Siftome Phase 3L

GSE107502

Defining the Triple Negative Breast Cancer Kinome Response to GSK1120212 (RNA-Seq)

Not suitable Dataset does not meet the current suitability threshold.

Sample grouping CSV Contrast CSV DESeq2 metadata CSV R handoff notes Handoff report Download instructions Open GEO dataset

Source: GEO
Search intent: Patient tissue tumor-vs-normal
Intent behavior: search-intent-behavior-v1
Submission date: 2017-11-29
Last update: 2019-03-27
Organization: University of North Carolina School of Medicine
Department: Pharmacology
Public date: 2017-11-29
Experiment types: Expression profiling by high throughput sequencing
Platforms: GPL11154 Illumina HiSeq 2000 (Homo sapiens)
Series type: SubSeries
SubSeries: Not available
BioProject: PRJNA420378
Supplementary files: TXT: GSE107502_LCCC1122_DESeq2_trametinibresponse.txt.gz; TXT: GSE107502_LCCC1122_normalizedLog2RSEM.txt.gz; TXT: GSE107502_LCCC1122_rawRSEM.txt.gz
Organism: Homo sapiens
Assay: bulk RNA-seq
Samples: 28
Study design: Tumor vs unmatched normal
Specimen/source: Biopsy
Scoring version: intent-aware-scoring-v15
Ranking batch: b69568dd1e4fe1b9ee2d880bf5495d748a7e4c5c11e4107f02528c3be0e76012
Ranking created: 2026-06-05T20:20:27.088676Z
Warning version: intent-aware-warnings-v2

Current Intent Interpretation

Patient tissue tumor-vs-normal

Expectations

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

Rules

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

Study Classification

Tumor vs unmatched normal Biopsy

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

Analysis Readiness

Ready after review

100% 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

10/10 pts

No dataset warnings are present.

Metadata normalization

10/10 pts

Metadata quality is high enough to support downstream handoff.

Blockers

No readiness blockers detected.

Next Steps

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

Analysis Preparation Checklist

5/6 ready

Group labels reviewed

Needs review

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

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

Minimum sample count met

Ready

Both groups meet the minimum of 2 samples.

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

Processed counts available

Ready

Processed data availability is marked true in the GEO index.

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

Ambiguous samples handled

Ready

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

Still scan the grouping table for biology-specific ambiguity.

Exclusion decisions recorded

Ready

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

Record any manual exclusions in the downstream analysis notes.

Source links preserved

Ready

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

Keep GEO dataset and sample links with exported metadata.

Bioinformatician Review

Standard analyst review

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

No expert-review triggers were detected by Siftome.

Why This Is Ranked Here

Patient tissue tumor-vs-normal

Not suitable Dataset does not meet the current suitability threshold.

Score Components

relevance 100% Disease or condition metadata normalized. Organism normalized. Assay type normalized. Tissue metadata normalized.
comparison suitability 0% Tumor and normal sample groups detected. No excluded sample type flags detected. Tumor/normal design boosted for colorectal tumor-vs-normal tissue triage. Patient tissue or biopsy specimens boosted for tissue comparison triage. Non-colorectal cancer context downgraded for colorectal tumor-vs-normal tissue ranking.
metadata quality 100% Sample source clarity: All samples have source metadata and clear GSE/GSM accessions. Group clarity: Rule-based grouping found both case and control samples. Disease clarity: Disease or condition metadata normalized. Tissue clarity: Tissue metadata normalized. Treatment clarity: No unclear treatment split detected in the sample metadata. Replicate clarity: No pooled sample or technical replicate flags detected. Data availability clarity: Dataset-level processed or raw data availability is explicit.
data availability 100% Processed data available. Raw data available.
overall 34% Weighted score: 30% relevance, 30% comparison suitability, 25% metadata quality, 15% data availability. Overall score capped because comparison suitability is weak for the selected search intent. Overall score capped because tumor/normal grouping is from a non-colorectal cancer context.

Derived Classifications

Organism Homo sapiens Organism remains rule-derived: Homo sapiens.
Assay bulk RNA-seq Assay remains rule-derived: bulk RNA-seq.
Study design Tumor vs unmatched normal Study design remains rule-derived: Tumor vs unmatched normal.
Specimen/source Biopsy Specimen/source remains rule-derived: Biopsy.
Likely case group tumor sample 23 samples
Likely control group normal tissue 5 samples

Warnings

No ranking warnings are active.

Intent Interpretation

Active intent Patient tissue tumor-vs-normal Ranks human colorectal tissue or biopsy cohorts where tumor samples can be compared with normal controls.
Organism expectation Homo sapiens Dataset organism is interpreted as Homo sapiens.
Assay expectation bulk RNA-seq Dataset assay is interpreted as bulk RNA-seq.
Specimen assumption patient tissue or biopsy Derived specimen/source is Biopsy.
Control-group assumption matched normal, adjacent normal, paired normal, healthy tissue control, or otherwise normal tissue control Derived study design is Tumor vs unmatched normal; likely groups are tumor sample vs normal tissue.
Score caps Applied when matching conditions are present non-human datasets stay below the primary recommendation band, missing colorectal/colon/rectal/CRC context stays below the primary recommendation band, biofluid and model-system datasets cannot reach Recommended by default, microarray and secondary assays are capped unless explicitly enabled, or small cohorts are capped below high-confidence recommendations
Warning rules 0 active warnings missing or unclear control group, unclear disease context, unclear tissue source, mixed sample types, model-system markers, secondary assay context, missing processed data, or small cohort size
Downgrade or exclusion reason Downgraded disease context: not a colorectal/GI cancer cohort. Derived from current-intent ranking reasons and warnings.

Applied Review Decisions

No active review decisions affect this ranking.

Ranking Facts

Recommendation Not suitable Dataset does not meet the current suitability threshold.
Supporting fact Tumor vs unmatched normal · Biopsy · suitability 0%. Contributed to match or upgrade evidence.
Supporting fact Prioritized assay: bulk RNA-seq is the active assay expectation. Contributed to match or upgrade evidence.
Supporting fact Downgraded disease context: not a colorectal/GI cancer cohort. Contributed to match or upgrade evidence.
Supporting fact Processed data is available for downstream review. Contributed to match or upgrade evidence.
Caution fact Non-colorectal cancer context downgraded for colorectal tumor-vs-normal tissue ranking. Contributed to downgrade or manual-review evidence.
Caution fact Missing or unclear metadata: Treatment clarity: No unclear treatment split detected in the sample metadata. Contributed to downgrade or manual-review evidence.
Caution fact Overall score capped because comparison suitability is weak for the selected search intent. Contributed to downgrade or manual-review evidence.
Caution fact Overall score capped because tumor/normal grouping is from a non-colorectal cancer context. Contributed to downgrade or manual-review evidence.
Caution fact Downgraded disease context: not a colorectal/GI cancer cohort. Contributed to downgrade or manual-review evidence.
Caution fact Comparison suitability score is below the Phase 1 recommended threshold. Contributed to downgrade or manual-review evidence.

Manual Corrections

0 active

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 unmatched normal.
Specimen/source · Normalization rules Specimen/source remains rule-derived: Biopsy.

Dataset organism

Dataset field · Organism · Global correction

Wrong organism

Current derived value

Homo sapiens

Raw GEO organism

dataset_accession: GSE107502
organism: Homo sapiens
dataset_title: Defining the Triple Negative Breast Cancer Kinome Response to GSK1120212 (RNA-Seq)

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: GPL11154 Illumina HiSeq 2000 (Homo sapiens)
dataset_title: Defining the Triple Negative Breast Cancer Kinome Response to GSK1120212 (RNA-Seq)

Study design

Dataset field · Study design · Global correction

Wrong study design

Current derived value

Tumor vs unmatched normal

Raw GEO study and sample metadata

dataset_title: Defining the Triple Negative Breast Cancer Kinome Response to GSK1120212 (RNA-Seq)
experiment_types: Expression profiling by high throughput sequencing
sample_context: GSM2869456: source_name=breast carcinoma; characteristics=disease state: TNBC; individual: Patient 6; protocol: pre-treatment needle core biospy; tumor sample subtype: claudin low
GSM2869457: source_name=breast carcinoma; characteristics=disease state: TNBC; individual: Patient 6; protocol: post-treatment surgical resection; tumor sample subtype: claudin low
GSM2869458: source_name=breast carcinoma; characteristics=disease state: TNBC; individual: Patient 5; protocol: pre-treatment needle core biospy; tumor sample subtype: basal
GSM2869459: source_name=breast carcinoma; characteristics=disease state: TNBC; individual: Patient 5; protocol: pre-treatment needle core biospy; tumor sample subtype: basal
GSM28694
[Correction source preview truncated.]

Specimen/source type

Dataset field · Specimen/source · Global correction

Wrong specimen/source

Current derived value

Biopsy

Raw GEO sample source metadata

dataset_title: Defining the Triple Negative Breast Cancer Kinome Response to GSK1120212 (RNA-Seq)
sample_context: GSM2869456: source_name=breast carcinoma; characteristics=disease state: TNBC; individual: Patient 6; protocol: pre-treatment needle core biospy; tumor sample subtype: claudin low
GSM2869457: source_name=breast carcinoma; characteristics=disease state: TNBC; individual: Patient 6; protocol: post-treatment surgical resection; tumor sample subtype: claudin low
GSM2869458: source_name=breast carcinoma; characteristics=disease state: TNBC; individual: Patient 5; protocol: pre-treatment needle core biospy; tumor sample subtype: basal
GSM2869459: source_name=breast carcinoma; characteristics=disease state: TNBC; individual: Patient 5; protocol: pre-treatment needle core biospy; tumor sample subtype: basal
GSM2869460: source_name=breast carcinoma; characteristics=disease state: TNBC
[Correction source preview truncated.]

Disease context

Dataset field · Disease context · Global correction

Wrong disease context

Current derived value

breast cancer

Raw GEO disease context metadata

dataset_title: Defining the Triple Negative Breast Cancer Kinome Response to GSK1120212 (RNA-Seq)
sample_context: GSM2869456: source_name=breast carcinoma; characteristics=disease state: TNBC; individual: Patient 6; protocol: pre-treatment needle core biospy; tumor sample subtype: claudin low
GSM2869457: source_name=breast carcinoma; characteristics=disease state: TNBC; individual: Patient 6; protocol: post-treatment surgical resection; tumor sample subtype: claudin low
GSM2869458: source_name=breast carcinoma; characteristics=disease state: TNBC; individual: Patient 5; protocol: pre-treatment needle core biospy; tumor sample subtype: basal
GSM2869459: source_name=breast carcinoma; characteristics=disease state: TNBC; individual: Patient 5; protocol: pre-treatment needle core biospy; tumor sample subtype: basal
GSM2869460: source_name=breast carcinoma; characteristics=disease state: TNBC
[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: GSE107502
dataset_title: Defining the Triple Negative Breast Cancer Kinome Response to GSK1120212 (RNA-Seq)
organism: Homo sapiens
assay_type: bulk RNA-seq
sample_context: GSM2869456: source_name=breast carcinoma; characteristics=disease state: TNBC; individual: Patient 6; protocol: pre-treatment needle core biospy; tumor sample subtype: claudin low
GSM2869457: source_name=breast carcinoma; characteristics=disease state: TNBC; individual: Patient 6; protocol: post-treatment surgical resection; tumor sample subtype: claudin low
GSM2869458: source_name=breast carcinoma; characteristics=disease state: TNBC; individual: Patient 5; protocol: pre-treatment needle core biospy; tumor sample subtype: basal
GSM2869459: source_name=breast carcinoma; characteristics=disease state: TNBC; individual: Patient 5; protocol: pre-treatment needle core biospy; tumor sample subtype: basal

[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: GSE107502
dataset_title: Defining the Triple Negative Breast Cancer Kinome Response to GSK1120212 (RNA-Seq)
organism: Homo sapiens
assay_type: bulk RNA-seq
sample_context: GSM2869456: source_name=breast carcinoma; characteristics=disease state: TNBC; individual: Patient 6; protocol: pre-treatment needle core biospy; tumor sample subtype: claudin low
GSM2869457: source_name=breast carcinoma; characteristics=disease state: TNBC; individual: Patient 6; protocol: post-treatment surgical resection; tumor sample subtype: claudin low
GSM2869458: source_name=breast carcinoma; characteristics=disease state: TNBC; individual: Patient 5; protocol: pre-treatment needle core biospy; tumor sample subtype: basal
GSM2869459: source_name=breast carcinoma; characteristics=disease state: TNBC; individual: Patient 5; protocol: pre-treatment needle core biospy; tumor sample subtype: basal

[Correction source preview truncated.]

