Siftome Phase 3L

GSE160626

Identification of transcriptional difference between platinum-sensitive and resistant patients with ovarian cancer (OV)

Not suitable Dataset does not meet the current suitability threshold.
Sample grouping CSV Contrast CSV DESeq2 metadata CSV R handoff notes Handoff report Download instructions Open GEO dataset
Source
GEO
Search intent
Patient tissue tumor-vs-normal
Intent behavior
search-intent-behavior-v1
Submission date
2020-11-02
Last update
2023-11-01
Organization
Shanghai Jiao Tong University School of Medicine
Department
Not available
Public date
2023-11-01
Experiment types
Expression profiling by high throughput sequencing
Platforms
GPL21290 Illumina HiSeq 3000 (Homo sapiens)
Series type
Series
SubSeries
Not available
BioProject
PRJNA673814
Supplementary files
TXT: GSE160626_ov_gene_TPM_profile.txt.gz
Organism
Homo sapiens
Assay
bulk RNA-seq
Samples
25
Study design
Tumor vs unmatched normal
Specimen/source
Tissue
Scoring version
intent-aware-scoring-v15
Ranking batch
b69568dd1e4fe1b9ee2d880bf5495d748a7e4c5c11e4107f02528c3be0e76012
Ranking created
2026-06-05T20:20:27.088676Z
Warning version
intent-aware-warnings-v2

Current Intent Interpretation

Patient tissue tumor-vs-normal

Expectations

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

Rules

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

Study Classification

Tumor vs unmatched normal Tissue

Analysis Readiness

Ready after review
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% Case and control sample groups detected: ovarian cancer vs normal tissue. 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 Tissue Specimen/source remains rule-derived: Tissue.
  • Likely case group ovarian cancer 18 samples
  • Likely control group normal tissue 7 samples

Warnings

No ranking warnings are active.

Intent Interpretation

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

Applied Review Decisions

No active review decisions affect this ranking.

Ranking Facts

  • Recommendation Not suitable Dataset does not meet the current suitability threshold.
  • Supporting fact Tumor vs unmatched normal · Tissue · suitability 0%. Contributed to match or upgrade evidence.
  • Supporting fact Prioritized assay: bulk RNA-seq is the active assay expectation. Contributed to match or upgrade evidence.
  • Supporting fact Downgraded disease context: not a colorectal/GI cancer cohort. Contributed to match or upgrade evidence.
  • Supporting fact Processed data is available for downstream review. Contributed to match or upgrade evidence.
  • Caution fact Non-colorectal cancer context downgraded for colorectal tumor-vs-normal tissue ranking. Contributed to downgrade or manual-review evidence.
  • Caution fact Missing or unclear metadata: Treatment clarity: No unclear treatment split detected in the sample metadata. Contributed to downgrade or manual-review evidence.
  • Caution fact Overall score capped because comparison suitability is weak for the selected search intent. Contributed to downgrade or manual-review evidence.
  • Caution fact Overall score capped because 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
GSE160626
Sample records
25 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
GSE160626
  • 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
GSE160626
  • 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
GSE160626
  • 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: GSE160626
dataset_title: Identification of transcriptional difference between platinum-sensitive and resistant patients with ovarian cancer (OV)
organism: Homo sapiens
assay_type: bulk RNA-seq
processed_data_available: true
raw_data_available: true
submission_date: 2020-11-02
last_update_date: 2023-11-01
organization_name: Shanghai Jiao Tong University School of Medicine
department: Not available
public_date: 2023-11-01
experiment_types: Expression profiling by high throughput sequencing
platforms: GPL21290 Illumina HiSeq 3000 (Homo sapiens)
sub_series: Not available
bioproject: PRJNA673814
supplementary_files: TXT: GSE160626_ov_gene_TPM_profile.txt.gz
series_type: Series

Why It Matched

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

Why It May Not Be Suitable

  • Non-colorectal cancer context downgraded for colorectal tumor-vs-normal tissue ranking.
  • Missing or unclear metadata: Treatment clarity: No unclear treatment split detected in the sample metadata.
  • Overall score capped because comparison suitability is weak for the selected search intent.
  • Overall score capped because 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

