Siftome Phase 3L

GSE110114

A practical evaluation of alignment algorithms for RNA variant calling analysis

Not suitable Dataset does not meet the current suitability threshold.
Sample grouping CSV Contrast CSV DESeq2 metadata CSV R handoff notes Handoff report Download instructions Open GEO dataset
Source
GEO
Search intent
Patient tissue tumor-vs-normal
Intent behavior
search-intent-behavior-v1
Submission date
2018-02-05
Last update
2019-03-27
Organization
Dankook University
Department
Not available
Public date
2018-02-06
Experiment types
Expression profiling by high throughput sequencing
Platforms
GPL16791 Illumina HiSeq 2500 (Homo sapiens)
Series type
Series
SubSeries
Not available
BioProject
PRJNA432903
Supplementary files
TXT: GSE110114_FPKM_table.txt.gz
Organism
Homo sapiens
Assay
bulk RNA-seq
Samples
13
Study design
Tumor vs matched normal
Specimen/source
Tissue
Scoring version
intent-aware-scoring-v15
Ranking batch
b69568dd1e4fe1b9ee2d880bf5495d748a7e4c5c11e4107f02528c3be0e76012
Ranking created
2026-06-05T20:20:27.088676Z
Warning version
intent-aware-warnings-v2

Current Intent Interpretation

Patient tissue tumor-vs-normal

Expectations

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

Rules

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

Study Classification

Tumor vs matched normal Tissue

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. Matched tumor/normal design boosted for colorectal tumor-vs-normal tissue triage. Patient tissue or biopsy specimens boosted for tissue comparison triage. Non-colorectal cancer context downgraded for colorectal tumor-vs-normal tissue ranking.
  • metadata quality 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 matched normal Study design remains rule-derived: Tumor vs matched normal.
  • Specimen/source Tissue Specimen/source remains rule-derived: Tissue.
  • Likely case group tumor sample 10 samples
  • Likely control group normal tissue 3 samples

Warnings

No ranking warnings are active.

Intent Interpretation

  • Active intent Patient tissue tumor-vs-normal Ranks human colorectal tissue or biopsy cohorts where tumor samples can be compared with normal controls.
  • Organism expectation Homo sapiens Dataset organism is interpreted as Homo sapiens.
  • Assay expectation bulk RNA-seq Dataset assay is interpreted as bulk RNA-seq.
  • Specimen assumption patient tissue or biopsy Derived specimen/source is Tissue.
  • Control-group assumption matched normal, adjacent normal, paired normal, healthy tissue control, or otherwise normal tissue control Derived study design is Tumor vs matched normal; likely groups are tumor sample vs normal tissue.
  • Score caps Applied when matching conditions are present non-human datasets stay below the primary recommendation band, missing colorectal/colon/rectal/CRC context stays below the primary recommendation band, biofluid and model-system datasets cannot reach Recommended by default, microarray and secondary assays are capped unless explicitly enabled, or small cohorts are capped below high-confidence recommendations
  • Warning rules 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 matched normal · Tissue · suitability 0%. Contributed to match or upgrade evidence.
  • Supporting fact Prioritized for patient tissue tumor-vs-normal triage. Contributed to match or upgrade evidence.
  • Supporting fact Prioritized assay: bulk RNA-seq is the active assay expectation. Contributed to match or upgrade evidence.
  • Supporting fact Downgraded disease context: not a colorectal/GI cancer cohort. Contributed to match or upgrade evidence.
  • Supporting fact Processed data is available for downstream review. Contributed to match or upgrade evidence.
  • Caution fact Non-colorectal cancer context downgraded for colorectal tumor-vs-normal tissue ranking. Contributed to downgrade or manual-review evidence.
  • Caution fact Missing or unclear metadata: Treatment clarity: No unclear treatment split detected in the sample metadata. Contributed to downgrade or manual-review evidence.
  • Caution fact Overall score capped because comparison suitability is weak for the selected search intent. Contributed to downgrade or manual-review evidence.
  • Caution fact Overall score capped because tumor/normal grouping is from a non-colorectal cancer context. Contributed to downgrade or manual-review evidence.
  • Caution fact Downgraded disease context: not a colorectal/GI cancer cohort. Contributed to downgrade or manual-review evidence.
  • Caution fact Comparison suitability score is below the Phase 1 recommended threshold. Contributed to downgrade or manual-review evidence.