GSM2869456 grouping

Sample field · Grouping · Global correction · GSM2869456

Wrong grouping

Current derived value

tumor sample (case)

Raw GEO sample metadata

sample_accession: GSM2869456
sample_title: Patient 6 needle core biospy - pre treatment
source_name: breast carcinoma
characteristics: disease state: TNBC; individual: Patient 6; protocol: pre-treatment needle core biospy; tumor sample subtype: claudin low

GSM2869456 exclusion decision

Sample field · Sample exclusion · Global correction · GSM2869456

Wrong sample exclusion

Current derived value

Included in derived sample grouping as tumor sample

Raw GEO sample metadata

sample_accession: GSM2869456
sample_title: Patient 6 needle core biospy - pre treatment
source_name: breast carcinoma
characteristics: disease state: TNBC; individual: Patient 6; protocol: pre-treatment needle core biospy; tumor sample subtype: claudin low

GSM2869457 grouping

Sample field · Grouping · Global correction · GSM2869457

Wrong grouping

Current derived value

tumor sample (case)

Raw GEO sample metadata

sample_accession: GSM2869457
sample_title: Patient 6 surgical resection - post treatment
source_name: breast carcinoma
characteristics: disease state: TNBC; individual: Patient 6; protocol: post-treatment surgical resection; tumor sample subtype: claudin low

GSM2869457 exclusion decision

Sample field · Sample exclusion · Global correction · GSM2869457

Wrong sample exclusion

Current derived value

Included in derived sample grouping as tumor sample

Raw GEO sample metadata

sample_accession: GSM2869457
sample_title: Patient 6 surgical resection - post treatment
source_name: breast carcinoma
characteristics: disease state: TNBC; individual: Patient 6; protocol: post-treatment surgical resection; tumor sample subtype: claudin low

GSM2869458 grouping

Sample field · Grouping · Global correction · GSM2869458

Wrong grouping

Current derived value

tumor sample (case)

Raw GEO sample metadata

sample_accession: GSM2869458
sample_title: Patient 5 needle core biopsy - pre treatment_2
source_name: breast carcinoma
characteristics: disease state: TNBC; individual: Patient 5; protocol: pre-treatment needle core biospy; tumor sample subtype: basal

GSM2869458 exclusion decision

Sample field · Sample exclusion · Global correction · GSM2869458

Wrong sample exclusion

Current derived value

Included in derived sample grouping as tumor sample

Raw GEO sample metadata

sample_accession: GSM2869458
sample_title: Patient 5 needle core biopsy - pre treatment_2
source_name: breast carcinoma
characteristics: disease state: TNBC; individual: Patient 5; protocol: pre-treatment needle core biospy; tumor sample subtype: basal

GSM2869459 grouping

Sample field · Grouping · Global correction · GSM2869459

Wrong grouping

Current derived value

tumor sample (case)

Raw GEO sample metadata

sample_accession: GSM2869459
sample_title: Patient 5 needle core biopsy - pre treatment
source_name: breast carcinoma
characteristics: disease state: TNBC; individual: Patient 5; protocol: pre-treatment needle core biospy; tumor sample subtype: basal

GSM2869459 exclusion decision

Sample field · Sample exclusion · Global correction · GSM2869459

Wrong sample exclusion

Current derived value

Included in derived sample grouping as tumor sample

Raw GEO sample metadata

sample_accession: GSM2869459
sample_title: Patient 5 needle core biopsy - pre treatment
source_name: breast carcinoma
characteristics: disease state: TNBC; individual: Patient 5; protocol: pre-treatment needle core biospy; tumor sample subtype: basal

GSM2869460 grouping

Sample field · Grouping · Global correction · GSM2869460

Wrong grouping

Current derived value

tumor sample (case)

Raw GEO sample metadata

sample_accession: GSM2869460
sample_title: Patient 5 surgical resection - post treatment_2
source_name: breast carcinoma
characteristics: disease state: TNBC; individual: Patient 5; protocol: post-treatment surgical resection; tumor sample subtype: basal

GSM2869460 exclusion decision

Sample field · Sample exclusion · Global correction · GSM2869460

Wrong sample exclusion

Current derived value

Included in derived sample grouping as tumor sample

Raw GEO sample metadata

sample_accession: GSM2869460
sample_title: Patient 5 surgical resection - post treatment_2
source_name: breast carcinoma
characteristics: disease state: TNBC; individual: Patient 5; protocol: post-treatment surgical resection; tumor sample subtype: basal

GSM2869461 grouping

Sample field · Grouping · Global correction · GSM2869461

Wrong grouping

Current derived value

tumor sample (case)

Raw GEO sample metadata

sample_accession: GSM2869461
sample_title: Patient 5 surgical resection - post treatment
source_name: breast carcinoma
characteristics: disease state: TNBC; individual: Patient 5; protocol: post-treatment surgical resection; tumor sample subtype: basal

GSM2869461 exclusion decision

Sample field · Sample exclusion · Global correction · GSM2869461

Wrong sample exclusion

Current derived value

Included in derived sample grouping as tumor sample

Raw GEO sample metadata

sample_accession: GSM2869461
sample_title: Patient 5 surgical resection - post treatment
source_name: breast carcinoma
characteristics: disease state: TNBC; individual: Patient 5; protocol: post-treatment surgical resection; tumor sample subtype: basal

GSM2869462 grouping

Sample field · Grouping · Global correction · GSM2869462

Wrong grouping

Current derived value

tumor sample (case)

Raw GEO sample metadata

sample_accession: GSM2869462
sample_title: Patient 6 needle core biospy - pre treatment_2
source_name: breast carcinoma
characteristics: disease state: TNBC; individual: Patient 6; protocol: pre-treatment needle core biospy; tumor sample subtype: claudin low

GSM2869462 exclusion decision

Sample field · Sample exclusion · Global correction · GSM2869462

Wrong sample exclusion

Current derived value

Included in derived sample grouping as tumor sample

Raw GEO sample metadata

sample_accession: GSM2869462
sample_title: Patient 6 needle core biospy - pre treatment_2
source_name: breast carcinoma
characteristics: disease state: TNBC; individual: Patient 6; protocol: pre-treatment needle core biospy; tumor sample subtype: claudin low

GSM2869463 grouping

Sample field · Grouping · Global correction · GSM2869463

Wrong grouping

Current derived value

tumor sample (case)

Raw GEO sample metadata

sample_accession: GSM2869463
sample_title: Patient 6 surgical resection - post treatment_2
source_name: breast carcinoma
characteristics: disease state: TNBC; individual: Patient 6; protocol: post-treatment surgical resection; tumor sample subtype: claudin low

GSM2869463 exclusion decision

Sample field · Sample exclusion · Global correction · GSM2869463

Wrong sample exclusion

Current derived value

Included in derived sample grouping as tumor sample

Raw GEO sample metadata

sample_accession: GSM2869463
sample_title: Patient 6 surgical resection - post treatment_2
source_name: breast carcinoma
characteristics: disease state: TNBC; individual: Patient 6; protocol: post-treatment surgical resection; tumor sample subtype: claudin low

GSM2869464 grouping

Sample field · Grouping · Global correction · GSM2869464

Wrong grouping

Current derived value

normal tissue (control)

Raw GEO sample metadata

sample_accession: GSM2869464
sample_title: Patient 7 needle core biopsy - pre treatment
source_name: breast carcinoma
characteristics: disease state: TNBC; individual: Patient 7; protocol: pre-treatment needle core biospy; tumor sample subtype: normal breast

GSM2869464 exclusion decision

Sample field · Sample exclusion · Global correction · GSM2869464

Wrong sample exclusion

Current derived value

Included in derived sample grouping as normal tissue

Raw GEO sample metadata

sample_accession: GSM2869464
sample_title: Patient 7 needle core biopsy - pre treatment
source_name: breast carcinoma
characteristics: disease state: TNBC; individual: Patient 7; protocol: pre-treatment needle core biospy; tumor sample subtype: normal breast

GSM2869465 grouping

Sample field · Grouping · Global correction · GSM2869465

Wrong grouping

Current derived value

normal tissue (control)

Raw GEO sample metadata

sample_accession: GSM2869465
sample_title: Patient 7 surgical resection - post treatment
source_name: breast carcinoma
characteristics: disease state: TNBC; individual: Patient 7; protocol: post-treatment surgical resection; tumor sample subtype: normal breast

GSM2869465 exclusion decision

Sample field · Sample exclusion · Global correction · GSM2869465

Wrong sample exclusion

Current derived value

Included in derived sample grouping as normal tissue

Raw GEO sample metadata

sample_accession: GSM2869465
sample_title: Patient 7 surgical resection - post treatment
source_name: breast carcinoma
characteristics: disease state: TNBC; individual: Patient 7; protocol: post-treatment surgical resection; tumor sample subtype: normal breast

GSM2869466 grouping

Sample field · Grouping · Global correction · GSM2869466

Wrong grouping

Current derived value

tumor sample (case)

Raw GEO sample metadata

sample_accession: GSM2869466
sample_title: Patient 8 needle core biopsy - pre treatment
source_name: breast carcinoma
characteristics: disease state: TNBC; individual: Patient 8; protocol: pre-treatment needle core biospy; tumor sample subtype: claudin low

GSM2869466 exclusion decision

Sample field · Sample exclusion · Global correction · GSM2869466

Wrong sample exclusion

Current derived value

Included in derived sample grouping as tumor sample

Raw GEO sample metadata

sample_accession: GSM2869466
sample_title: Patient 8 needle core biopsy - pre treatment
source_name: breast carcinoma
characteristics: disease state: TNBC; individual: Patient 8; protocol: pre-treatment needle core biospy; tumor sample subtype: claudin low

GSM2869467 grouping

Sample field · Grouping · Global correction · GSM2869467

Wrong grouping

Current derived value

tumor sample (case)

Raw GEO sample metadata

sample_accession: GSM2869467
sample_title: Patient 8 surgical resection - post treatment
source_name: breast carcinoma
characteristics: disease state: TNBC; individual: Patient 8; protocol: post-treatment surgical resection; tumor sample subtype: basal

GSM2869467 exclusion decision

Sample field · Sample exclusion · Global correction · GSM2869467

Wrong sample exclusion

Current derived value

Included in derived sample grouping as tumor sample

Raw GEO sample metadata

sample_accession: GSM2869467
sample_title: Patient 8 surgical resection - post treatment
source_name: breast carcinoma
characteristics: disease state: TNBC; individual: Patient 8; protocol: post-treatment surgical resection; tumor sample subtype: basal

GSM2869468 grouping

Sample field · Grouping · Global correction · GSM2869468

Wrong grouping

Current derived value

tumor sample (case)

Raw GEO sample metadata

sample_accession: GSM2869468
sample_title: Patient 1 needle core biopsy - pre treatment
source_name: breast carcinoma
characteristics: disease state: TNBC; individual: Patient 1; protocol: pre-treatment needle core biospy; tumor sample subtype: basal

GSM2869468 exclusion decision

Sample field · Sample exclusion · Global correction · GSM2869468

Wrong sample exclusion

Current derived value

Included in derived sample grouping as tumor sample

Raw GEO sample metadata

sample_accession: GSM2869468
sample_title: Patient 1 needle core biopsy - pre treatment
source_name: breast carcinoma
characteristics: disease state: TNBC; individual: Patient 1; protocol: pre-treatment needle core biospy; tumor sample subtype: basal

GSM2869469 grouping

Sample field · Grouping · Global correction · GSM2869469

Wrong grouping

Current derived value

tumor sample (case)

Raw GEO sample metadata

sample_accession: GSM2869469
sample_title: Patient 1 surgical resection - post treatment
source_name: breast carcinoma
characteristics: disease state: TNBC; individual: Patient 1; protocol: post-treatment surgical resection; tumor sample subtype: basal

GSM2869469 exclusion decision

Sample field · Sample exclusion · Global correction · GSM2869469

Wrong sample exclusion

Current derived value

Included in derived sample grouping as tumor sample

Raw GEO sample metadata

sample_accession: GSM2869469
sample_title: Patient 1 surgical resection - post treatment
source_name: breast carcinoma
characteristics: disease state: TNBC; individual: Patient 1; protocol: post-treatment surgical resection; tumor sample subtype: basal

GSM2869470 grouping

Sample field · Grouping · Global correction · GSM2869470

Wrong grouping

Current derived value

tumor sample (case)

Raw GEO sample metadata

sample_accession: GSM2869470
sample_title: Patient 2 needle core biopsy - pre treatment
source_name: breast carcinoma
characteristics: disease state: TNBC; individual: Patient 2; protocol: pre-treatment needle core biospy; tumor sample subtype: basal