54 fields
Field Value Source Origin Confidence Evidence Reason
assay_type bulk RNA-seq dataset GSE160626 Runtime Siftome inference GEO:dataset:GSE160626:62157cd813c12d473718dbdcc9099c47252bf4e66d48546425b4ac0558600f73 high confidence bulk rna-seq dataset_accession: GSE160626 dataset_title: Identification of transcriptional difference between platinum-sensitive and resistant patients with ovarian cancer (OV) organism: Hom... keyword match keyword match: bulk rna-seq
disease ovarian cancer dataset GSE160626 Runtime Siftome inference GEO:dataset:GSE160626:62157cd813c12d473718dbdcc9099c47252bf4e66d48546425b4ac0558600f73 high confidence ovarian cancer dataset_accession: GSE160626 dataset_title: Identification of transcriptional difference between platinum-sensitive and resistant patients with ovarian cancer (OV) organism: Hom... controlled vocabulary controlled vocabulary disease match: ovarian cancer
disease ovarian cancer sample GSM4876147 Runtime Siftome inference GEO:sample:GSM4876147:5848c928f57d1bcccfde40e56c4b4c4789b649c381e56fc8e288ee9e6318b5da high confidence ovarian cancer sample_accession: GSM4876147 sample_title: Resistance_01 source_name: Ovary characteristics: tissue: Ovary; disease: Ovarian cancer; phenotype: Platinum resistant patient Resist... controlled vocabulary controlled vocabulary disease match: ovarian cancer
disease ovarian cancer sample GSM4876148 Runtime Siftome inference GEO:sample:GSM4876148:186253691e316a65173e1d8b91f15ac0f72af42375ebd56eccb6be35076e560e high confidence ovarian cancer sample_accession: GSM4876148 sample_title: Resistance_03 source_name: Ovary characteristics: tissue: Ovary; disease: Ovarian cancer; phenotype: Platinum resistant patient Resist... controlled vocabulary controlled vocabulary disease match: ovarian cancer
disease ovarian cancer sample GSM4876149 Runtime Siftome inference GEO:sample:GSM4876149:210171affb484bbe9a3a45a84d0bfc42b3b2cac3b10269e2bacc06c2a176a63b high confidence ovarian cancer sample_accession: GSM4876149 sample_title: Resistance_04 source_name: Ovary characteristics: tissue: Ovary; disease: Ovarian cancer; phenotype: Platinum resistant patient Resist... controlled vocabulary controlled vocabulary disease match: ovarian cancer
disease ovarian cancer sample GSM4876150 Runtime Siftome inference GEO:sample:GSM4876150:621f7faaed85bc4aa90e44d09583fb052b251d2996869e772ce51a421d6617bc high confidence ovarian cancer sample_accession: GSM4876150 sample_title: Resistance_05 source_name: Ovary characteristics: tissue: Ovary; disease: Ovarian cancer; phenotype: Platinum resistant patient Resist... controlled vocabulary controlled vocabulary disease match: ovarian cancer
disease ovarian cancer sample GSM4876151 Runtime Siftome inference GEO:sample:GSM4876151:d29c9b14b7dc52dbd44913d94a40891f2b4a217fcd179b91fff31d0e7c7e9223 high confidence ovarian cancer sample_accession: GSM4876151 sample_title: Resistance_06 source_name: Ovary characteristics: tissue: Ovary; disease: Ovarian cancer; phenotype: Platinum resistant patient Resist... controlled vocabulary controlled vocabulary disease match: ovarian cancer
disease ovarian cancer sample GSM4876152 Runtime Siftome inference GEO:sample:GSM4876152:061a5455ca615d4c2dbed90ac8deeea5ba5c30f93b7814a91a2a4b4f199a7039 high confidence ovarian cancer sample_accession: GSM4876152 sample_title: Resistance_07 source_name: Ovary characteristics: tissue: Ovary; disease: Ovarian cancer; phenotype: Platinum resistant patient Resist... controlled vocabulary controlled vocabulary disease match: ovarian cancer