Manual Corrections

0 active

Source Evidence

4 sources

GEO

Primary source

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

Dataset accession
GSE110114
Sample records
13 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
GSE110114
  • No recount3 project identifier has been imported for this dataset.
  • Once imported, recount3 has priority for processed count availability.
  • The recount3 source filter excludes this dataset until that linkage exists.
No recount3 sync data available.

Expression Atlas

Not imported

Planned source for curated expression experiment links.

GEO accession
GSE110114
  • No Expression Atlas experiment identifier has been imported for this dataset.
  • Once imported, Expression Atlas has priority for curated expression experiment links.
  • The Expression Atlas source filter excludes this dataset until that linkage exists.
No Expression Atlas sync data available.

PubMed

Unavailable

Publication context when PubMed identifiers are already known.

GEO accession
GSE110114
  • No PubMed identifier is present in the current runtime metadata.
  • No live PubMed search is performed from the dataset detail page.
No publication identifier imported.

Dataset Feedback

0 stored

Original GEO Metadata

dataset_accession: GSE110114
dataset_title: A practical evaluation of alignment algorithms for RNA variant calling analysis
organism: Homo sapiens
assay_type: bulk RNA-seq
processed_data_available: true
raw_data_available: true
submission_date: 2018-02-05
last_update_date: 2019-03-27
organization_name: Dankook University
department: Not available
public_date: 2018-02-06
experiment_types: Expression profiling by high throughput sequencing
platforms: GPL16791 Illumina HiSeq 2500 (Homo sapiens)
sub_series: Not available
bioproject: PRJNA432903
supplementary_files: TXT: GSE110114_FPKM_table.txt.gz
series_type: Series