GSM2869470 exclusion decision

Sample field · Sample exclusion · Global correction · GSM2869470

Wrong sample exclusion

Current derived value

Included in derived sample grouping as tumor sample

Raw GEO sample metadata

sample_accession: GSM2869470
sample_title: Patient 2 needle core biopsy - pre treatment
source_name: breast carcinoma
characteristics: disease state: TNBC; individual: Patient 2; protocol: pre-treatment needle core biospy; tumor sample subtype: basal

GSM2869471 grouping

Sample field · Grouping · Global correction · GSM2869471

Wrong grouping

Current derived value

tumor sample (case)

Raw GEO sample metadata

sample_accession: GSM2869471
sample_title: Patient 2 surgical resection - post treatment
source_name: breast carcinoma
characteristics: disease state: TNBC; individual: Patient 2; protocol: post-treatment surgical resection; tumor sample subtype: basal

GSM2869471 exclusion decision

Sample field · Sample exclusion · Global correction · GSM2869471

Wrong sample exclusion

Current derived value

Included in derived sample grouping as tumor sample

Raw GEO sample metadata

sample_accession: GSM2869471
sample_title: Patient 2 surgical resection - post treatment
source_name: breast carcinoma
characteristics: disease state: TNBC; individual: Patient 2; protocol: post-treatment surgical resection; tumor sample subtype: basal

GSM2869472 grouping

Sample field · Grouping · Global correction · GSM2869472

Wrong grouping

Current derived value

tumor sample (case)

Raw GEO sample metadata

sample_accession: GSM2869472
sample_title: Patient 9 needle core biopsy - pre treatment
source_name: breast carcinoma
characteristics: disease state: TNBC; individual: Patient 9; protocol: pre-treatment needle core biospy; tumor sample subtype: basal

GSM2869472 exclusion decision

Sample field · Sample exclusion · Global correction · GSM2869472

Wrong sample exclusion

Current derived value

Included in derived sample grouping as tumor sample

Raw GEO sample metadata

sample_accession: GSM2869472
sample_title: Patient 9 needle core biopsy - pre treatment
source_name: breast carcinoma
characteristics: disease state: TNBC; individual: Patient 9; protocol: pre-treatment needle core biospy; tumor sample subtype: basal

GSM2869473 grouping

Sample field · Grouping · Global correction · GSM2869473

Wrong grouping

Current derived value

normal tissue (control)

Raw GEO sample metadata

sample_accession: GSM2869473
sample_title: Patient 9 surgical resection - post treatment
source_name: breast carcinoma
characteristics: disease state: TNBC; individual: Patient 9; protocol: post-treatment surgical resection; tumor sample subtype: normal breast

GSM2869473 exclusion decision

Sample field · Sample exclusion · Global correction · GSM2869473

Wrong sample exclusion

Current derived value

Included in derived sample grouping as normal tissue

Raw GEO sample metadata

sample_accession: GSM2869473
sample_title: Patient 9 surgical resection - post treatment
source_name: breast carcinoma
characteristics: disease state: TNBC; individual: Patient 9; protocol: post-treatment surgical resection; tumor sample subtype: normal breast

GSM2869474 grouping

Sample field · Grouping · Global correction · GSM2869474

Wrong grouping

Current derived value

tumor sample (case)

Raw GEO sample metadata

sample_accession: GSM2869474
sample_title: Patient 10 needle core biopsy - pre treatment
source_name: breast carcinoma
characteristics: disease state: TNBC; individual: Patient 10; protocol: pre-treatment needle core biospy; tumor sample subtype: claudin low

GSM2869474 exclusion decision

Sample field · Sample exclusion · Global correction · GSM2869474

Wrong sample exclusion

Current derived value

Included in derived sample grouping as tumor sample

Raw GEO sample metadata

sample_accession: GSM2869474
sample_title: Patient 10 needle core biopsy - pre treatment
source_name: breast carcinoma
characteristics: disease state: TNBC; individual: Patient 10; protocol: pre-treatment needle core biospy; tumor sample subtype: claudin low

GSM2869475 grouping

Sample field · Grouping · Global correction · GSM2869475

Wrong grouping

Current derived value

tumor sample (case)

Raw GEO sample metadata

sample_accession: GSM2869475
sample_title: Patient 10 surgical resection - post treatment
source_name: breast carcinoma
characteristics: disease state: TNBC; individual: Patient 10; protocol: post-treatment surgical resection; tumor sample subtype: basal

GSM2869475 exclusion decision

Sample field · Sample exclusion · Global correction · GSM2869475

Wrong sample exclusion

Current derived value

Included in derived sample grouping as tumor sample

Raw GEO sample metadata

sample_accession: GSM2869475
sample_title: Patient 10 surgical resection - post treatment
source_name: breast carcinoma
characteristics: disease state: TNBC; individual: Patient 10; protocol: post-treatment surgical resection; tumor sample subtype: basal

GSM2869476 grouping

Sample field · Grouping · Global correction · GSM2869476

Wrong grouping

Current derived value

tumor sample (case)

Raw GEO sample metadata

sample_accession: GSM2869476
sample_title: Patient 4 Needle Core Biopsy - pre treatment
source_name: breast carcinoma
characteristics: disease state: TNBC; individual: Patient 4; protocol: pre-treatment needle core biospy; tumor sample subtype: basal

GSM2869476 exclusion decision

Sample field · Sample exclusion · Global correction · GSM2869476

Wrong sample exclusion

Current derived value

Included in derived sample grouping as tumor sample

Raw GEO sample metadata

sample_accession: GSM2869476
sample_title: Patient 4 Needle Core Biopsy - pre treatment
source_name: breast carcinoma
characteristics: disease state: TNBC; individual: Patient 4; protocol: pre-treatment needle core biospy; tumor sample subtype: basal

GSM2869477 grouping

Sample field · Grouping · Global correction · GSM2869477

Wrong grouping

Current derived value

tumor sample (case)

Raw GEO sample metadata

sample_accession: GSM2869477
sample_title: Patient 4 surgical resection - post treatment
source_name: breast carcinoma
characteristics: disease state: TNBC; individual: Patient 4; protocol: post-treatment surgical resection; tumor sample subtype: basal

GSM2869477 exclusion decision

Sample field · Sample exclusion · Global correction · GSM2869477

Wrong sample exclusion

Current derived value

Included in derived sample grouping as tumor sample

Raw GEO sample metadata

sample_accession: GSM2869477
sample_title: Patient 4 surgical resection - post treatment
source_name: breast carcinoma
characteristics: disease state: TNBC; individual: Patient 4; protocol: post-treatment surgical resection; tumor sample subtype: basal

GSM2869478 grouping

Sample field · Grouping · Global correction · GSM2869478

Wrong grouping

Current derived value

tumor sample (case)

Raw GEO sample metadata

sample_accession: GSM2869478
sample_title: Patient 3 Needle Core Biopsy - pre treatment
source_name: breast carcinoma
characteristics: disease state: TNBC; individual: Patient 3; protocol: pre-treatment needle core biospy; tumor sample subtype: basal

GSM2869478 exclusion decision

Sample field · Sample exclusion · Global correction · GSM2869478

Wrong sample exclusion

Current derived value

Included in derived sample grouping as tumor sample

Raw GEO sample metadata

sample_accession: GSM2869478
sample_title: Patient 3 Needle Core Biopsy - pre treatment
source_name: breast carcinoma
characteristics: disease state: TNBC; individual: Patient 3; protocol: pre-treatment needle core biospy; tumor sample subtype: basal

GSM2869479 grouping

Sample field · Grouping · Global correction · GSM2869479

Wrong grouping

Current derived value

tumor sample (case)

Raw GEO sample metadata

sample_accession: GSM2869479
sample_title: Patient 3 surgical resection - post treatment
source_name: breast carcinoma
characteristics: disease state: TNBC; individual: Patient 3; protocol: post-treatment surgical resection; tumor sample subtype: basal

GSM2869479 exclusion decision

Sample field · Sample exclusion · Global correction · GSM2869479

Wrong sample exclusion

Current derived value

Included in derived sample grouping as tumor sample

Raw GEO sample metadata

sample_accession: GSM2869479
sample_title: Patient 3 surgical resection - post treatment
source_name: breast carcinoma
characteristics: disease state: TNBC; individual: Patient 3; protocol: post-treatment surgical resection; tumor sample subtype: basal

GSM2869480 grouping

Sample field · Grouping · Global correction · GSM2869480

Wrong grouping

Current derived value

tumor sample (case)

Raw GEO sample metadata

sample_accession: GSM2869480
sample_title: Patient 11 needle core biopsy - pre treatment
source_name: breast carcinoma
characteristics: disease state: TNBC; individual: Patient 11; protocol: pre-treatment needle core biospy; tumor sample subtype: basal

GSM2869480 exclusion decision

Sample field · Sample exclusion · Global correction · GSM2869480

Wrong sample exclusion

Current derived value

Included in derived sample grouping as tumor sample

Raw GEO sample metadata

sample_accession: GSM2869480
sample_title: Patient 11 needle core biopsy - pre treatment
source_name: breast carcinoma
characteristics: disease state: TNBC; individual: Patient 11; protocol: pre-treatment needle core biospy; tumor sample subtype: basal

GSM2869481 grouping

Sample field · Grouping · Global correction · GSM2869481

Wrong grouping

Current derived value

tumor sample (case)

Raw GEO sample metadata

sample_accession: GSM2869481
sample_title: Patient 11 surgical resection - post treatment
source_name: breast carcinoma
characteristics: disease state: TNBC; individual: Patient 11; protocol: post-treatment surgical resection; tumor sample subtype: claudin low

GSM2869481 exclusion decision

Sample field · Sample exclusion · Global correction · GSM2869481

Wrong sample exclusion

Current derived value

Included in derived sample grouping as tumor sample

Raw GEO sample metadata

sample_accession: GSM2869481
sample_title: Patient 11 surgical resection - post treatment
source_name: breast carcinoma
characteristics: disease state: TNBC; individual: Patient 11; protocol: post-treatment surgical resection; tumor sample subtype: claudin low

GSM2869482 grouping

Sample field · Grouping · Global correction · GSM2869482

Wrong grouping

Current derived value

normal tissue (control)

Raw GEO sample metadata

sample_accession: GSM2869482
sample_title: Patient 12 needle core biopsy - pre treatment
source_name: breast carcinoma
characteristics: disease state: TNBC; individual: Patient 12; protocol: pre-treatment needle core biospy; tumor sample subtype: normal breast

GSM2869482 exclusion decision

Sample field · Sample exclusion · Global correction · GSM2869482

Wrong sample exclusion

Current derived value

Included in derived sample grouping as normal tissue

Raw GEO sample metadata

sample_accession: GSM2869482
sample_title: Patient 12 needle core biopsy - pre treatment
source_name: breast carcinoma
characteristics: disease state: TNBC; individual: Patient 12; protocol: pre-treatment needle core biospy; tumor sample subtype: normal breast

GSM2869483 grouping

Sample field · Grouping · Global correction · GSM2869483

Wrong grouping

Current derived value

normal tissue (control)

Raw GEO sample metadata

sample_accession: GSM2869483
sample_title: Patient 12 surgical resection - post treatment
source_name: breast carcinoma
characteristics: disease state: TNBC; individual: Patient 12; protocol: post-treatment surgical resection; tumor sample subtype: normal breast

GSM2869483 exclusion decision

Sample field · Sample exclusion · Global correction · GSM2869483

Wrong sample exclusion

Current derived value

Included in derived sample grouping as normal tissue

Raw GEO sample metadata

sample_accession: GSM2869483
sample_title: Patient 12 surgical resection - post treatment
source_name: breast carcinoma
characteristics: disease state: TNBC; individual: Patient 12; protocol: post-treatment surgical resection; tumor sample subtype: normal breast

Source Evidence

4 sources

GEO

Primary source

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

Dataset accession: GSE107502
Sample records: 28 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: GSE107502

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: GSE107502

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: GSE107502

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: GSE107502
dataset_title: Defining the Triple Negative Breast Cancer Kinome Response to GSK1120212 (RNA-Seq)
organism: Homo sapiens
assay_type: bulk RNA-seq
processed_data_available: true
raw_data_available: true
submission_date: 2017-11-29
last_update_date: 2019-03-27
organization_name: University of North Carolina School of Medicine
department: Pharmacology
public_date: 2017-11-29
experiment_types: Expression profiling by high throughput sequencing
platforms: GPL11154 Illumina HiSeq 2000 (Homo sapiens)
sub_series: Not available
bioproject: PRJNA420378
supplementary_files: TXT: GSE107502_LCCC1122_DESeq2_trametinibresponse.txt.gz; TXT: GSE107502_LCCC1122_normalizedLog2RSEM.txt.gz; TXT: GSE107502_LCCC1122_rawRSEM.txt.gz
series_type: SubSeries

Why It Matched

Tumor vs unmatched normal · Biopsy · suitability 0%.
Prioritized assay: bulk RNA-seq is the active assay expectation.
Downgraded disease context: not a colorectal/GI cancer cohort.
Processed data is available for downstream review.