disease ovarian cancer sample GSM4876153 Runtime Siftome inference GEO:sample:GSM4876153:b4e5953c581e748b6761cf31fd2bb7f4c9fc57e496e74310c919a2162c12b024 high confidence ovarian cancer sample_accession: GSM4876153 sample_title: Resistance_08 source_name: Ovary characteristics: tissue: Ovary; disease: Ovarian cancer; phenotype: Platinum resistant patient Resist... controlled vocabulary controlled vocabulary disease match: ovarian cancer
disease ovarian cancer sample GSM4876154 Runtime Siftome inference GEO:sample:GSM4876154:f4ea6e344736f9762df4dad2c4f022fe916443449d9a1158a0bc00712e385512 high confidence ovarian cancer sample_accession: GSM4876154 sample_title: Resistance_09 source_name: Ovary characteristics: tissue: Ovary; disease: Ovarian cancer; phenotype: Platinum resistant patient Resist... controlled vocabulary controlled vocabulary disease match: ovarian cancer
disease ovarian cancer sample GSM4876155 Runtime Siftome inference GEO:sample:GSM4876155:64545645601f8336543429cf54851d5f858d927102fb8ab11051ee92956d9e8b high confidence ovarian cancer sample_accession: GSM4876155 sample_title: Sensitive_01 source_name: Ovary characteristics: tissue: Ovary; disease: Ovarian cancer; phenotype: Platinum sensitive patient Sensiti... controlled vocabulary controlled vocabulary disease match: ovarian cancer
disease ovarian cancer sample GSM4876156 Runtime Siftome inference GEO:sample:GSM4876156:ebf0deb622ac6d2491976c5824a321d5b30fc1da5b2ee48b088a28c9c9fddedf high confidence ovarian cancer sample_accession: GSM4876156 sample_title: Sensitive_02 source_name: Ovary characteristics: tissue: Ovary; disease: Ovarian cancer; phenotype: Platinum sensitive patient Sensiti... controlled vocabulary controlled vocabulary disease match: ovarian cancer
disease ovarian cancer sample GSM4876157 Runtime Siftome inference GEO:sample:GSM4876157:a772a86f51c62a8ad54d1e342286617df1e862a21fcd628426e2e8fbba5f6846 high confidence ovarian cancer sample_accession: GSM4876157 sample_title: Sensitive_03 source_name: Ovary characteristics: tissue: Ovary; disease: Ovarian cancer; phenotype: Platinum sensitive patient Sensiti... controlled vocabulary controlled vocabulary disease match: ovarian cancer
disease ovarian cancer sample GSM4876158 Runtime Siftome inference GEO:sample:GSM4876158:31453feddc3bfc63f9322dbf9c3d9d8faeb67b90d05fdaf5f63c6134704dabe4 high confidence ovarian cancer sample_accession: GSM4876158 sample_title: Sensitive_04 source_name: Ovary characteristics: tissue: Ovary; disease: Ovarian cancer; phenotype: Platinum sensitive patient Sensiti... controlled vocabulary controlled vocabulary disease match: ovarian cancer
disease ovarian cancer sample GSM4876159 Runtime Siftome inference GEO:sample:GSM4876159:6d725663a04aac58c84a2a39ee94aa3d643f13ae4db19c97d30e87f52c663df3 high confidence ovarian cancer sample_accession: GSM4876159 sample_title: Sensitive_05 source_name: Ovary characteristics: tissue: Ovary; disease: Ovarian cancer; phenotype: Platinum sensitive patient Sensiti... controlled vocabulary controlled vocabulary disease match: ovarian cancer
disease ovarian cancer sample GSM4876160 Runtime Siftome inference GEO:sample:GSM4876160:e0374e350ce553cfb1002b30bae11dbff24fe2f815edd23c63cc1894102eaf12 high confidence ovarian cancer sample_accession: GSM4876160 sample_title: Sensitive_06 source_name: Ovary characteristics: tissue: Ovary; disease: Ovarian cancer; phenotype: Platinum sensitive patient Sensiti... controlled vocabulary controlled vocabulary disease match: ovarian cancer
disease ovarian cancer sample GSM4876161 Runtime Siftome inference GEO:sample:GSM4876161:d95d450ec26fb1ef2b1ba6af7b934e811d904caae3748b20237ee0fa25fb00f9 high confidence ovarian cancer sample_accession: GSM4876161 sample_title: Sensitive_07 source_name: Ovary characteristics: tissue: Ovary; disease: Ovarian cancer; phenotype: Platinum sensitive patient Sensiti... controlled vocabulary controlled vocabulary disease match: ovarian cancer