Why It Matched

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

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

38 fields
Field Value Source Origin Confidence Evidence Reason
assay_type bulk RNA-seq dataset GSE110114 Runtime Siftome inference GEO:dataset:GSE110114:339b9224ea22a77a1624d85fa0172151b8acd7bd1c4b7f395dc4e1c010a0a3ff high confidence bulk rna-seq dataset_accession: GSE110114 dataset_title: A practical evaluation of alignment algorithms for RNA variant calling analysis organism: Homo sapiens assay_type: bulk RNA-seq proce... keyword match keyword match: bulk rna-seq
disease breast cancer sample GSM2977775 Runtime Siftome inference GEO:sample:GSM2977775:1df0c34ba04a5f9e6abe46368896f334a91c7e778aec859b481695cd247bd133 high confidence breast cancer sample_accession: GSM2977775 sample_title: C0 source_name: Breast cancer tissue characteristics: tissue: breast cancer tissue; cancer type: Invasive ductal carcinoma; cancer sub... controlled vocabulary controlled vocabulary disease match: breast cancer
disease breast cancer sample GSM2977776 Runtime Siftome inference GEO:sample:GSM2977776:2e3fb24f95f4a391b1563221321c4b321eeebf43292a318d2b27e2cdcb6e535b high confidence breast cancer sample_accession: GSM2977776 sample_title: C1 source_name: Breast cancer tissue characteristics: tissue: breast cancer tissue; cancer type: Invasive ductal carcinoma; cancer sub... controlled vocabulary controlled vocabulary disease match: breast cancer
disease breast cancer sample GSM2977777 Runtime Siftome inference GEO:sample:GSM2977777:155d6ee1b5683c81c32530138f0e9398c30d4ddd34f217b62add8ff6d7990147 high confidence breast cancer sample_accession: GSM2977777 sample_title: C2 source_name: Breast cancer tissue characteristics: tissue: breast cancer tissue; cancer type: Invasive ductal carcinoma; cancer sub... controlled vocabulary controlled vocabulary disease match: breast cancer
disease breast cancer sample GSM2977778 Runtime Siftome inference GEO:sample:GSM2977778:785b7e3ea66c160b95169f81555983768c5c002a827f28b8384f85c144c8d2c5 high confidence breast cancer sample_accession: GSM2977778 sample_title: C3 source_name: Breast cancer tissue characteristics: tissue: breast cancer tissue; cancer type: Invasive ductal carcinoma; cancer sub... controlled vocabulary controlled vocabulary disease match: breast cancer
disease breast cancer sample GSM2977779 Runtime Siftome inference GEO:sample:GSM2977779:0e3aee2f6e6961aab358c082ee576afc4127d2c8825e3809428295fad2deec5b high confidence breast cancer sample_accession: GSM2977779 sample_title: C4 source_name: Breast cancer tissue characteristics: tissue: breast cancer tissue; cancer type: Invasive ductal carcinoma; cancer sub... controlled vocabulary controlled vocabulary disease match: breast cancer
disease breast cancer sample GSM2977780 Runtime Siftome inference GEO:sample:GSM2977780:1eb05bd5444290ed5e5f1c6dcd10e9d43b043e5a56ac4ce05eb236149e4cf49c high confidence breast cancer sample_accession: GSM2977780 sample_title: C5 source_name: Breast cancer tissue characteristics: tissue: breast cancer tissue; cancer type: Invasive ductal carcinoma; cancer sub... controlled vocabulary controlled vocabulary disease match: breast cancer
disease breast cancer sample GSM2977781 Runtime Siftome inference GEO:sample:GSM2977781:a3e6b32dd0f9994f146754a7ecbac2f9dac6430f4e3d5b191435c5d14a70be84 high confidence breast cancer sample_accession: GSM2977781 sample_title: C6 source_name: Breast cancer tissue characteristics: tissue: breast cancer tissue; cancer type: Invasive ductal carcinoma; cancer sub... controlled vocabulary controlled vocabulary disease match: breast cancer
disease breast cancer sample GSM2977782 Runtime Siftome inference GEO:sample:GSM2977782:5703af6c4caf012b2d640f978a891ab8580499ffb804e3d6df740480e92c31bb high confidence breast cancer sample_accession: GSM2977782 sample_title: C7 source_name: Breast cancer tissue characteristics: tissue: breast cancer tissue; cancer type: Invasive ductal carcinoma; cancer sub... controlled vocabulary controlled vocabulary disease match: breast cancer
