue Control marker detected. Floor of mouth patient diagnosis: HPV-negative Oral Squamous Cell Carcinoma; patient id: OSCC_4; tissue: oral mucosa; condition: Adjacent Normal; age: 48; gender: Male; smoking: Yes
GSM5593755 OSCC_5-N normal tissue Control marker detected. Tongue patient diagnosis: HPV-negative Oral Squamous Cell Carcinoma; patient id: OSCC_5; tissue: oral mucosa; condition: Adjacent Normal; age: 22; gender: Male; smoking: Yes
GSM5593757 OSCC_6-N normal tissue Control marker detected. Tongue patient diagnosis: HPV-negative Oral Squamous Cell Carcinoma; patient id: OSCC_6; tissue: oral mucosa; condition: Adjacent Normal; age: 48; gender: Female; smoking: No
GSM5593759 OSCC_7-N normal tissue Control marker detected. Palatal mucosa to maxilla patient diagnosis: HPV-negative Oral Squamous Cell Carcinoma; patient id: OSCC_7; tissue: oral mucosa; condition: Adjacent Normal; age: 49; gender: Male; smoking: Yes
GSM5593761 OSCC_8-N normal tissue Control marker detected. Tongue patient diagnosis: HPV-negative Oral Squamous Cell Carcinoma; patient id: OSCC_8; tissue: oral mucosa; condition: Adjacent Normal; age: 37; gender: Female; smoking: No
GSM5593763 OSCC_9-N normal tissue Control marker detected. Tongue patient diagnosis: HPV-negative Oral Squamous Cell Carcinoma; patient id: OSCC_9; tissue: oral mucosa; condition: Adjacent Normal; age: 21; gender: Female; smoking: No
GSM5593765 OSCC_10-N normal tissue Control marker detected. Tongue patient diagnosis: HPV-negative Oral Squamous Cell Carcinoma; patient id: OSCC_10; tissue: oral mucosa; condition: Adjacent Normal; age: 46; gender: Male; smoking: No
GSM5593767 OSCC_11-N normal tissue Control marker detected. Floor of mouth patient diagnosis: HPV-negative Oral Squamous Cell Carcinoma; patient id: OSCC_11; tissue: oral mucosa; condition: Adjacent Normal; age: 50; gender: Female; smoking: No
GSM5593769 OSCC_12-N normal tissue Control marker detected. Tongue patient diagnosis: HPV-negative Oral Squamous Cell Carcinoma; patient id: OSCC_12; tissue: oral mucosa; condition: Adjacent Normal; age: 34; gender: Female; smoking: No
GSM5593771 OSCC_13-N normal tissue Control marker detected. Tongue patient diagnosis: HPV-negative Oral Squamous Cell Carcinoma; patient id: OSCC_13; tissue: oral mucosa; condition: Adjacent Normal; age: 37; gender: Male; smoking: Yes
GSM5593773 OSCC_14-N normal tissue Control marker detected. Tongue patient diagnosis: HPV-negative Oral Squamous Cell Carcinoma; patient id: OSCC_14; tissue: oral mucosa; condition: Adjacent Normal; age: 36; gender: Female; smoking: No
GSM5593775 OSCC_16-N normal tissue Control marker detected. Tongue patient diagnosis: HPV-negative Oral Squamous Cell Carcinoma; patient id: OSCC_16; tissue: oral mucosa; condition: Adjacent Normal; age: 42; gender: Male; smoking: Yes

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

70 pts

Clarity: 70%
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 was not 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