Why It May Not Be Suitable

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

Warnings

No warnings

Normalized Fields

105 fields

Field Value Source Origin Confidence Evidence Reason

assay_type bulk RNA-seq dataset GSE107502 Runtime Siftome inference GEO:dataset:GSE107502:427a0952bc54dcba3a4efcebf84c8d85785e16ead5e245fbac8e512cba819d73 high confidence bulk rna-seq dataset_accession: GSE107502 dataset_title: Defining the Triple Negative Breast Cancer Kinome Response to GSK1120212 (RNA-Seq) organism: Homo sapiens assay_type: bulk RNA-seq pr... keyword match keyword match: bulk rna-seq

disease breast cancer dataset GSE107502 Runtime Siftome inference GEO:dataset:GSE107502:427a0952bc54dcba3a4efcebf84c8d85785e16ead5e245fbac8e512cba819d73 high confidence breast cancer dataset_accession: GSE107502 dataset_title: Defining the Triple Negative Breast Cancer Kinome Response to GSK1120212 (RNA-Seq) organism: Homo sapiens assay_type: bulk RNA-seq pr... controlled vocabulary controlled vocabulary disease match: breast cancer

disease breast cancer sample GSM2869456 Runtime Siftome inference GEO:sample:GSM2869456:6178d1051873b9f3a0d9a0821c18b28c9b088cbfadf20f37324410420f7a49bf high confidence breast carcinoma sample_accession: GSM2869456 sample_title: Patient 6 needle core biospy - pre treatment source_name: breast carcinoma characteristics: disease state: TNBC; individual: Patient 6... controlled vocabulary controlled vocabulary disease match: breast carcinoma

disease breast cancer sample GSM2869457 Runtime Siftome inference GEO:sample:GSM2869457:39a66f9be90892815bfb8c225d1f59495d770d913e83e2bbf1af4b8d0044a919 high confidence breast carcinoma sample_accession: GSM2869457 sample_title: Patient 6 surgical resection - post treatment source_name: breast carcinoma characteristics: disease state: TNBC; individual: Patient ... controlled vocabulary controlled vocabulary disease match: breast carcinoma

disease breast cancer sample GSM2869458 Runtime Siftome inference GEO:sample:GSM2869458:5e4edcaaba9eb03506c4b7460817d9ca7dd626f47d97a6fcbce1181ecc33ef3a high confidence breast carcinoma sample_accession: GSM2869458 sample_title: Patient 5 needle core biopsy - pre treatment_2 source_name: breast carcinoma characteristics: disease state: TNBC; individual: Patient... controlled vocabulary controlled vocabulary disease match: breast carcinoma

disease breast cancer sample GSM2869459 Runtime Siftome inference GEO:sample:GSM2869459:321f46d4e261215a6dcf759126a9d0bc5e71e1de8a8839b2246c837de9e4e002 high confidence breast carcinoma sample_accession: GSM2869459 sample_title: Patient 5 needle core biopsy - pre treatment source_name: breast carcinoma characteristics: disease state: TNBC; individual: Patient 5... controlled vocabulary controlled vocabulary disease match: breast carcinoma

disease breast cancer sample GSM2869460 Runtime Siftome inference GEO:sample:GSM2869460:69dd8e5d160c584f2d25405054d791880c20da16e13bdafbacca5b2a724267a7 high confidence breast carcinoma sample_accession: GSM2869460 sample_title: Patient 5 surgical resection - post treatment_2 source_name: breast carcinoma characteristics: disease state: TNBC; individual: Patien... controlled vocabulary controlled vocabulary disease match: breast carcinoma

disease breast cancer sample GSM2869461 Runtime Siftome inference GEO:sample:GSM2869461:54eb4e38fdd60a391390c1c9ff275bb33624d0d11907f755aa553772d4c61f5a high confidence breast carcinoma sample_accession: GSM2869461 sample_title: Patient 5 surgical resection - post treatment source_name: breast carcinoma characteristics: disease state: TNBC; individual: Patient ... controlled vocabulary controlled vocabulary disease match: breast carcinoma

disease breast cancer sample GSM2869462 Runtime Siftome inference GEO:sample:GSM2869462:d93930c081cfa7f84126d4f858c9eb7a92b2cfb0c2bc9b2d597fa76bd70daa2a high confidence breast carcinoma sample_accession: GSM2869462 sample_title: Patient 6 needle core biospy - pre treatment_2 source_name: breast carcinoma characteristics: disease state: TNBC; individual: Patient... controlled vocabulary controlled vocabulary disease match: breast carcinoma

disease breast cancer sample GSM2869463 Runtime Siftome inference GEO:sample:GSM2869463:0f484f676a79f1215b49a70b84dbeb55210496278ba39eff8fd62b88af966a02 high confidence breast carcinoma sample_accession: GSM2869463 sample_title: Patient 6 surgical resection - post treatment_2 source_name: breast carcinoma characteristics: disease state: TNBC; individual: Patien... controlled vocabulary controlled vocabulary disease match: breast carcinoma

disease breast cancer sample GSM2869464 Runtime Siftome inference GEO:sample:GSM2869464:38f8e064f7f081f5a3b82d333a0e67a3fefaaf20cab2d3f10789154824196442 high confidence breast carcinoma sample_accession: GSM2869464 sample_title: Patient 7 needle core biopsy - pre treatment source_name: breast carcinoma characteristics: disease state: TNBC; individual: Patient 7... controlled vocabulary controlled vocabulary disease match: breast carcinoma

disease breast cancer sample GSM2869465 Runtime Siftome inference GEO:sample:GSM2869465:a06e75f64b807afbc88df47d9de4b294d7f875ba9dda03da2f419458d7e4fbdd high confidence breast carcinoma sample_accession: GSM2869465 sample_title: Patient 7 surgical resection - post treatment source_name: breast carcinoma characteristics: disease state: TNBC; individual: Patient ... controlled vocabulary controlled vocabulary disease match: breast carcinoma

disease breast cancer sample GSM2869466 Runtime Siftome inference GEO:sample:GSM2869466:5f90b89fe6341e14302e86a1f7e674116c521f6224582f781b04021b7af36d01 high confidence breast carcinoma sample_accession: GSM2869466 sample_title: Patient 8 needle core biopsy - pre treatment source_name: breast carcinoma characteristics: disease state: TNBC; individual: Patient 8... controlled vocabulary controlled vocabulary disease match: breast carcinoma

disease breast cancer sample GSM2869467 Runtime Siftome inference GEO:sample:GSM2869467:19d7fd3ba8af2e8d632479aa733698b3d0ee4174007bb0770285aade9795ebb8 high confidence breast carcinoma sample_accession: GSM2869467 sample_title: Patient 8 surgical resection - post treatment source_name: breast carcinoma characteristics: disease state: TNBC; individual: Patient ... controlled vocabulary controlled vocabulary disease match: breast carcinoma

disease breast cancer sample GSM2869468 Runtime Siftome inference GEO:sample:GSM2869468:45b7065fd2b9aa4eb2212f6e618698a43994f31d0db6579b6182717b85bc6d20 high confidence breast carcinoma sample_accession: GSM2869468 sample_title: Patient 1 needle core biopsy - pre treatment source_name: breast carcinoma characteristics: disease state: TNBC; individual: Patient 1... controlled vocabulary controlled vocabulary disease match: breast carcinoma

disease breast cancer sample GSM2869469 Runtime Siftome inference GEO:sample:GSM2869469:2977295c09649b901461a215db37dffd547951cd6ab2cfb0562b0c131626d6f3 high confidence breast carcinoma sample_accession: GSM2869469 sample_title: Patient 1 surgical resection - post treatment source_name: breast carcinoma characteristics: disease state: TNBC; individual: Patient ... controlled vocabulary controlled vocabulary disease match: breast carcinoma

disease breast cancer sample GSM2869470 Runtime Siftome inference GEO:sample:GSM2869470:b43e629862976783f07cde6708ffe30963a677163b27cc17720b7794eb5cdb52 high confidence breast carcinoma sample_accession: GSM2869470 sample_title: Patient 2 needle core biopsy - pre treatment source_name: breast carcinoma characteristics: disease state: TNBC; individual: Patient 2... controlled vocabulary controlled vocabulary disease match: breast carcinoma

disease breast cancer sample GSM2869471 Runtime Siftome inference GEO:sample:GSM2869471:6e43e86c809979366a715ca2549abba13341d138e276fa3a9735e8e73d79c5d6 high confidence breast carcinoma sample_accession: GSM2869471 sample_title: Patient 2 surgical resection - post treatment source_name: breast carcinoma characteristics: disease state: TNBC; individual: Patient ... controlled vocabulary controlled vocabulary disease match: breast carcinoma

disease breast cancer sample GSM2869472 Runtime Siftome inference GEO:sample:GSM2869472:3b9cfd141897c6903c5e0f3998fdd86bbaea12d8dc119740623bcf757587a487 high confidence breast carcinoma sample_accession: GSM2869472 sample_title: Patient 9 needle core biopsy - pre treatment source_name: breast carcinoma characteristics: disease state: TNBC; individual: Patient 9... controlled vocabulary controlled vocabulary disease match: breast carcinoma

disease breast cancer sample GSM2869473 Runtime Siftome inference GEO:sample:GSM2869473:ee53428d612e1d876ec35b4b0619de559bdc32d590f35c506a91090016bf5db4 high confidence breast carcinoma sample_accession: GSM2869473 sample_title: Patient 9 surgical resection - post treatment source_name: breast carcinoma characteristics: disease state: TNBC; individual: Patient ... controlled vocabulary controlled vocabulary disease match: breast carcinoma

disease breast cancer sample GSM2869474 Runtime Siftome inference GEO:sample:GSM2869474:78478bc5914a3f6146aafc57f035c8b5430359744dc3fe8b223925ee89948da0 high confidence breast carcinoma sample_accession: GSM2869474 sample_title: Patient 10 needle core biopsy - pre treatment source_name: breast carcinoma characteristics: disease state: TNBC; individual: Patient ... controlled vocabulary controlled vocabulary disease match: breast carcinoma

disease breast cancer sample GSM2869475 Runtime Siftome inference GEO:sample:GSM2869475:091279fbfc1164e4f84903262576ba85744641be1402e35689f1deb7cdc71c96 high confidence breast carcinoma sample_accession: GSM2869475 sample_title: Patient 10 surgical resection - post treatment source_name: breast carcinoma characteristics: disease state: TNBC; individual: Patient... controlled vocabulary controlled vocabulary disease match: breast carcinoma

disease breast cancer sample GSM2869476 Runtime Siftome inference GEO:sample:GSM2869476:6fd1cac86be15517c6d703235fbc7e6bafc2e59ca3e24f6dfd7bfe152b87212e high confidence breast carcinoma sample_accession: GSM2869476 sample_title: Patient 4 Needle Core Biopsy - pre treatment source_name: breast carcinoma characteristics: disease state: TNBC; individual: Patient 4... controlled vocabulary controlled vocabulary disease match: breast carcinoma

disease breast cancer sample GSM2869477 Runtime Siftome inference GEO:sample:GSM2869477:647d52cdb77b41f21bcaacd0a305421c5b4b9c48de5f1797a5f24c2e70b346b9 high confidence breast carcinoma sample_accession: GSM2869477 sample_title: Patient 4 surgical resection - post treatment source_name: breast carcinoma characteristics: disease state: TNBC; individual: Patient ... controlled vocabulary controlled vocabulary disease match: breast carcinoma

disease breast cancer sample GSM2869478 Runtime Siftome inference GEO:sample:GSM2869478:b16123e48049e734d34785ffb6866b7119533972fdd89d5b442cc6bed824d87d high confidence breast carcinoma sample_accession: GSM2869478 sample_title: Patient 3 Needle Core Biopsy - pre treatment source_name: breast carcinoma characteristics: disease state: TNBC; individual: Patient 3... controlled vocabulary controlled vocabulary disease match: breast carcinoma

disease breast cancer sample GSM2869479 Runtime Siftome inference GEO:sample:GSM2869479:fd8d86ae92e55340329d175703c339b4cb5c7dc0e410c0aabdb62ae3a6f06d60 high confidence breast carcinoma sample_accession: GSM2869479 sample_title: Patient 3 surgical resection - post treatment source_name: breast carcinoma characteristics: disease state: TNBC; individual: Patient ... controlled vocabulary controlled vocabulary disease match: breast carcinoma