disease breast cancer sample GSM2977783 Runtime Siftome inference GEO:sample:GSM2977783:d3978d6029cc96a6deff17a5c85c1ea51d495b97e65055187c11d3c527d19548 high confidence breast cancer sample_accession: GSM2977783 sample_title: C8 source_name: Breast cancer tissue characteristics: tissue: breast cancer tissue; cancer type: Invasive ductal carcinoma; cancer sub... controlled vocabulary controlled vocabulary disease match: breast cancer
disease breast cancer sample GSM2977784 Runtime Siftome inference GEO:sample:GSM2977784:44d5582609abecb5be0207ffc0b76d5a6c0d38fe50b20b989fefe19e26348d69 high confidence breast cancer sample_accession: GSM2977784 sample_title: C9 source_name: Breast cancer tissue characteristics: tissue: breast cancer tissue; cancer type: Invasive ductal carcinoma; cancer sub... controlled vocabulary controlled vocabulary disease match: breast cancer
normal_tissue_type adjacent normal sample GSM2977785 Runtime Siftome inference GEO:sample:GSM2977785:39ef2b8d1a8bab77d49040a413cd6fbe67551963262ec75159f1bb3ebe53d4b4 high confidence adjacent normal sample_accession: GSM2977785 sample_title: N1 source_name: Adjacent normal tissue characteristics: tissue: adjacent normal tissue N1 controlled vocabulary controlled vocabulary normal tissue type match: adjacent normal
normal_tissue_type adjacent normal sample GSM2977786 Runtime Siftome inference GEO:sample:GSM2977786:fb179c3f22246aad7d5f8e4d7f972099cc9cd95c56ac6c61beceaa4f8ca33f58 high confidence adjacent normal sample_accession: GSM2977786 sample_title: N2 source_name: Adjacent normal tissue characteristics: tissue: adjacent normal tissue N2 controlled vocabulary controlled vocabulary normal tissue type match: adjacent normal
normal_tissue_type adjacent normal sample GSM2977787 Runtime Siftome inference GEO:sample:GSM2977787:0d1753cc6a0a1f9b70af5701c430954ef4d31e52cdf610d1abee7ae24c1b4e21 high confidence adjacent normal sample_accession: GSM2977787 sample_title: N3 source_name: Adjacent normal tissue characteristics: tissue: adjacent normal tissue N3 controlled vocabulary controlled vocabulary normal tissue type match: adjacent normal
organism Homo sapiens dataset GSE110114 Runtime Siftome inference GEO:dataset:GSE110114:339b9224ea22a77a1624d85fa0172151b8acd7bd1c4b7f395dc4e1c010a0a3ff high confidence homo sapiens dataset_accession: GSE110114 dataset_title: A practical evaluation of alignment algorithms for RNA variant calling analysis organism: Homo sapiens assay_type: bulk RNA-seq proce... keyword match keyword match: homo sapiens
sample_type tumor sample sample GSM2977775 Runtime Siftome inference GEO:sample:GSM2977775:1df0c34ba04a5f9e6abe46368896f334a91c7e778aec859b481695cd247bd133 medium confidence carcinoma sample_accession: GSM2977775 sample_title: C0 source_name: Breast cancer tissue characteristics: tissue: breast cancer tissue; cancer type: Invasive ductal carcinoma; cancer sub... controlled vocabulary controlled vocabulary sample type match: carcinoma
sample_type tumor sample sample GSM2977776 Runtime Siftome inference GEO:sample:GSM2977776:2e3fb24f95f4a391b1563221321c4b321eeebf43292a318d2b27e2cdcb6e535b medium confidence carcinoma sample_accession: GSM2977776 sample_title: C1 source_name: Breast cancer tissue characteristics: tissue: breast cancer tissue; cancer type: Invasive ductal carcinoma; cancer sub... controlled vocabulary controlled vocabulary sample type match: carcinoma
sample_type tumor sample sample GSM2977777 Runtime Siftome inference GEO:sample:GSM2977777:155d6ee1b5683c81c32530138f0e9398c30d4ddd34f217b62add8ff6d7990147 medium confidence carcinoma sample_accession: GSM2977777 sample_title: C2 source_name: Breast cancer tissue characteristics: tissue: breast cancer tissue; cancer type: Invasive ductal carcinoma; cancer sub... controlled vocabulary controlled vocabulary sample type match: carcinoma
sample_type tumor sample sample GSM2977778 Runtime Siftome inference GEO:sample:GSM2977778:785b7e3ea66c160b95169f81555983768c5c002a827f28b8384f85c144c8d2c5 medium confidence carcinoma sample_accession: GSM2977778 sample_title: C3 source_name: Breast cancer tissue characteristics: tissue: breast cancer tissue; cancer type: Invasive ductal carcinoma; cancer sub... controlled vocabulary controlled vocabulary sample type match: carcinoma