disease ovarian cancer sample GSM4876162 Runtime Siftome inference GEO:sample:GSM4876162:20d440fb8c4cd07d1627380c9a8fd5a0983e377b5f3ecf5e3bea0463007163c5 high confidence ovarian cancer sample_accession: GSM4876162 sample_title: Sensitive_08 source_name: Ovary characteristics: tissue: Ovary; disease: Ovarian cancer; phenotype: Platinum sensitive patient Sensiti... controlled vocabulary controlled vocabulary disease match: ovarian cancer
disease ovarian cancer sample GSM4876163 Runtime Siftome inference GEO:sample:GSM4876163:0b33b0aff5176c6cf92a53bc5be8733f43047fd84c73ad3a1480383b3fcec70c high confidence ovarian cancer sample_accession: GSM4876163 sample_title: Sensitive_09 source_name: Ovary characteristics: tissue: Ovary; disease: Ovarian cancer; phenotype: Platinum sensitive patient Sensiti... controlled vocabulary controlled vocabulary disease match: ovarian cancer
disease ovarian cancer sample GSM4876164 Runtime Siftome inference GEO:sample:GSM4876164:7965956d11404c46856bcb189f3e7d3879328b39beecce9f4559463f1938883d high confidence ovarian cancer sample_accession: GSM4876164 sample_title: Sensitive_10 source_name: Ovary characteristics: tissue: Ovary; disease: Ovarian cancer; phenotype: Platinum sensitive patient Sensiti... controlled vocabulary controlled vocabulary disease match: ovarian cancer
organism Homo sapiens dataset GSE160626 Runtime Siftome inference GEO:dataset:GSE160626:62157cd813c12d473718dbdcc9099c47252bf4e66d48546425b4ac0558600f73 high confidence homo sapiens dataset_accession: GSE160626 dataset_title: Identification of transcriptional difference between platinum-sensitive and resistant patients with ovarian cancer (OV) organism: Hom... keyword match keyword match: homo sapiens
sample_type normal tissue sample GSM4876140 Runtime Siftome inference GEO:sample:GSM4876140:00f78a799422041820f1c25c93c3abd9e1e882b04ad17438272bec3a622d8b17 low confidence normal sample_accession: GSM4876140 sample_title: Normal_01 source_name: Ovary characteristics: tissue: Ovary; disease: Normal ovary; phenotype: NA Normal_01 controlled vocabulary controlled vocabulary sample type match: normal
sample_type normal tissue sample GSM4876141 Runtime Siftome inference GEO:sample:GSM4876141:bca01a57d0762d84e9fed4e11b2a1681a842ca5ed8134b1e1ba4a14b704f40ac low confidence normal sample_accession: GSM4876141 sample_title: Normal_02 source_name: Ovary characteristics: tissue: Ovary; disease: Normal ovary; phenotype: NA Normal_02 controlled vocabulary controlled vocabulary sample type match: normal
sample_type normal tissue sample GSM4876142 Runtime Siftome inference GEO:sample:GSM4876142:b5efeab68e9da79cffacb22b5abdf1f2205aab6ee5fec4c8a4665e0da2c415f1 low confidence normal sample_accession: GSM4876142 sample_title: Normal_03 source_name: Ovary characteristics: tissue: Ovary; disease: Normal ovary; phenotype: NA Normal_03 controlled vocabulary controlled vocabulary sample type match: normal
sample_type normal tissue sample GSM4876143 Runtime Siftome inference GEO:sample:GSM4876143:05e486d1e3f62d0618c3f14a2461f597aaa80e5c424cd9fc94610cd8d743cddf low confidence normal sample_accession: GSM4876143 sample_title: Normal_05 source_name: Ovary characteristics: tissue: Ovary; disease: Normal ovary; phenotype: NA Normal_05 controlled vocabulary controlled vocabulary sample type match: normal
sample_type normal tissue sample GSM4876144 Runtime Siftome inference GEO:sample:GSM4876144:46ffa71416d6bf900755dafb29378450da352613cc01044f337ab9c075f5f5b9 low confidence normal sample_accession: GSM4876144 sample_title: Normal_06 source_name: Ovary characteristics: tissue: Ovary; disease: Normal ovary; phenotype: NA Normal_06 controlled vocabulary controlled vocabulary sample type match: normal