disease breast cancer sample GSM2869480 Runtime Siftome inference GEO:sample:GSM2869480:5368260ab0154d6d24a3916ad9e47692dc2786cfeafa96f6f384efaaa4f52e4f high confidence breast carcinoma sample_accession: GSM2869480 sample_title: Patient 11 needle core biopsy - pre treatment source_name: breast carcinoma characteristics: disease state: TNBC; individual: Patient ... controlled vocabulary controlled vocabulary disease match: breast carcinoma

disease breast cancer sample GSM2869481 Runtime Siftome inference GEO:sample:GSM2869481:baa56bae0e23b1e4242cb686a33d349f5216806e9cf3b79d414493a1f743b66a high confidence breast carcinoma sample_accession: GSM2869481 sample_title: Patient 11 surgical resection - post treatment source_name: breast carcinoma characteristics: disease state: TNBC; individual: Patient... controlled vocabulary controlled vocabulary disease match: breast carcinoma

disease breast cancer sample GSM2869482 Runtime Siftome inference GEO:sample:GSM2869482:14f2ac4dc4e3e7b3ac0762020f56c0b506f442f4a2945e709695f9bb3c86b7a8 high confidence breast carcinoma sample_accession: GSM2869482 sample_title: Patient 12 needle core biopsy - pre treatment source_name: breast carcinoma characteristics: disease state: TNBC; individual: Patient ... controlled vocabulary controlled vocabulary disease match: breast carcinoma

disease breast cancer sample GSM2869483 Runtime Siftome inference GEO:sample:GSM2869483:46e3b505d4f41ae78e1fcba7ee5e2065792821fde87161ee3da8eeb15590852b high confidence breast carcinoma sample_accession: GSM2869483 sample_title: Patient 12 surgical resection - post treatment source_name: breast carcinoma characteristics: disease state: TNBC; individual: Patient... controlled vocabulary controlled vocabulary disease match: breast carcinoma

organism Homo sapiens dataset GSE107502 Runtime Siftome inference GEO:dataset:GSE107502:427a0952bc54dcba3a4efcebf84c8d85785e16ead5e245fbac8e512cba819d73 high confidence homo sapiens dataset_accession: GSE107502 dataset_title: Defining the Triple Negative Breast Cancer Kinome Response to GSK1120212 (RNA-Seq) organism: Homo sapiens assay_type: bulk RNA-seq pr... keyword match keyword match: homo sapiens

primary_tissue primary tissue sample GSM2869458 Runtime Siftome inference GEO:sample:GSM2869458:5e4edcaaba9eb03506c4b7460817d9ca7dd626f47d97a6fcbce1181ecc33ef3a low confidence biopsy sample_accession: GSM2869458 sample_title: Patient 5 needle core biopsy - pre treatment_2 source_name: breast carcinoma characteristics: disease state: TNBC; individual: Patient... controlled vocabulary controlled vocabulary primary tissue match: biopsy

primary_tissue primary tissue sample GSM2869459 Runtime Siftome inference GEO:sample:GSM2869459:321f46d4e261215a6dcf759126a9d0bc5e71e1de8a8839b2246c837de9e4e002 low confidence biopsy sample_accession: GSM2869459 sample_title: Patient 5 needle core biopsy - pre treatment source_name: breast carcinoma characteristics: disease state: TNBC; individual: Patient 5... controlled vocabulary controlled vocabulary primary tissue match: biopsy

primary_tissue primary tissue sample GSM2869464 Runtime Siftome inference GEO:sample:GSM2869464:38f8e064f7f081f5a3b82d333a0e67a3fefaaf20cab2d3f10789154824196442 low confidence biopsy sample_accession: GSM2869464 sample_title: Patient 7 needle core biopsy - pre treatment source_name: breast carcinoma characteristics: disease state: TNBC; individual: Patient 7... controlled vocabulary controlled vocabulary primary tissue match: biopsy

primary_tissue primary tissue sample GSM2869466 Runtime Siftome inference GEO:sample:GSM2869466:5f90b89fe6341e14302e86a1f7e674116c521f6224582f781b04021b7af36d01 low confidence biopsy sample_accession: GSM2869466 sample_title: Patient 8 needle core biopsy - pre treatment source_name: breast carcinoma characteristics: disease state: TNBC; individual: Patient 8... controlled vocabulary controlled vocabulary primary tissue match: biopsy

primary_tissue primary tissue sample GSM2869468 Runtime Siftome inference GEO:sample:GSM2869468:45b7065fd2b9aa4eb2212f6e618698a43994f31d0db6579b6182717b85bc6d20 low confidence biopsy sample_accession: GSM2869468 sample_title: Patient 1 needle core biopsy - pre treatment source_name: breast carcinoma characteristics: disease state: TNBC; individual: Patient 1... controlled vocabulary controlled vocabulary primary tissue match: biopsy

primary_tissue primary tissue sample GSM2869470 Runtime Siftome inference GEO:sample:GSM2869470:b43e629862976783f07cde6708ffe30963a677163b27cc17720b7794eb5cdb52 low confidence biopsy sample_accession: GSM2869470 sample_title: Patient 2 needle core biopsy - pre treatment source_name: breast carcinoma characteristics: disease state: TNBC; individual: Patient 2... controlled vocabulary controlled vocabulary primary tissue match: biopsy

primary_tissue primary tissue sample GSM2869472 Runtime Siftome inference GEO:sample:GSM2869472:3b9cfd141897c6903c5e0f3998fdd86bbaea12d8dc119740623bcf757587a487 low confidence biopsy sample_accession: GSM2869472 sample_title: Patient 9 needle core biopsy - pre treatment source_name: breast carcinoma characteristics: disease state: TNBC; individual: Patient 9... controlled vocabulary controlled vocabulary primary tissue match: biopsy

primary_tissue primary tissue sample GSM2869474 Runtime Siftome inference GEO:sample:GSM2869474:78478bc5914a3f6146aafc57f035c8b5430359744dc3fe8b223925ee89948da0 low confidence biopsy sample_accession: GSM2869474 sample_title: Patient 10 needle core biopsy - pre treatment source_name: breast carcinoma characteristics: disease state: TNBC; individual: Patient ... controlled vocabulary controlled vocabulary primary tissue match: biopsy

primary_tissue primary tissue sample GSM2869476 Runtime Siftome inference GEO:sample:GSM2869476:6fd1cac86be15517c6d703235fbc7e6bafc2e59ca3e24f6dfd7bfe152b87212e low confidence biopsy sample_accession: GSM2869476 sample_title: Patient 4 Needle Core Biopsy - pre treatment source_name: breast carcinoma characteristics: disease state: TNBC; individual: Patient 4... controlled vocabulary controlled vocabulary primary tissue match: biopsy

primary_tissue primary tissue sample GSM2869478 Runtime Siftome inference GEO:sample:GSM2869478:b16123e48049e734d34785ffb6866b7119533972fdd89d5b442cc6bed824d87d low confidence biopsy sample_accession: GSM2869478 sample_title: Patient 3 Needle Core Biopsy - pre treatment source_name: breast carcinoma characteristics: disease state: TNBC; individual: Patient 3... controlled vocabulary controlled vocabulary primary tissue match: biopsy

primary_tissue primary tissue sample GSM2869480 Runtime Siftome inference GEO:sample:GSM2869480:5368260ab0154d6d24a3916ad9e47692dc2786cfeafa96f6f384efaaa4f52e4f low confidence biopsy sample_accession: GSM2869480 sample_title: Patient 11 needle core biopsy - pre treatment source_name: breast carcinoma characteristics: disease state: TNBC; individual: Patient ... controlled vocabulary controlled vocabulary primary tissue match: biopsy

primary_tissue primary tissue sample GSM2869482 Runtime Siftome inference GEO:sample:GSM2869482:14f2ac4dc4e3e7b3ac0762020f56c0b506f442f4a2945e709695f9bb3c86b7a8 low confidence biopsy sample_accession: GSM2869482 sample_title: Patient 12 needle core biopsy - pre treatment source_name: breast carcinoma characteristics: disease state: TNBC; individual: Patient ... controlled vocabulary controlled vocabulary primary tissue match: biopsy

sample_type tumor sample sample GSM2869456 Runtime Siftome inference GEO:sample:GSM2869456:6178d1051873b9f3a0d9a0821c18b28c9b088cbfadf20f37324410420f7a49bf low confidence tumor sample_accession: GSM2869456 sample_title: Patient 6 needle core biospy - pre treatment source_name: breast carcinoma characteristics: disease state: TNBC; individual: Patient 6... controlled vocabulary controlled vocabulary sample type match: tumor

sample_type tumor sample sample GSM2869457 Runtime Siftome inference GEO:sample:GSM2869457:39a66f9be90892815bfb8c225d1f59495d770d913e83e2bbf1af4b8d0044a919 low confidence tumor sample_accession: GSM2869457 sample_title: Patient 6 surgical resection - post treatment source_name: breast carcinoma characteristics: disease state: TNBC; individual: Patient ... controlled vocabulary controlled vocabulary sample type match: tumor

sample_type tumor sample sample GSM2869458 Runtime Siftome inference GEO:sample:GSM2869458:5e4edcaaba9eb03506c4b7460817d9ca7dd626f47d97a6fcbce1181ecc33ef3a low confidence tumor sample_accession: GSM2869458 sample_title: Patient 5 needle core biopsy - pre treatment_2 source_name: breast carcinoma characteristics: disease state: TNBC; individual: Patient... controlled vocabulary controlled vocabulary sample type match: tumor

sample_type tumor sample sample GSM2869459 Runtime Siftome inference GEO:sample:GSM2869459:321f46d4e261215a6dcf759126a9d0bc5e71e1de8a8839b2246c837de9e4e002 low confidence tumor sample_accession: GSM2869459 sample_title: Patient 5 needle core biopsy - pre treatment source_name: breast carcinoma characteristics: disease state: TNBC; individual: Patient 5... controlled vocabulary controlled vocabulary sample type match: tumor

sample_type tumor sample sample GSM2869460 Runtime Siftome inference GEO:sample:GSM2869460:69dd8e5d160c584f2d25405054d791880c20da16e13bdafbacca5b2a724267a7 low confidence tumor sample_accession: GSM2869460 sample_title: Patient 5 surgical resection - post treatment_2 source_name: breast carcinoma characteristics: disease state: TNBC; individual: Patien... controlled vocabulary controlled vocabulary sample type match: tumor

sample_type tumor sample sample GSM2869461 Runtime Siftome inference GEO:sample:GSM2869461:54eb4e38fdd60a391390c1c9ff275bb33624d0d11907f755aa553772d4c61f5a low confidence tumor sample_accession: GSM2869461 sample_title: Patient 5 surgical resection - post treatment source_name: breast carcinoma characteristics: disease state: TNBC; individual: Patient ... controlled vocabulary controlled vocabulary sample type match: tumor

sample_type tumor sample sample GSM2869462 Runtime Siftome inference GEO:sample:GSM2869462:d93930c081cfa7f84126d4f858c9eb7a92b2cfb0c2bc9b2d597fa76bd70daa2a low confidence tumor sample_accession: GSM2869462 sample_title: Patient 6 needle core biospy - pre treatment_2 source_name: breast carcinoma characteristics: disease state: TNBC; individual: Patient... controlled vocabulary controlled vocabulary sample type match: tumor

sample_type tumor sample sample GSM2869463 Runtime Siftome inference GEO:sample:GSM2869463:0f484f676a79f1215b49a70b84dbeb55210496278ba39eff8fd62b88af966a02 low confidence tumor sample_accession: GSM2869463 sample_title: Patient 6 surgical resection - post treatment_2 source_name: breast carcinoma characteristics: disease state: TNBC; individual: Patien... controlled vocabulary controlled vocabulary sample type match: tumor

sample_type normal tissue sample GSM2869464 Runtime Siftome inference GEO:sample:GSM2869464:38f8e064f7f081f5a3b82d333a0e67a3fefaaf20cab2d3f10789154824196442 low confidence normal sample_accession: GSM2869464 sample_title: Patient 7 needle core biopsy - pre treatment source_name: breast carcinoma characteristics: disease state: TNBC; individual: Patient 7... controlled vocabulary controlled vocabulary sample type match: normal

sample_type tumor sample sample GSM2869464 Runtime Siftome inference GEO:sample:GSM2869464:38f8e064f7f081f5a3b82d333a0e67a3fefaaf20cab2d3f10789154824196442 low confidence tumor sample_accession: GSM2869464 sample_title: Patient 7 needle core biopsy - pre treatment source_name: breast carcinoma characteristics: disease state: TNBC; individual: Patient 7... controlled vocabulary controlled vocabulary sample type match: tumor

sample_type normal tissue sample GSM2869465 Runtime Siftome inference GEO:sample:GSM2869465:a06e75f64b807afbc88df47d9de4b294d7f875ba9dda03da2f419458d7e4fbdd low confidence normal sample_accession: GSM2869465 sample_title: Patient 7 surgical resection - post treatment source_name: breast carcinoma characteristics: disease state: TNBC; individual: Patient ... controlled vocabulary controlled vocabulary sample type match: normal