sample_type tumor sample sample GSM2977779 Runtime Siftome inference GEO:sample:GSM2977779:0e3aee2f6e6961aab358c082ee576afc4127d2c8825e3809428295fad2deec5b medium confidence carcinoma sample_accession: GSM2977779 sample_title: C4 source_name: Breast cancer tissue characteristics: tissue: breast cancer tissue; cancer type: Invasive ductal carcinoma; cancer sub... controlled vocabulary controlled vocabulary sample type match: carcinoma
sample_type tumor sample sample GSM2977780 Runtime Siftome inference GEO:sample:GSM2977780:1eb05bd5444290ed5e5f1c6dcd10e9d43b043e5a56ac4ce05eb236149e4cf49c medium confidence carcinoma sample_accession: GSM2977780 sample_title: C5 source_name: Breast cancer tissue characteristics: tissue: breast cancer tissue; cancer type: Invasive ductal carcinoma; cancer sub... controlled vocabulary controlled vocabulary sample type match: carcinoma
sample_type tumor sample sample GSM2977781 Runtime Siftome inference GEO:sample:GSM2977781:a3e6b32dd0f9994f146754a7ecbac2f9dac6430f4e3d5b191435c5d14a70be84 medium confidence carcinoma sample_accession: GSM2977781 sample_title: C6 source_name: Breast cancer tissue characteristics: tissue: breast cancer tissue; cancer type: Invasive ductal carcinoma; cancer sub... controlled vocabulary controlled vocabulary sample type match: carcinoma
sample_type tumor sample sample GSM2977782 Runtime Siftome inference GEO:sample:GSM2977782:5703af6c4caf012b2d640f978a891ab8580499ffb804e3d6df740480e92c31bb medium confidence carcinoma sample_accession: GSM2977782 sample_title: C7 source_name: Breast cancer tissue characteristics: tissue: breast cancer tissue; cancer type: Invasive ductal carcinoma; cancer sub... controlled vocabulary controlled vocabulary sample type match: carcinoma
sample_type tumor sample sample GSM2977783 Runtime Siftome inference GEO:sample:GSM2977783:d3978d6029cc96a6deff17a5c85c1ea51d495b97e65055187c11d3c527d19548 medium confidence carcinoma sample_accession: GSM2977783 sample_title: C8 source_name: Breast cancer tissue characteristics: tissue: breast cancer tissue; cancer type: Invasive ductal carcinoma; cancer sub... controlled vocabulary controlled vocabulary sample type match: carcinoma
sample_type tumor sample sample GSM2977784 Runtime Siftome inference GEO:sample:GSM2977784:44d5582609abecb5be0207ffc0b76d5a6c0d38fe50b20b989fefe19e26348d69 medium confidence carcinoma sample_accession: GSM2977784 sample_title: C9 source_name: Breast cancer tissue characteristics: tissue: breast cancer tissue; cancer type: Invasive ductal carcinoma; cancer sub... controlled vocabulary controlled vocabulary sample type match: carcinoma
sample_type normal tissue sample GSM2977785 Runtime Siftome inference GEO:sample:GSM2977785:39ef2b8d1a8bab77d49040a413cd6fbe67551963262ec75159f1bb3ebe53d4b4 high confidence adjacent normal sample_accession: GSM2977785 sample_title: N1 source_name: Adjacent normal tissue characteristics: tissue: adjacent normal tissue N1 controlled vocabulary controlled vocabulary sample type match: adjacent normal
sample_type normal tissue sample GSM2977786 Runtime Siftome inference GEO:sample:GSM2977786:fb179c3f22246aad7d5f8e4d7f972099cc9cd95c56ac6c61beceaa4f8ca33f58 high confidence adjacent normal sample_accession: GSM2977786 sample_title: N2 source_name: Adjacent normal tissue characteristics: tissue: adjacent normal tissue N2 controlled vocabulary controlled vocabulary sample type match: adjacent normal
sample_type normal tissue sample GSM2977787 Runtime Siftome inference GEO:sample:GSM2977787:0d1753cc6a0a1f9b70af5701c430954ef4d31e52cdf610d1abee7ae24c1b4e21 high confidence adjacent normal sample_accession: GSM2977787 sample_title: N3 source_name: Adjacent normal tissue characteristics: tissue: adjacent normal tissue N3 controlled vocabulary controlled vocabulary sample type match: adjacent normal