sample_type normal tissue sample GSM4876145 Runtime Siftome inference GEO:sample:GSM4876145:d236878c0291a0bdb34df81fa9661dcc8097798fd4ddf6850721bc6ae721a15d low confidence normal sample_accession: GSM4876145 sample_title: Normal_07 source_name: Ovary characteristics: tissue: Ovary; disease: Normal ovary; phenotype: NA Normal_07 controlled vocabulary controlled vocabulary sample type match: normal
sample_type normal tissue sample GSM4876146 Runtime Siftome inference GEO:sample:GSM4876146:12c17065bd539f0164f1f6ef316d30c001b3e68f06724613771c2da78ffd64f6 low confidence normal sample_accession: GSM4876146 sample_title: Normal_08 source_name: Ovary characteristics: tissue: Ovary; disease: Normal ovary; phenotype: NA Normal_08 controlled vocabulary controlled vocabulary sample type match: normal
tissue ovary dataset GSE160626 Runtime Siftome inference GEO:dataset:GSE160626:62157cd813c12d473718dbdcc9099c47252bf4e66d48546425b4ac0558600f73 medium confidence ovarian dataset_accession: GSE160626 dataset_title: Identification of transcriptional difference between platinum-sensitive and resistant patients with ovarian cancer (OV) organism: Hom... controlled vocabulary controlled vocabulary tissue match: ovarian
tissue ovary sample GSM4876140 Runtime Siftome inference GEO:sample:GSM4876140:00f78a799422041820f1c25c93c3abd9e1e882b04ad17438272bec3a622d8b17 low confidence ovary sample_accession: GSM4876140 sample_title: Normal_01 source_name: Ovary characteristics: tissue: Ovary; disease: Normal ovary; phenotype: NA Normal_01 controlled vocabulary controlled vocabulary tissue match: ovary
tissue ovary sample GSM4876141 Runtime Siftome inference GEO:sample:GSM4876141:bca01a57d0762d84e9fed4e11b2a1681a842ca5ed8134b1e1ba4a14b704f40ac low confidence ovary sample_accession: GSM4876141 sample_title: Normal_02 source_name: Ovary characteristics: tissue: Ovary; disease: Normal ovary; phenotype: NA Normal_02 controlled vocabulary controlled vocabulary tissue match: ovary
tissue ovary sample GSM4876142 Runtime Siftome inference GEO:sample:GSM4876142:b5efeab68e9da79cffacb22b5abdf1f2205aab6ee5fec4c8a4665e0da2c415f1 low confidence ovary sample_accession: GSM4876142 sample_title: Normal_03 source_name: Ovary characteristics: tissue: Ovary; disease: Normal ovary; phenotype: NA Normal_03 controlled vocabulary controlled vocabulary tissue match: ovary
tissue ovary sample GSM4876143 Runtime Siftome inference GEO:sample:GSM4876143:05e486d1e3f62d0618c3f14a2461f597aaa80e5c424cd9fc94610cd8d743cddf low confidence ovary sample_accession: GSM4876143 sample_title: Normal_05 source_name: Ovary characteristics: tissue: Ovary; disease: Normal ovary; phenotype: NA Normal_05 controlled vocabulary controlled vocabulary tissue match: ovary
tissue ovary sample GSM4876144 Runtime Siftome inference GEO:sample:GSM4876144:46ffa71416d6bf900755dafb29378450da352613cc01044f337ab9c075f5f5b9 low confidence ovary sample_accession: GSM4876144 sample_title: Normal_06 source_name: Ovary characteristics: tissue: Ovary; disease: Normal ovary; phenotype: NA Normal_06 controlled vocabulary controlled vocabulary tissue match: ovary
tissue ovary sample GSM4876145 Runtime Siftome inference GEO:sample:GSM4876145:d236878c0291a0bdb34df81fa9661dcc8097798fd4ddf6850721bc6ae721a15d low confidence ovary sample_accession: GSM4876145 sample_title: Normal_07 source_name: Ovary characteristics: tissue: Ovary; disease: Normal ovary; phenotype: NA Normal_07 controlled vocabulary controlled vocabulary tissue match: ovary
tissue ovary sample GSM4876146 Runtime Siftome inference GEO:sample:GSM4876146:12c17065bd539f0164f1f6ef316d30c001b3e68f06724613771c2da78ffd64f6 low confidence ovary sample_accession: GSM4876146 sample_title: Normal_08 source_name: Ovary characteristics: tissue: Ovary; disease: Normal ovary; phenotype: NA Normal_08 controlled vocabulary controlled vocabulary tissue match: ovary