sample_type tumor sample sample GSM2869465 Runtime Siftome inference GEO:sample:GSM2869465:a06e75f64b807afbc88df47d9de4b294d7f875ba9dda03da2f419458d7e4fbdd low confidence tumor sample_accession: GSM2869465 sample_title: Patient 7 surgical resection - post treatment source_name: breast carcinoma characteristics: disease state: TNBC; individual: Patient ... controlled vocabulary controlled vocabulary sample type match: tumor

sample_type tumor sample sample GSM2869466 Runtime Siftome inference GEO:sample:GSM2869466:5f90b89fe6341e14302e86a1f7e674116c521f6224582f781b04021b7af36d01 low confidence tumor sample_accession: GSM2869466 sample_title: Patient 8 needle core biopsy - pre treatment source_name: breast carcinoma characteristics: disease state: TNBC; individual: Patient 8... controlled vocabulary controlled vocabulary sample type match: tumor

sample_type tumor sample sample GSM2869467 Runtime Siftome inference GEO:sample:GSM2869467:19d7fd3ba8af2e8d632479aa733698b3d0ee4174007bb0770285aade9795ebb8 low confidence tumor sample_accession: GSM2869467 sample_title: Patient 8 surgical resection - post treatment source_name: breast carcinoma characteristics: disease state: TNBC; individual: Patient ... controlled vocabulary controlled vocabulary sample type match: tumor

sample_type tumor sample sample GSM2869468 Runtime Siftome inference GEO:sample:GSM2869468:45b7065fd2b9aa4eb2212f6e618698a43994f31d0db6579b6182717b85bc6d20 low confidence tumor sample_accession: GSM2869468 sample_title: Patient 1 needle core biopsy - pre treatment source_name: breast carcinoma characteristics: disease state: TNBC; individual: Patient 1... controlled vocabulary controlled vocabulary sample type match: tumor

sample_type tumor sample sample GSM2869469 Runtime Siftome inference GEO:sample:GSM2869469:2977295c09649b901461a215db37dffd547951cd6ab2cfb0562b0c131626d6f3 low confidence tumor sample_accession: GSM2869469 sample_title: Patient 1 surgical resection - post treatment source_name: breast carcinoma characteristics: disease state: TNBC; individual: Patient ... controlled vocabulary controlled vocabulary sample type match: tumor

sample_type tumor sample sample GSM2869470 Runtime Siftome inference GEO:sample:GSM2869470:b43e629862976783f07cde6708ffe30963a677163b27cc17720b7794eb5cdb52 low confidence tumor sample_accession: GSM2869470 sample_title: Patient 2 needle core biopsy - pre treatment source_name: breast carcinoma characteristics: disease state: TNBC; individual: Patient 2... controlled vocabulary controlled vocabulary sample type match: tumor

sample_type tumor sample sample GSM2869471 Runtime Siftome inference GEO:sample:GSM2869471:6e43e86c809979366a715ca2549abba13341d138e276fa3a9735e8e73d79c5d6 low confidence tumor sample_accession: GSM2869471 sample_title: Patient 2 surgical resection - post treatment source_name: breast carcinoma characteristics: disease state: TNBC; individual: Patient ... controlled vocabulary controlled vocabulary sample type match: tumor

sample_type tumor sample sample GSM2869472 Runtime Siftome inference GEO:sample:GSM2869472:3b9cfd141897c6903c5e0f3998fdd86bbaea12d8dc119740623bcf757587a487 low confidence tumor sample_accession: GSM2869472 sample_title: Patient 9 needle core biopsy - pre treatment source_name: breast carcinoma characteristics: disease state: TNBC; individual: Patient 9... controlled vocabulary controlled vocabulary sample type match: tumor

sample_type normal tissue sample GSM2869473 Runtime Siftome inference GEO:sample:GSM2869473:ee53428d612e1d876ec35b4b0619de559bdc32d590f35c506a91090016bf5db4 low confidence normal sample_accession: GSM2869473 sample_title: Patient 9 surgical resection - post treatment source_name: breast carcinoma characteristics: disease state: TNBC; individual: Patient ... controlled vocabulary controlled vocabulary sample type match: normal

sample_type tumor sample sample GSM2869473 Runtime Siftome inference GEO:sample:GSM2869473:ee53428d612e1d876ec35b4b0619de559bdc32d590f35c506a91090016bf5db4 low confidence tumor sample_accession: GSM2869473 sample_title: Patient 9 surgical resection - post treatment source_name: breast carcinoma characteristics: disease state: TNBC; individual: Patient ... controlled vocabulary controlled vocabulary sample type match: tumor

sample_type tumor sample sample GSM2869474 Runtime Siftome inference GEO:sample:GSM2869474:78478bc5914a3f6146aafc57f035c8b5430359744dc3fe8b223925ee89948da0 low confidence tumor sample_accession: GSM2869474 sample_title: Patient 10 needle core biopsy - pre treatment source_name: breast carcinoma characteristics: disease state: TNBC; individual: Patient ... controlled vocabulary controlled vocabulary sample type match: tumor

sample_type tumor sample sample GSM2869475 Runtime Siftome inference GEO:sample:GSM2869475:091279fbfc1164e4f84903262576ba85744641be1402e35689f1deb7cdc71c96 low confidence tumor sample_accession: GSM2869475 sample_title: Patient 10 surgical resection - post treatment source_name: breast carcinoma characteristics: disease state: TNBC; individual: Patient... controlled vocabulary controlled vocabulary sample type match: tumor

sample_type tumor sample sample GSM2869476 Runtime Siftome inference GEO:sample:GSM2869476:6fd1cac86be15517c6d703235fbc7e6bafc2e59ca3e24f6dfd7bfe152b87212e low confidence tumor sample_accession: GSM2869476 sample_title: Patient 4 Needle Core Biopsy - pre treatment source_name: breast carcinoma characteristics: disease state: TNBC; individual: Patient 4... controlled vocabulary controlled vocabulary sample type match: tumor

sample_type tumor sample sample GSM2869477 Runtime Siftome inference GEO:sample:GSM2869477:647d52cdb77b41f21bcaacd0a305421c5b4b9c48de5f1797a5f24c2e70b346b9 low confidence tumor sample_accession: GSM2869477 sample_title: Patient 4 surgical resection - post treatment source_name: breast carcinoma characteristics: disease state: TNBC; individual: Patient ... controlled vocabulary controlled vocabulary sample type match: tumor

sample_type tumor sample sample GSM2869478 Runtime Siftome inference GEO:sample:GSM2869478:b16123e48049e734d34785ffb6866b7119533972fdd89d5b442cc6bed824d87d low confidence tumor sample_accession: GSM2869478 sample_title: Patient 3 Needle Core Biopsy - pre treatment source_name: breast carcinoma characteristics: disease state: TNBC; individual: Patient 3... controlled vocabulary controlled vocabulary sample type match: tumor

sample_type tumor sample sample GSM2869479 Runtime Siftome inference GEO:sample:GSM2869479:fd8d86ae92e55340329d175703c339b4cb5c7dc0e410c0aabdb62ae3a6f06d60 low confidence tumor sample_accession: GSM2869479 sample_title: Patient 3 surgical resection - post treatment source_name: breast carcinoma characteristics: disease state: TNBC; individual: Patient ... controlled vocabulary controlled vocabulary sample type match: tumor

sample_type tumor sample sample GSM2869480 Runtime Siftome inference GEO:sample:GSM2869480:5368260ab0154d6d24a3916ad9e47692dc2786cfeafa96f6f384efaaa4f52e4f low confidence tumor sample_accession: GSM2869480 sample_title: Patient 11 needle core biopsy - pre treatment source_name: breast carcinoma characteristics: disease state: TNBC; individual: Patient ... controlled vocabulary controlled vocabulary sample type match: tumor

sample_type tumor sample sample GSM2869481 Runtime Siftome inference GEO:sample:GSM2869481:baa56bae0e23b1e4242cb686a33d349f5216806e9cf3b79d414493a1f743b66a low confidence tumor sample_accession: GSM2869481 sample_title: Patient 11 surgical resection - post treatment source_name: breast carcinoma characteristics: disease state: TNBC; individual: Patient... controlled vocabulary controlled vocabulary sample type match: tumor

sample_type normal tissue sample GSM2869482 Runtime Siftome inference GEO:sample:GSM2869482:14f2ac4dc4e3e7b3ac0762020f56c0b506f442f4a2945e709695f9bb3c86b7a8 low confidence normal sample_accession: GSM2869482 sample_title: Patient 12 needle core biopsy - pre treatment source_name: breast carcinoma characteristics: disease state: TNBC; individual: Patient ... controlled vocabulary controlled vocabulary sample type match: normal

sample_type tumor sample sample GSM2869482 Runtime Siftome inference GEO:sample:GSM2869482:14f2ac4dc4e3e7b3ac0762020f56c0b506f442f4a2945e709695f9bb3c86b7a8 low confidence tumor sample_accession: GSM2869482 sample_title: Patient 12 needle core biopsy - pre treatment source_name: breast carcinoma characteristics: disease state: TNBC; individual: Patient ... controlled vocabulary controlled vocabulary sample type match: tumor

sample_type normal tissue sample GSM2869483 Runtime Siftome inference GEO:sample:GSM2869483:46e3b505d4f41ae78e1fcba7ee5e2065792821fde87161ee3da8eeb15590852b low confidence normal sample_accession: GSM2869483 sample_title: Patient 12 surgical resection - post treatment source_name: breast carcinoma characteristics: disease state: TNBC; individual: Patient... controlled vocabulary controlled vocabulary sample type match: normal

sample_type tumor sample sample GSM2869483 Runtime Siftome inference GEO:sample:GSM2869483:46e3b505d4f41ae78e1fcba7ee5e2065792821fde87161ee3da8eeb15590852b low confidence tumor sample_accession: GSM2869483 sample_title: Patient 12 surgical resection - post treatment source_name: breast carcinoma characteristics: disease state: TNBC; individual: Patient... controlled vocabulary controlled vocabulary sample type match: tumor

tissue breast dataset GSE107502 Runtime Siftome inference GEO:dataset:GSE107502:427a0952bc54dcba3a4efcebf84c8d85785e16ead5e245fbac8e512cba819d73 low confidence breast dataset_accession: GSE107502 dataset_title: Defining the Triple Negative Breast Cancer Kinome Response to GSK1120212 (RNA-Seq) organism: Homo sapiens assay_type: bulk RNA-seq pr... controlled vocabulary controlled vocabulary tissue match: breast

tissue breast sample GSM2869456 Runtime Siftome inference GEO:sample:GSM2869456:6178d1051873b9f3a0d9a0821c18b28c9b088cbfadf20f37324410420f7a49bf low confidence breast sample_accession: GSM2869456 sample_title: Patient 6 needle core biospy - pre treatment source_name: breast carcinoma characteristics: disease state: TNBC; individual: Patient 6... controlled vocabulary controlled vocabulary tissue match: breast

tissue breast sample GSM2869457 Runtime Siftome inference GEO:sample:GSM2869457:39a66f9be90892815bfb8c225d1f59495d770d913e83e2bbf1af4b8d0044a919 low confidence breast sample_accession: GSM2869457 sample_title: Patient 6 surgical resection - post treatment source_name: breast carcinoma characteristics: disease state: TNBC; individual: Patient ... controlled vocabulary controlled vocabulary tissue match: breast

tissue breast sample GSM2869458 Runtime Siftome inference GEO:sample:GSM2869458:5e4edcaaba9eb03506c4b7460817d9ca7dd626f47d97a6fcbce1181ecc33ef3a low confidence breast sample_accession: GSM2869458 sample_title: Patient 5 needle core biopsy - pre treatment_2 source_name: breast carcinoma characteristics: disease state: TNBC; individual: Patient... controlled vocabulary controlled vocabulary tissue match: breast

tissue breast sample GSM2869459 Runtime Siftome inference GEO:sample:GSM2869459:321f46d4e261215a6dcf759126a9d0bc5e71e1de8a8839b2246c837de9e4e002 low confidence breast sample_accession: GSM2869459 sample_title: Patient 5 needle core biopsy - pre treatment source_name: breast carcinoma characteristics: disease state: TNBC; individual: Patient 5... controlled vocabulary controlled vocabulary tissue match: breast

tissue breast sample GSM2869460 Runtime Siftome inference GEO:sample:GSM2869460:69dd8e5d160c584f2d25405054d791880c20da16e13bdafbacca5b2a724267a7 low confidence breast sample_accession: GSM2869460 sample_title: Patient 5 surgical resection - post treatment_2 source_name: breast carcinoma characteristics: disease state: TNBC; individual: Patien... controlled vocabulary controlled vocabulary tissue match: breast