tissue breast sample GSM2977775 Runtime Siftome inference GEO:sample:GSM2977775:1df0c34ba04a5f9e6abe46368896f334a91c7e778aec859b481695cd247bd133 low confidence breast sample_accession: GSM2977775 sample_title: C0 source_name: Breast cancer tissue characteristics: tissue: breast cancer tissue; cancer type: Invasive ductal carcinoma; cancer sub... controlled vocabulary controlled vocabulary tissue match: breast
tissue breast sample GSM2977776 Runtime Siftome inference GEO:sample:GSM2977776:2e3fb24f95f4a391b1563221321c4b321eeebf43292a318d2b27e2cdcb6e535b low confidence breast sample_accession: GSM2977776 sample_title: C1 source_name: Breast cancer tissue characteristics: tissue: breast cancer tissue; cancer type: Invasive ductal carcinoma; cancer sub... controlled vocabulary controlled vocabulary tissue match: breast
tissue breast sample GSM2977777 Runtime Siftome inference GEO:sample:GSM2977777:155d6ee1b5683c81c32530138f0e9398c30d4ddd34f217b62add8ff6d7990147 low confidence breast sample_accession: GSM2977777 sample_title: C2 source_name: Breast cancer tissue characteristics: tissue: breast cancer tissue; cancer type: Invasive ductal carcinoma; cancer sub... controlled vocabulary controlled vocabulary tissue match: breast
tissue breast sample GSM2977778 Runtime Siftome inference GEO:sample:GSM2977778:785b7e3ea66c160b95169f81555983768c5c002a827f28b8384f85c144c8d2c5 low confidence breast sample_accession: GSM2977778 sample_title: C3 source_name: Breast cancer tissue characteristics: tissue: breast cancer tissue; cancer type: Invasive ductal carcinoma; cancer sub... controlled vocabulary controlled vocabulary tissue match: breast
tissue breast sample GSM2977779 Runtime Siftome inference GEO:sample:GSM2977779:0e3aee2f6e6961aab358c082ee576afc4127d2c8825e3809428295fad2deec5b low confidence breast sample_accession: GSM2977779 sample_title: C4 source_name: Breast cancer tissue characteristics: tissue: breast cancer tissue; cancer type: Invasive ductal carcinoma; cancer sub... controlled vocabulary controlled vocabulary tissue match: breast
tissue breast sample GSM2977780 Runtime Siftome inference GEO:sample:GSM2977780:1eb05bd5444290ed5e5f1c6dcd10e9d43b043e5a56ac4ce05eb236149e4cf49c low confidence breast sample_accession: GSM2977780 sample_title: C5 source_name: Breast cancer tissue characteristics: tissue: breast cancer tissue; cancer type: Invasive ductal carcinoma; cancer sub... controlled vocabulary controlled vocabulary tissue match: breast
tissue breast sample GSM2977781 Runtime Siftome inference GEO:sample:GSM2977781:a3e6b32dd0f9994f146754a7ecbac2f9dac6430f4e3d5b191435c5d14a70be84 low confidence breast sample_accession: GSM2977781 sample_title: C6 source_name: Breast cancer tissue characteristics: tissue: breast cancer tissue; cancer type: Invasive ductal carcinoma; cancer sub... controlled vocabulary controlled vocabulary tissue match: breast
tissue breast sample GSM2977782 Runtime Siftome inference GEO:sample:GSM2977782:5703af6c4caf012b2d640f978a891ab8580499ffb804e3d6df740480e92c31bb low confidence breast sample_accession: GSM2977782 sample_title: C7 source_name: Breast cancer tissue characteristics: tissue: breast cancer tissue; cancer type: Invasive ductal carcinoma; cancer sub... controlled vocabulary controlled vocabulary tissue match: breast
tissue breast sample GSM2977783 Runtime Siftome inference GEO:sample:GSM2977783:d3978d6029cc96a6deff17a5c85c1ea51d495b97e65055187c11d3c527d19548 low confidence breast sample_accession: GSM2977783 sample_title: C8 source_name: Breast cancer tissue characteristics: tissue: breast cancer tissue; cancer type: Invasive ductal carcinoma; cancer sub... controlled vocabulary controlled vocabulary tissue match: breast
tissue breast sample GSM2977784 Runtime Siftome inference GEO:sample:GSM2977784:44d5582609abecb5be0207ffc0b76d5a6c0d38fe50b20b989fefe19e26348d69 low confidence breast sample_accession: GSM2977784 sample_title: C9 source_name: Breast cancer tissue characteristics: tissue: breast cancer tissue; cancer type: Invasive ductal carcinoma; cancer sub... controlled vocabulary controlled vocabulary tissue match: breast