tissue ovary sample GSM4876147 Runtime Siftome inference GEO:sample:GSM4876147:5848c928f57d1bcccfde40e56c4b4c4789b649c381e56fc8e288ee9e6318b5da low confidence ovary sample_accession: GSM4876147 sample_title: Resistance_01 source_name: Ovary characteristics: tissue: Ovary; disease: Ovarian cancer; phenotype: Platinum resistant patient Resist... controlled vocabulary controlled vocabulary tissue match: ovary
tissue ovary sample GSM4876148 Runtime Siftome inference GEO:sample:GSM4876148:186253691e316a65173e1d8b91f15ac0f72af42375ebd56eccb6be35076e560e low confidence ovary sample_accession: GSM4876148 sample_title: Resistance_03 source_name: Ovary characteristics: tissue: Ovary; disease: Ovarian cancer; phenotype: Platinum resistant patient Resist... controlled vocabulary controlled vocabulary tissue match: ovary
tissue ovary sample GSM4876149 Runtime Siftome inference GEO:sample:GSM4876149:210171affb484bbe9a3a45a84d0bfc42b3b2cac3b10269e2bacc06c2a176a63b low confidence ovary sample_accession: GSM4876149 sample_title: Resistance_04 source_name: Ovary characteristics: tissue: Ovary; disease: Ovarian cancer; phenotype: Platinum resistant patient Resist... controlled vocabulary controlled vocabulary tissue match: ovary
tissue ovary sample GSM4876150 Runtime Siftome inference GEO:sample:GSM4876150:621f7faaed85bc4aa90e44d09583fb052b251d2996869e772ce51a421d6617bc low confidence ovary sample_accession: GSM4876150 sample_title: Resistance_05 source_name: Ovary characteristics: tissue: Ovary; disease: Ovarian cancer; phenotype: Platinum resistant patient Resist... controlled vocabulary controlled vocabulary tissue match: ovary
tissue ovary sample GSM4876151 Runtime Siftome inference GEO:sample:GSM4876151:d29c9b14b7dc52dbd44913d94a40891f2b4a217fcd179b91fff31d0e7c7e9223 low confidence ovary sample_accession: GSM4876151 sample_title: Resistance_06 source_name: Ovary characteristics: tissue: Ovary; disease: Ovarian cancer; phenotype: Platinum resistant patient Resist... controlled vocabulary controlled vocabulary tissue match: ovary
tissue ovary sample GSM4876152 Runtime Siftome inference GEO:sample:GSM4876152:061a5455ca615d4c2dbed90ac8deeea5ba5c30f93b7814a91a2a4b4f199a7039 low confidence ovary sample_accession: GSM4876152 sample_title: Resistance_07 source_name: Ovary characteristics: tissue: Ovary; disease: Ovarian cancer; phenotype: Platinum resistant patient Resist... controlled vocabulary controlled vocabulary tissue match: ovary
tissue ovary sample GSM4876153 Runtime Siftome inference GEO:sample:GSM4876153:b4e5953c581e748b6761cf31fd2bb7f4c9fc57e496e74310c919a2162c12b024 low confidence ovary sample_accession: GSM4876153 sample_title: Resistance_08 source_name: Ovary characteristics: tissue: Ovary; disease: Ovarian cancer; phenotype: Platinum resistant patient Resist... controlled vocabulary controlled vocabulary tissue match: ovary
tissue ovary sample GSM4876154 Runtime Siftome inference GEO:sample:GSM4876154:f4ea6e344736f9762df4dad2c4f022fe916443449d9a1158a0bc00712e385512 low confidence ovary sample_accession: GSM4876154 sample_title: Resistance_09 source_name: Ovary characteristics: tissue: Ovary; disease: Ovarian cancer; phenotype: Platinum resistant patient Resist... controlled vocabulary controlled vocabulary tissue match: ovary
tissue ovary sample GSM4876155 Runtime Siftome inference GEO:sample:GSM4876155:64545645601f8336543429cf54851d5f858d927102fb8ab11051ee92956d9e8b low confidence ovary sample_accession: GSM4876155 sample_title: Sensitive_01 source_name: Ovary characteristics: tissue: Ovary; disease: Ovarian cancer; phenotype: Platinum sensitive patient Sensiti... controlled vocabulary controlled vocabulary tissue match: ovary