tissue breast sample GSM2869461 Runtime Siftome inference GEO:sample:GSM2869461:54eb4e38fdd60a391390c1c9ff275bb33624d0d11907f755aa553772d4c61f5a low confidence breast sample_accession: GSM2869461 sample_title: Patient 5 surgical resection - post treatment source_name: breast carcinoma characteristics: disease state: TNBC; individual: Patient ... controlled vocabulary controlled vocabulary tissue match: breast

tissue breast sample GSM2869462 Runtime Siftome inference GEO:sample:GSM2869462:d93930c081cfa7f84126d4f858c9eb7a92b2cfb0c2bc9b2d597fa76bd70daa2a low confidence breast sample_accession: GSM2869462 sample_title: Patient 6 needle core biospy - pre treatment_2 source_name: breast carcinoma characteristics: disease state: TNBC; individual: Patient... controlled vocabulary controlled vocabulary tissue match: breast

tissue breast sample GSM2869463 Runtime Siftome inference GEO:sample:GSM2869463:0f484f676a79f1215b49a70b84dbeb55210496278ba39eff8fd62b88af966a02 low confidence breast sample_accession: GSM2869463 sample_title: Patient 6 surgical resection - post treatment_2 source_name: breast carcinoma characteristics: disease state: TNBC; individual: Patien... controlled vocabulary controlled vocabulary tissue match: breast

tissue breast sample GSM2869464 Runtime Siftome inference GEO:sample:GSM2869464:38f8e064f7f081f5a3b82d333a0e67a3fefaaf20cab2d3f10789154824196442 low confidence breast sample_accession: GSM2869464 sample_title: Patient 7 needle core biopsy - pre treatment source_name: breast carcinoma characteristics: disease state: TNBC; individual: Patient 7... controlled vocabulary controlled vocabulary tissue match: breast

tissue breast sample GSM2869465 Runtime Siftome inference GEO:sample:GSM2869465:a06e75f64b807afbc88df47d9de4b294d7f875ba9dda03da2f419458d7e4fbdd low confidence breast sample_accession: GSM2869465 sample_title: Patient 7 surgical resection - post treatment source_name: breast carcinoma characteristics: disease state: TNBC; individual: Patient ... controlled vocabulary controlled vocabulary tissue match: breast

tissue breast sample GSM2869466 Runtime Siftome inference GEO:sample:GSM2869466:5f90b89fe6341e14302e86a1f7e674116c521f6224582f781b04021b7af36d01 low confidence breast sample_accession: GSM2869466 sample_title: Patient 8 needle core biopsy - pre treatment source_name: breast carcinoma characteristics: disease state: TNBC; individual: Patient 8... controlled vocabulary controlled vocabulary tissue match: breast

tissue breast sample GSM2869467 Runtime Siftome inference GEO:sample:GSM2869467:19d7fd3ba8af2e8d632479aa733698b3d0ee4174007bb0770285aade9795ebb8 low confidence breast sample_accession: GSM2869467 sample_title: Patient 8 surgical resection - post treatment source_name: breast carcinoma characteristics: disease state: TNBC; individual: Patient ... controlled vocabulary controlled vocabulary tissue match: breast

tissue breast sample GSM2869468 Runtime Siftome inference GEO:sample:GSM2869468:45b7065fd2b9aa4eb2212f6e618698a43994f31d0db6579b6182717b85bc6d20 low confidence breast sample_accession: GSM2869468 sample_title: Patient 1 needle core biopsy - pre treatment source_name: breast carcinoma characteristics: disease state: TNBC; individual: Patient 1... controlled vocabulary controlled vocabulary tissue match: breast

tissue breast sample GSM2869469 Runtime Siftome inference GEO:sample:GSM2869469:2977295c09649b901461a215db37dffd547951cd6ab2cfb0562b0c131626d6f3 low confidence breast sample_accession: GSM2869469 sample_title: Patient 1 surgical resection - post treatment source_name: breast carcinoma characteristics: disease state: TNBC; individual: Patient ... controlled vocabulary controlled vocabulary tissue match: breast

tissue breast sample GSM2869470 Runtime Siftome inference GEO:sample:GSM2869470:b43e629862976783f07cde6708ffe30963a677163b27cc17720b7794eb5cdb52 low confidence breast sample_accession: GSM2869470 sample_title: Patient 2 needle core biopsy - pre treatment source_name: breast carcinoma characteristics: disease state: TNBC; individual: Patient 2... controlled vocabulary controlled vocabulary tissue match: breast

tissue breast sample GSM2869471 Runtime Siftome inference GEO:sample:GSM2869471:6e43e86c809979366a715ca2549abba13341d138e276fa3a9735e8e73d79c5d6 low confidence breast sample_accession: GSM2869471 sample_title: Patient 2 surgical resection - post treatment source_name: breast carcinoma characteristics: disease state: TNBC; individual: Patient ... controlled vocabulary controlled vocabulary tissue match: breast

tissue breast sample GSM2869472 Runtime Siftome inference GEO:sample:GSM2869472:3b9cfd141897c6903c5e0f3998fdd86bbaea12d8dc119740623bcf757587a487 low confidence breast sample_accession: GSM2869472 sample_title: Patient 9 needle core biopsy - pre treatment source_name: breast carcinoma characteristics: disease state: TNBC; individual: Patient 9... controlled vocabulary controlled vocabulary tissue match: breast

tissue breast sample GSM2869473 Runtime Siftome inference GEO:sample:GSM2869473:ee53428d612e1d876ec35b4b0619de559bdc32d590f35c506a91090016bf5db4 low confidence breast sample_accession: GSM2869473 sample_title: Patient 9 surgical resection - post treatment source_name: breast carcinoma characteristics: disease state: TNBC; individual: Patient ... controlled vocabulary controlled vocabulary tissue match: breast

tissue breast sample GSM2869474 Runtime Siftome inference GEO:sample:GSM2869474:78478bc5914a3f6146aafc57f035c8b5430359744dc3fe8b223925ee89948da0 low confidence breast sample_accession: GSM2869474 sample_title: Patient 10 needle core biopsy - pre treatment source_name: breast carcinoma characteristics: disease state: TNBC; individual: Patient ... controlled vocabulary controlled vocabulary tissue match: breast

tissue breast sample GSM2869475 Runtime Siftome inference GEO:sample:GSM2869475:091279fbfc1164e4f84903262576ba85744641be1402e35689f1deb7cdc71c96 low confidence breast sample_accession: GSM2869475 sample_title: Patient 10 surgical resection - post treatment source_name: breast carcinoma characteristics: disease state: TNBC; individual: Patient... controlled vocabulary controlled vocabulary tissue match: breast

tissue breast sample GSM2869476 Runtime Siftome inference GEO:sample:GSM2869476:6fd1cac86be15517c6d703235fbc7e6bafc2e59ca3e24f6dfd7bfe152b87212e low confidence breast sample_accession: GSM2869476 sample_title: Patient 4 Needle Core Biopsy - pre treatment source_name: breast carcinoma characteristics: disease state: TNBC; individual: Patient 4... controlled vocabulary controlled vocabulary tissue match: breast

tissue breast sample GSM2869477 Runtime Siftome inference GEO:sample:GSM2869477:647d52cdb77b41f21bcaacd0a305421c5b4b9c48de5f1797a5f24c2e70b346b9 low confidence breast sample_accession: GSM2869477 sample_title: Patient 4 surgical resection - post treatment source_name: breast carcinoma characteristics: disease state: TNBC; individual: Patient ... controlled vocabulary controlled vocabulary tissue match: breast

tissue breast sample GSM2869478 Runtime Siftome inference GEO:sample:GSM2869478:b16123e48049e734d34785ffb6866b7119533972fdd89d5b442cc6bed824d87d low confidence breast sample_accession: GSM2869478 sample_title: Patient 3 Needle Core Biopsy - pre treatment source_name: breast carcinoma characteristics: disease state: TNBC; individual: Patient 3... controlled vocabulary controlled vocabulary tissue match: breast

tissue breast sample GSM2869479 Runtime Siftome inference GEO:sample:GSM2869479:fd8d86ae92e55340329d175703c339b4cb5c7dc0e410c0aabdb62ae3a6f06d60 low confidence breast sample_accession: GSM2869479 sample_title: Patient 3 surgical resection - post treatment source_name: breast carcinoma characteristics: disease state: TNBC; individual: Patient ... controlled vocabulary controlled vocabulary tissue match: breast

tissue breast sample GSM2869480 Runtime Siftome inference GEO:sample:GSM2869480:5368260ab0154d6d24a3916ad9e47692dc2786cfeafa96f6f384efaaa4f52e4f low confidence breast sample_accession: GSM2869480 sample_title: Patient 11 needle core biopsy - pre treatment source_name: breast carcinoma characteristics: disease state: TNBC; individual: Patient ... controlled vocabulary controlled vocabulary tissue match: breast

tissue breast sample GSM2869481 Runtime Siftome inference GEO:sample:GSM2869481:baa56bae0e23b1e4242cb686a33d349f5216806e9cf3b79d414493a1f743b66a low confidence breast sample_accession: GSM2869481 sample_title: Patient 11 surgical resection - post treatment source_name: breast carcinoma characteristics: disease state: TNBC; individual: Patient... controlled vocabulary controlled vocabulary tissue match: breast

tissue breast sample GSM2869482 Runtime Siftome inference GEO:sample:GSM2869482:14f2ac4dc4e3e7b3ac0762020f56c0b506f442f4a2945e709695f9bb3c86b7a8 low confidence breast sample_accession: GSM2869482 sample_title: Patient 12 needle core biopsy - pre treatment source_name: breast carcinoma characteristics: disease state: TNBC; individual: Patient ... controlled vocabulary controlled vocabulary tissue match: breast

tissue breast sample GSM2869483 Runtime Siftome inference GEO:sample:GSM2869483:46e3b505d4f41ae78e1fcba7ee5e2065792821fde87161ee3da8eeb15590852b low confidence breast sample_accession: GSM2869483 sample_title: Patient 12 surgical resection - post treatment source_name: breast carcinoma characteristics: disease state: TNBC; individual: Patient... controlled vocabulary controlled vocabulary tissue match: breast

Sample Group Preview

Possible case samples

Samples currently treated as the comparison case group.