15 samples

GSM5593747 OSCC_1-N Tongue patient diagnosis: HPV-negative Oral Squamous Cell Carcinoma; patient id: OSCC_1; tissue: oral mucosa; condition: Adjacent Normal; age: 50; gender: Male; smoking: No
GSM5593749 OSCC_2-N Tongue patient diagnosis: HPV-negative Oral Squamous Cell Carcinoma; patient id: OSCC_2; tissue: oral mucosa; condition: Adjacent Normal; age: 33; gender: Male; smoking: No
GSM5593751 OSCC_3-N Gingivolingual sulcus patient diagnosis: HPV-negative Oral Squamous Cell Carcinoma; patient id: OSCC_3; tissue: oral mucosa; condition: Adjacent Normal; age: 45; gender: Male; smoking: Yes
GSM5593753 OSCC_4-N Floor of mouth patient diagnosis: HPV-negative Oral Squamous Cell Carcinoma; patient id: OSCC_4; tissue: oral mucosa; condition: Adjacent Normal; age: 48; gender: Male; smoking: Yes
GSM5593755 OSCC_5-N Tongue patient diagnosis: HPV-negative Oral Squamous Cell Carcinoma; patient id: OSCC_5; tissue: oral mucosa; condition: Adjacent Normal; age: 22; gender: Male; smoking: Yes
GSM5593757 OSCC_6-N Tongue patient diagnosis: HPV-negative Oral Squamous Cell Carcinoma; patient id: OSCC_6; tissue: oral mucosa; condition: Adjacent Normal; age: 48; gender: Female; smoking: No
GSM5593759 OSCC_7-N Palatal mucosa to maxilla patient diagnosis: HPV-negative Oral Squamous Cell Carcinoma; patient id: OSCC_7; tissue: oral mucosa; condition: Adjacent Normal; age: 49; gender: Male; smoking: Yes
GSM5593761 OSCC_8-N Tongue patient diagnosis: HPV-negative Oral Squamous Cell Carcinoma; patient id: OSCC_8; tissue: oral mucosa; condition: Adjacent Normal; age: 37; gender: Female; smoking: No
GSM5593763 OSCC_9-N Tongue patient diagnosis: HPV-negative Oral Squamous Cell Carcinoma; patient id: OSCC_9; tissue: oral mucosa; condition: Adjacent Normal; age: 21; gender: Female; smoking: No
GSM5593765 OSCC_10-N Tongue patient diagnosis: HPV-negative Oral Squamous Cell Carcinoma; patient id: OSCC_10; tissue: oral mucosa; condition: Adjacent Normal; age: 46; gender: Male; smoking: No
GSM5593767 OSCC_11-N Floor of mouth patient diagnosis: HPV-negative Oral Squamous Cell Carcinoma; patient id: OSCC_11; tissue: oral mucosa; condition: Adjacent Normal; age: 50; gender: Female; smoking: No
GSM5593769 OSCC_12-N Tongue patient diagnosis: HPV-negative Oral Squamous Cell Carcinoma; patient id: OSCC_12; tissue: oral mucosa; condition: Adjacent Normal; age: 34; gender: Female; smoking: No
GSM5593771 OSCC_13-N Tongue patient diagnosis: HPV-negative Oral Squamous Cell Carcinoma; patient id: OSCC_13; tissue: oral mucosa; condition: Adjacent Normal; age: 37; gender: Male; smoking: Yes
GSM5593773 OSCC_14-N Tongue patient diagnosis: HPV-negative Oral Squamous Cell Carcinoma; patient id: OSCC_14; tissue: oral mucosa; condition: Adjacent Normal; age: 36; gender: Female; smoking: No
GSM5593775 OSCC_16-N Tongue patient diagnosis: HPV-negative Oral Squamous Cell Carcinoma; patient id: OSCC_16; tissue: oral mucosa; condition: Adjacent Normal; age: 42; gender: Male; smoking: Yes