Sample Group Preview

Possible case samples

Samples currently treated as the comparison case group.

10
  • GSM2977775 C0 tumor sample Case marker detected. Breast cancer tissue tissue: breast cancer tissue; cancer type: Invasive ductal carcinoma; cancer subtype: Luminal B type
  • GSM2977776 C1 tumor sample Case marker detected. Breast cancer tissue tissue: breast cancer tissue; cancer type: Invasive ductal carcinoma; cancer subtype: Luminal B type
  • GSM2977777 C2 tumor sample Case marker detected. Breast cancer tissue tissue: breast cancer tissue; cancer type: Invasive ductal carcinoma; cancer subtype: Luminal B type
  • GSM2977778 C3 tumor sample Case marker detected. Breast cancer tissue tissue: breast cancer tissue; cancer type: Invasive ductal carcinoma; cancer subtype: Luminal B type
  • GSM2977779 C4 tumor sample Case marker detected. Breast cancer tissue tissue: breast cancer tissue; cancer type: Invasive ductal carcinoma; cancer subtype: Luminal B type
  • GSM2977780 C5 tumor sample Case marker detected. Breast cancer tissue tissue: breast cancer tissue; cancer type: Invasive ductal carcinoma; cancer subtype: Luminal B type
  • GSM2977781 C6 tumor sample Case marker detected. Breast cancer tissue tissue: breast cancer tissue; cancer type: Invasive ductal carcinoma; cancer subtype: Luminal B type
  • GSM2977782 C7 tumor sample Case marker detected. Breast cancer tissue tissue: breast cancer tissue; cancer type: Invasive ductal carcinoma; cancer subtype: Luminal B type
  • GSM2977783 C8 tumor sample Case marker detected. Breast cancer tissue tissue: breast cancer tissue; cancer type: Invasive ductal carcinoma; cancer subtype: Luminal B type
  • GSM2977784 C9 tumor sample Case marker detected. Breast cancer tissue tissue: breast cancer tissue; cancer type: Invasive ductal carcinoma; cancer subtype: Luminal B type

Possible control samples

Samples currently treated as controls or baseline.

3
  • GSM2977785 N1 normal tissue Control marker detected. Adjacent normal tissue tissue: adjacent normal tissue
  • GSM2977786 N2 normal tissue Control marker detected. Adjacent normal tissue tissue: adjacent normal tissue
  • GSM2977787 N3 normal tissue Control marker detected. Adjacent normal tissue tissue: adjacent normal tissue

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

10 samples
  • GSM2977775 C0 Breast cancer tissue tissue: breast cancer tissue; cancer type: Invasive ductal carcinoma; cancer subtype: Luminal B type
  • GSM2977776 C1 Breast cancer tissue tissue: breast cancer tissue; cancer type: Invasive ductal carcinoma; cancer subtype: Luminal B type
  • GSM2977777 C2 Breast cancer tissue tissue: breast cancer tissue; cancer type: Invasive ductal carcinoma; cancer subtype: Luminal B type
  • GSM2977778 C3 Breast cancer tissue tissue: breast cancer tissue; cancer type: Invasive ductal carcinoma; cancer subtype: Luminal B type
  • GSM2977779 C4 Breast cancer tissue tissue: breast cancer tissue; cancer type: Invasive ductal carcinoma; cancer subtype: Luminal B type
  • GSM2977780 C5 Breast cancer tissue tissue: breast cancer tissue; cancer type: Invasive ductal carcinoma; cancer subtype: Luminal B type
  • GSM2977781 C6 Breast cancer tissue tissue: breast cancer tissue; cancer type: Invasive ductal carcinoma; cancer subtype: Luminal B type
  • GSM2977782 C7 Breast cancer tissue tissue: breast cancer tissue; cancer type: Invasive ductal carcinoma; cancer subtype: Luminal B type
  • GSM2977783 C8 Breast cancer tissue tissue: breast cancer tissue; cancer type: Invasive ductal carcinoma; cancer subtype: Luminal B type
  • GSM2977784 C9 Breast cancer tissue tissue: breast cancer tissue; cancer type: Invasive ductal carcinoma; cancer subtype: Luminal B type

normal tissue

3 samples
  • GSM2977785 N1 Adjacent normal tissue tissue: adjacent normal tissue
  • GSM2977786 N2 Adjacent normal tissue tissue: adjacent normal tissue
  • GSM2977787 N3 Adjacent normal tissue tissue: adjacent normal tissue

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.
  • Matched tumor/normal design boosted for colorectal tumor-vs-normal tissue triage.
  • Patient tissue or biopsy specimens boosted for tissue comparison triage.
  • Non-colorectal cancer context downgraded for colorectal tumor-vs-normal tissue ranking.
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

13 samples

Review Audit Trail

0 decisions

No review decisions have been stored for this dataset.