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GSM2869456 Patient 6 needle core biospy - pre treatment tumor sample Case marker detected. breast carcinoma disease state: TNBC; individual: Patient 6; protocol: pre-treatment needle core biospy; tumor sample subtype: claudin low
GSM2869457 Patient 6 surgical resection - post treatment tumor sample Case marker detected. breast carcinoma disease state: TNBC; individual: Patient 6; protocol: post-treatment surgical resection; tumor sample subtype: claudin low
GSM2869458 Patient 5 needle core biopsy - pre treatment_2 tumor sample Case marker detected. breast carcinoma disease state: TNBC; individual: Patient 5; protocol: pre-treatment needle core biospy; tumor sample subtype: basal
GSM2869459 Patient 5 needle core biopsy - pre treatment tumor sample Case marker detected. breast carcinoma disease state: TNBC; individual: Patient 5; protocol: pre-treatment needle core biospy; tumor sample subtype: basal
GSM2869460 Patient 5 surgical resection - post treatment_2 tumor sample Case marker detected. breast carcinoma disease state: TNBC; individual: Patient 5; protocol: post-treatment surgical resection; tumor sample subtype: basal
GSM2869461 Patient 5 surgical resection - post treatment tumor sample Case marker detected. breast carcinoma disease state: TNBC; individual: Patient 5; protocol: post-treatment surgical resection; tumor sample subtype: basal
GSM2869462 Patient 6 needle core biospy - pre treatment_2 tumor sample Case marker detected. breast carcinoma disease state: TNBC; individual: Patient 6; protocol: pre-treatment needle core biospy; tumor sample subtype: claudin low
GSM2869463 Patient 6 surgical resection - post treatment_2 tumor sample Case marker detected. breast carcinoma disease state: TNBC; individual: Patient 6; protocol: post-treatment surgical resection; tumor sample subtype: claudin low
GSM2869466 Patient 8 needle core biopsy - pre treatment tumor sample Case marker detected. breast carcinoma disease state: TNBC; individual: Patient 8; protocol: pre-treatment needle core biospy; tumor sample subtype: claudin low
GSM2869467 Patient 8 surgical resection - post treatment tumor sample Case marker detected. breast carcinoma disease state: TNBC; individual: Patient 8; protocol: post-treatment surgical resection; tumor sample subtype: basal
GSM2869468 Patient 1 needle core biopsy - pre treatment tumor sample Case marker detected. breast carcinoma disease state: TNBC; individual: Patient 1; protocol: pre-treatment needle core biospy; tumor sample subtype: basal
GSM2869469 Patient 1 surgical resection - post treatment tumor sample Case marker detected. breast carcinoma disease state: TNBC; individual: Patient 1; protocol: post-treatment surgical resection; tumor sample subtype: basal
GSM2869470 Patient 2 needle core biopsy - pre treatment tumor sample Case marker detected. breast carcinoma disease state: TNBC; individual: Patient 2; protocol: pre-treatment needle core biospy; tumor sample subtype: basal
GSM2869471 Patient 2 surgical resection - post treatment tumor sample Case marker detected. breast carcinoma disease state: TNBC; individual: Patient 2; protocol: post-treatment surgical resection; tumor sample subtype: basal
GSM2869472 Patient 9 needle core biopsy - pre treatment tumor sample Case marker detected. breast carcinoma disease state: TNBC; individual: Patient 9; protocol: pre-treatment needle core biospy; tumor sample subtype: basal
GSM2869474 Patient 10 needle core biopsy - pre treatment tumor sample Case marker detected. breast carcinoma disease state: TNBC; individual: Patient 10; protocol: pre-treatment needle core biospy; tumor sample subtype: claudin low
GSM2869475 Patient 10 surgical resection - post treatment tumor sample Case marker detected. breast carcinoma disease state: TNBC; individual: Patient 10; protocol: post-treatment surgical resection; tumor sample subtype: basal
GSM2869476 Patient 4 Needle Core Biopsy - pre treatment tumor sample Case marker detected. breast carcinoma disease state: TNBC; individual: Patient 4; protocol: pre-treatment needle core biospy; tumor sample subtype: basal
GSM2869477 Patient 4 surgical resection - post treatment tumor sample Case marker detected. breast carcinoma disease state: TNBC; individual: Patient 4; protocol: post-treatment surgical resection; tumor sample subtype: basal
GSM2869478 Patient 3 Needle Core Biopsy - pre treatment tumor sample Case marker detected. breast carcinoma disease state: TNBC; individual: Patient 3; protocol: pre-treatment needle core biospy; tumor sample subtype: basal
GSM2869479 Patient 3 surgical resection - post treatment tumor sample Case marker detected. breast carcinoma disease state: TNBC; individual: Patient 3; protocol: post-treatment surgical resection; tumor sample subtype: basal
GSM2869480 Patient 11 needle core biopsy - pre treatment tumor sample Case marker detected. breast carcinoma disease state: TNBC; individual: Patient 11; protocol: pre-treatment needle core biospy; tumor sample subtype: basal
GSM2869481 Patient 11 surgical resection - post treatment tumor sample Case marker detected. breast carcinoma disease state: TNBC; individual: Patient 11; protocol: post-treatment surgical resection; tumor sample subtype: claudin low

Possible control samples

Samples currently treated as controls or baseline.

5

GSM2869464 Patient 7 needle core biopsy - pre treatment normal tissue Control marker detected. breast carcinoma disease state: TNBC; individual: Patient 7; protocol: pre-treatment needle core biospy; tumor sample subtype: normal breast
GSM2869465 Patient 7 surgical resection - post treatment normal tissue Control marker detected. breast carcinoma disease state: TNBC; individual: Patient 7; protocol: post-treatment surgical resection; tumor sample subtype: normal breast
GSM2869473 Patient 9 surgical resection - post treatment normal tissue Control marker detected. breast carcinoma disease state: TNBC; individual: Patient 9; protocol: post-treatment surgical resection; tumor sample subtype: normal breast
GSM2869482 Patient 12 needle core biopsy - pre treatment normal tissue Control marker detected. breast carcinoma disease state: TNBC; individual: Patient 12; protocol: pre-treatment needle core biospy; tumor sample subtype: normal breast
GSM2869483 Patient 12 surgical resection - post treatment normal tissue Control marker detected. breast carcinoma disease state: TNBC; individual: Patient 12; protocol: post-treatment surgical resection; tumor sample subtype: normal breast

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

100 pts

Clarity: 100%
Weight: 100 pts

Sample source clarity: All samples have source metadata and clear GSE/GSM accessions. Group clarity: Rule-based grouping found both case and control samples. Disease clarity: Disease or condition metadata normalized. Tissue clarity: Tissue metadata normalized. Treatment clarity: No unclear treatment split detected in the sample metadata. Replicate clarity: No pooled sample or technical replicate flags detected. Data availability clarity: Dataset-level processed or raw data availability is explicit.

Detected Sample Groups

tumor sample

23 samples

GSM2869456 Patient 6 needle core biospy - pre treatment breast carcinoma disease state: TNBC; individual: Patient 6; protocol: pre-treatment needle core biospy; tumor sample subtype: claudin low
GSM2869457 Patient 6 surgical resection - post treatment breast carcinoma disease state: TNBC; individual: Patient 6; protocol: post-treatment surgical resection; tumor sample subtype: claudin low
GSM2869458 Patient 5 needle core biopsy - pre treatment_2 breast carcinoma disease state: TNBC; individual: Patient 5; protocol: pre-treatment needle core biospy; tumor sample subtype: basal
GSM2869459 Patient 5 needle core biopsy - pre treatment breast carcinoma disease state: TNBC; individual: Patient 5; protocol: pre-treatment needle core biospy; tumor sample subtype: basal
GSM2869460 Patient 5 surgical resection - post treatment_2 breast carcinoma disease state: TNBC; individual: Patient 5; protocol: post-treatment surgical resection; tumor sample subtype: basal
GSM2869461 Patient 5 surgical resection - post treatment breast carcinoma disease state: TNBC; individual: Patient 5; protocol: post-treatment surgical resection; tumor sample subtype: basal
GSM2869462 Patient 6 needle core biospy - pre treatment_2 breast carcinoma disease state: TNBC; individual: Patient 6; protocol: pre-treatment needle core biospy; tumor sample subtype: claudin low
GSM2869463 Patient 6 surgical resection - post treatment_2 breast carcinoma disease state: TNBC; individual: Patient 6; protocol: post-treatment surgical resection; tumor sample subtype: claudin low
GSM2869466 Patient 8 needle core biopsy - pre treatment breast carcinoma disease state: TNBC; individual: Patient 8; protocol: pre-treatment needle core biospy; tumor sample subtype: claudin low
GSM2869467 Patient 8 surgical resection - post treatment breast carcinoma disease state: TNBC; individual: Patient 8; protocol: post-treatment surgical resection; tumor sample subtype: basal
GSM2869468 Patient 1 needle core biopsy - pre treatment breast carcinoma disease state: TNBC; individual: Patient 1; protocol: pre-treatment needle core biospy; tumor sample subtype: basal
GSM2869469 Patient 1 surgical resection - post treatment breast carcinoma disease state: TNBC; individual: Patient 1; protocol: post-treatment surgical resection; tumor sample subtype: basal
GSM2869470 Patient 2 needle core biopsy - pre treatment breast carcinoma disease state: TNBC; individual: Patient 2; protocol: pre-treatment needle core biospy; tumor sample subtype: basal
GSM2869471 Patient 2 surgical resection - post treatment breast carcinoma disease state: TNBC; individual: Patient 2; protocol: post-treatment surgical resection; tumor sample subtype: basal
GSM2869472 Patient 9 needle core biopsy - pre treatment breast carcinoma disease state: TNBC; individual: Patient 9; protocol: pre-treatment needle core biospy; tumor sample subtype: basal
GSM2869474 Patient 10 needle core biopsy - pre treatment breast carcinoma disease state: TNBC; individual: Patient 10; protocol: pre-treatment needle core biospy; tumor sample subtype: claudin low
GSM2869475 Patient 10 surgical resection - post treatment breast carcinoma disease state: TNBC; individual: Patient 10; protocol: post-treatment surgical resection; tumor sample subtype: basal
GSM2869476 Patient 4 Needle Core Biopsy - pre treatment breast carcinoma disease state: TNBC; individual: Patient 4; protocol: pre-treatment needle core biospy; tumor sample subtype: basal
GSM2869477 Patient 4 surgical resection - post treatment breast carcinoma disease state: TNBC; individual: Patient 4; protocol: post-treatment surgical resection; tumor sample subtype: basal
GSM2869478 Patient 3 Needle Core Biopsy - pre treatment breast carcinoma disease state: TNBC; individual: Patient 3; protocol: pre-treatment needle core biospy; tumor sample subtype: basal
GSM2869479 Patient 3 surgical resection - post treatment breast carcinoma disease state: TNBC; individual: Patient 3; protocol: post-treatment surgical resection; tumor sample subtype: basal
GSM2869480 Patient 11 needle core biopsy - pre treatment breast carcinoma disease state: TNBC; individual: Patient 11; protocol: pre-treatment needle core biospy; tumor sample subtype: basal
GSM2869481 Patient 11 surgical resection - post treatment breast carcinoma disease state: TNBC; individual: Patient 11; protocol: post-treatment surgical resection; tumor sample subtype: claudin low

normal tissue

5 samples

GSM2869464 Patient 7 needle core biopsy - pre treatment breast carcinoma disease state: TNBC; individual: Patient 7; protocol: pre-treatment needle core biospy; tumor sample subtype: normal breast
GSM2869465 Patient 7 surgical resection - post treatment breast carcinoma disease state: TNBC; individual: Patient 7; protocol: post-treatment surgical resection; tumor sample subtype: normal breast
GSM2869473 Patient 9 surgical resection - post treatment breast carcinoma disease state: TNBC; individual: Patient 9; protocol: post-treatment surgical resection; tumor sample subtype: normal breast
GSM2869482 Patient 12 needle core biopsy - pre treatment breast carcinoma disease state: TNBC; individual: Patient 12; protocol: pre-treatment needle core biospy; tumor sample subtype: normal breast
GSM2869483 Patient 12 surgical resection - post treatment breast carcinoma disease state: TNBC; individual: Patient 12; protocol: post-treatment surgical resection; tumor sample subtype: normal breast

Score Breakdown

100%

relevance

Disease or condition metadata normalized.
Organism normalized.
Assay type normalized.
Tissue metadata normalized.

0%

comparison suitability

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

100%

metadata quality

Sample source clarity: All samples have source metadata and clear GSE/GSM accessions.
Group clarity: Rule-based grouping found both case and control samples.
Disease clarity: Disease or condition metadata normalized.
Tissue clarity: Tissue metadata normalized.
Treatment clarity: No unclear treatment split detected in the sample metadata.
Replicate clarity: No pooled sample or technical replicate flags detected.
Data availability clarity: Dataset-level processed or raw data availability is explicit.

100%

data availability

Processed data available.
Raw data available.

34%

overall

Weighted score: 30% relevance, 30% comparison suitability, 25% metadata quality, 15% data availability.
Overall score capped because comparison suitability is weak for the selected search intent.
Overall score capped because tumor/normal grouping is from a non-colorectal cancer context.

Sample Links

28 samples

GSM2869456 Patient 6 needle core biospy - pre treatment
GSM2869457 Patient 6 surgical resection - post treatment
GSM2869458 Patient 5 needle core biopsy - pre treatment_2
GSM2869459 Patient 5 needle core biopsy - pre treatment
GSM2869460 Patient 5 surgical resection - post treatment_2
GSM2869461 Patient 5 surgical resection - post treatment
GSM2869462 Patient 6 needle core biospy - pre treatment_2
GSM2869463 Patient 6 surgical resection - post treatment_2
GSM2869464 Patient 7 needle core biopsy - pre treatment
GSM2869465 Patient 7 surgical resection - post treatment
GSM2869466 Patient 8 needle core biopsy - pre treatment
GSM2869467 Patient 8 surgical resection - post treatment
GSM2869468 Patient 1 needle core biopsy - pre treatment
GSM2869469 Patient 1 surgical resection - post treatment
GSM2869470 Patient 2 needle core biopsy - pre treatment
GSM2869471 Patient 2 surgical resection - post treatment
GSM2869472 Patient 9 needle core biopsy - pre treatment
GSM2869473 Patient 9 surgical resection - post treatment
GSM2869474 Patient 10 needle core biopsy - pre treatment
GSM2869475 Patient 10 surgical resection - post treatment
GSM2869476 Patient 4 Needle Core Biopsy - pre treatment
GSM2869477 Patient 4 surgical resection - post treatment
GSM2869478 Patient 3 Needle Core Biopsy - pre treatment
GSM2869479 Patient 3 surgical resection - post treatment
GSM2869480 Patient 11 needle core biopsy - pre treatment
GSM2869481 Patient 11 surgical resection - post treatment
GSM2869482 Patient 12 needle core biopsy - pre treatment
GSM2869483 Patient 12 surgical resection - post treatment

Review Audit Trail

0 decisions

No review decisions have been stored for this dataset.