tissue ovary sample GSM4876156 Runtime Siftome inference GEO:sample:GSM4876156:ebf0deb622ac6d2491976c5824a321d5b30fc1da5b2ee48b088a28c9c9fddedf low confidence ovary sample_accession: GSM4876156 sample_title: Sensitive_02 source_name: Ovary characteristics: tissue: Ovary; disease: Ovarian cancer; phenotype: Platinum sensitive patient Sensiti... controlled vocabulary controlled vocabulary tissue match: ovary
tissue ovary sample GSM4876157 Runtime Siftome inference GEO:sample:GSM4876157:a772a86f51c62a8ad54d1e342286617df1e862a21fcd628426e2e8fbba5f6846 low confidence ovary sample_accession: GSM4876157 sample_title: Sensitive_03 source_name: Ovary characteristics: tissue: Ovary; disease: Ovarian cancer; phenotype: Platinum sensitive patient Sensiti... controlled vocabulary controlled vocabulary tissue match: ovary
tissue ovary sample GSM4876158 Runtime Siftome inference GEO:sample:GSM4876158:31453feddc3bfc63f9322dbf9c3d9d8faeb67b90d05fdaf5f63c6134704dabe4 low confidence ovary sample_accession: GSM4876158 sample_title: Sensitive_04 source_name: Ovary characteristics: tissue: Ovary; disease: Ovarian cancer; phenotype: Platinum sensitive patient Sensiti... controlled vocabulary controlled vocabulary tissue match: ovary
tissue ovary sample GSM4876159 Runtime Siftome inference GEO:sample:GSM4876159:6d725663a04aac58c84a2a39ee94aa3d643f13ae4db19c97d30e87f52c663df3 low confidence ovary sample_accession: GSM4876159 sample_title: Sensitive_05 source_name: Ovary characteristics: tissue: Ovary; disease: Ovarian cancer; phenotype: Platinum sensitive patient Sensiti... controlled vocabulary controlled vocabulary tissue match: ovary
tissue ovary sample GSM4876160 Runtime Siftome inference GEO:sample:GSM4876160:e0374e350ce553cfb1002b30bae11dbff24fe2f815edd23c63cc1894102eaf12 low confidence ovary sample_accession: GSM4876160 sample_title: Sensitive_06 source_name: Ovary characteristics: tissue: Ovary; disease: Ovarian cancer; phenotype: Platinum sensitive patient Sensiti... controlled vocabulary controlled vocabulary tissue match: ovary
tissue ovary sample GSM4876161 Runtime Siftome inference GEO:sample:GSM4876161:d95d450ec26fb1ef2b1ba6af7b934e811d904caae3748b20237ee0fa25fb00f9 low confidence ovary sample_accession: GSM4876161 sample_title: Sensitive_07 source_name: Ovary characteristics: tissue: Ovary; disease: Ovarian cancer; phenotype: Platinum sensitive patient Sensiti... controlled vocabulary controlled vocabulary tissue match: ovary
tissue ovary sample GSM4876162 Runtime Siftome inference GEO:sample:GSM4876162:20d440fb8c4cd07d1627380c9a8fd5a0983e377b5f3ecf5e3bea0463007163c5 low confidence ovary sample_accession: GSM4876162 sample_title: Sensitive_08 source_name: Ovary characteristics: tissue: Ovary; disease: Ovarian cancer; phenotype: Platinum sensitive patient Sensiti... controlled vocabulary controlled vocabulary tissue match: ovary
tissue ovary sample GSM4876163 Runtime Siftome inference GEO:sample:GSM4876163:0b33b0aff5176c6cf92a53bc5be8733f43047fd84c73ad3a1480383b3fcec70c low confidence ovary sample_accession: GSM4876163 sample_title: Sensitive_09 source_name: Ovary characteristics: tissue: Ovary; disease: Ovarian cancer; phenotype: Platinum sensitive patient Sensiti... controlled vocabulary controlled vocabulary tissue match: ovary
tissue ovary sample GSM4876164 Runtime Siftome inference GEO:sample:GSM4876164:7965956d11404c46856bcb189f3e7d3879328b39beecce9f4559463f1938883d low confidence ovary sample_accession: GSM4876164 sample_title: Sensitive_10 source_name: Ovary characteristics: tissue: Ovary; disease: Ovarian cancer; phenotype: Platinum sensitive patient Sensiti... controlled vocabulary controlled vocabulary tissue match: ovary