tumor sample

15 samples

GSM5593748 OSCC_1-P Tongue patient diagnosis: HPV-negative Oral Squamous Cell Carcinoma; patient id: OSCC_1; tissue: fresh frozen OSCC; condition: Primary Tumour; age: 50; gender: Male; smoking: No
GSM5593750 OSCC_2-P Tongue patient diagnosis: HPV-negative Oral Squamous Cell Carcinoma; patient id: OSCC_2; tissue: fresh frozen OSCC; condition: Primary Tumour; age: 33; gender: Male; smoking: No
GSM5593752 OSCC_3-P Gingivolingual sulcus patient diagnosis: HPV-negative Oral Squamous Cell Carcinoma; patient id: OSCC_3; tissue: fresh frozen OSCC; condition: Primary Tumour; age: 45; gender: Male; smoking: Yes
GSM5593754 OSCC_4-P Floor of mouth patient diagnosis: HPV-negative Oral Squamous Cell Carcinoma; patient id: OSCC_4; tissue: fresh frozen OSCC; condition: Primary Tumour; age: 48; gender: Male; smoking: Yes
GSM5593756 OSCC_5-P Tongue patient diagnosis: HPV-negative Oral Squamous Cell Carcinoma; patient id: OSCC_5; tissue: fresh frozen OSCC; condition: Primary Tumour; age: 22; gender: Male; smoking: Yes
GSM5593758 OSCC_6-P Tongue patient diagnosis: HPV-negative Oral Squamous Cell Carcinoma; patient id: OSCC_6; tissue: fresh frozen OSCC; condition: Primary Tumour; age: 48; gender: Female; smoking: No
GSM5593760 OSCC_7-P Palatal mucosa to maxilla patient diagnosis: Oral Squamous Cell Carcinoma; patient id: OSCC_7; tissue: fresh frozen OSCC; condition: Primary Tumour; age: 49; gender: Male; smoking: Yes
GSM5593762 OSCC_8-P Tongue patient diagnosis: HPV-negative Oral Squamous Cell Carcinoma; patient id: OSCC_8; tissue: fresh frozen OSCC; condition: Primary Tumour; age: 37; gender: Female; smoking: No
GSM5593764 OSCC_9-P Tongue patient diagnosis: HPV-negative Oral Squamous Cell Carcinoma; patient id: OSCC_9; tissue: fresh frozen OSCC; condition: Primary Tumour; age: 21; gender: Female; smoking: No
GSM5593766 OSCC_10-P Tongue patient diagnosis: HPV-negative Oral Squamous Cell Carcinoma; patient id: OSCC_10; tissue: fresh frozen OSCC; condition: Primary Tumour; age: 46; gender: Male; smoking: No
GSM5593768 OSCC_11-P Floor of mouth patient diagnosis: HPV-negative Oral Squamous Cell Carcinoma; patient id: OSCC_11; tissue: fresh frozen OSCC; condition: Primary Tumour; age: 50; gender: Female; smoking: No
GSM5593770 OSCC_12-P Tongue patient diagnosis: HPV-negative Oral Squamous Cell Carcinoma; patient id: OSCC_12; tissue: fresh frozen OSCC; condition: Primary Tumour; age: 34; gender: Female; smoking: No
GSM5593772 OSCC_13-P Tongue patient diagnosis: HPV-negative Oral Squamous Cell Carcinoma; patient id: OSCC_13; tissue: fresh frozen OSCC; condition: Primary Tumour; age: 37; gender: Male; smoking: Yes
GSM5593774 OSCC_14-P Tongue patient diagnosis: HPV-negative Oral Squamous Cell Carcinoma; patient id: OSCC_14; tissue: fresh frozen OSCC; condition: Primary Tumour; age: 36; gender: Female; smoking: No
GSM5593776 OSCC_16-P Tongue patient diagnosis: HPV-negative Oral Squamous Cell Carcinoma; patient id: OSCC_16; tissue: fresh frozen OSCC; condition: Primary Tumour; age: 42; gender: Male; smoking: Yes

Score Breakdown

50%

relevance

Organism normalized.
Assay type normalized.

0%

comparison suitability

Tumor and normal sample groups detected.
No excluded sample type flags detected.
Matched tumor/normal design boosted for colorectal tumor-vs-normal tissue triage.
Patient tissue or biopsy specimens boosted for tissue comparison triage.
Non-colorectal cancer context downgraded for colorectal tumor-vs-normal tissue ranking.

70%

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 was not 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

30 samples

GSM5593747 OSCC_1-N
GSM5593748 OSCC_1-P
GSM5593749 OSCC_2-N
GSM5593750 OSCC_2-P
GSM5593751 OSCC_3-N
GSM5593752 OSCC_3-P
GSM5593753 OSCC_4-N
GSM5593754 OSCC_4-P
GSM5593755 OSCC_5-N
GSM5593756 OSCC_5-P
GSM5593757 OSCC_6-N
GSM5593758 OSCC_6-P
GSM5593759 OSCC_7-N
GSM5593760 OSCC_7-P
GSM5593761 OSCC_8-N
GSM5593762 OSCC_8-P
GSM5593763 OSCC_9-N
GSM5593764 OSCC_9-P
GSM5593765 OSCC_10-N
GSM5593766 OSCC_10-P
GSM5593767 OSCC_11-N
GSM5593768 OSCC_11-P
GSM5593769 OSCC_12-N
GSM5593770 OSCC_12-P
GSM5593771 OSCC_13-N
GSM5593772 OSCC_13-P
GSM5593773 OSCC_14-N
GSM5593774 OSCC_14-P
GSM5593775 OSCC_16-N
GSM5593776 OSCC_16-P

Review Audit Trail

0 decisions

No review decisions have been stored for this dataset.