Sample Group Preview

Possible case samples

Samples currently treated as the comparison case group.

18
  • GSM4876147 Resistance_01 ovarian cancer Case marker detected. Ovary tissue: Ovary; disease: Ovarian cancer; phenotype: Platinum resistant patient
  • GSM4876148 Resistance_03 ovarian cancer Case marker detected. Ovary tissue: Ovary; disease: Ovarian cancer; phenotype: Platinum resistant patient
  • GSM4876149 Resistance_04 ovarian cancer Case marker detected. Ovary tissue: Ovary; disease: Ovarian cancer; phenotype: Platinum resistant patient
  • GSM4876150 Resistance_05 ovarian cancer Case marker detected. Ovary tissue: Ovary; disease: Ovarian cancer; phenotype: Platinum resistant patient
  • GSM4876151 Resistance_06 ovarian cancer Case marker detected. Ovary tissue: Ovary; disease: Ovarian cancer; phenotype: Platinum resistant patient
  • GSM4876152 Resistance_07 ovarian cancer Case marker detected. Ovary tissue: Ovary; disease: Ovarian cancer; phenotype: Platinum resistant patient
  • GSM4876153 Resistance_08 ovarian cancer Case marker detected. Ovary tissue: Ovary; disease: Ovarian cancer; phenotype: Platinum resistant patient
  • GSM4876154 Resistance_09 ovarian cancer Case marker detected. Ovary tissue: Ovary; disease: Ovarian cancer; phenotype: Platinum resistant patient
  • GSM4876155 Sensitive_01 ovarian cancer Case marker detected. Ovary tissue: Ovary; disease: Ovarian cancer; phenotype: Platinum sensitive patient
  • GSM4876156 Sensitive_02 ovarian cancer Case marker detected. Ovary tissue: Ovary; disease: Ovarian cancer; phenotype: Platinum sensitive patient
  • GSM4876157 Sensitive_03 ovarian cancer Case marker detected. Ovary tissue: Ovary; disease: Ovarian cancer; phenotype: Platinum sensitive patient
  • GSM4876158 Sensitive_04 ovarian cancer Case marker detected. Ovary tissue: Ovary; disease: Ovarian cancer; phenotype: Platinum sensitive patient
  • GSM4876159 Sensitive_05 ovarian cancer Case marker detected. Ovary tissue: Ovary; disease: Ovarian cancer; phenotype: Platinum sensitive patient
  • GSM4876160 Sensitive_06 ovarian cancer Case marker detected. Ovary tissue: Ovary; disease: Ovarian cancer; phenotype: Platinum sensitive patient
  • GSM4876161 Sensitive_07 ovarian cancer Case marker detected. Ovary tissue: Ovary; disease: Ovarian cancer; phenotype: Platinum sensitive patient
  • GSM4876162 Sensitive_08 ovarian cancer Case marker detected. Ovary tissue: Ovary; disease: Ovarian cancer; phenotype: Platinum sensitive patient
  • GSM4876163 Sensitive_09 ovarian cancer Case marker detected. Ovary tissue: Ovary; disease: Ovarian cancer; phenotype: Platinum sensitive patient
  • GSM4876164 Sensitive_10 ovarian cancer Case marker detected. Ovary tissue: Ovary; disease: Ovarian cancer; phenotype: Platinum sensitive patient

Possible control samples

Samples currently treated as controls or baseline.

7
  • GSM4876140 Normal_01 normal tissue Control marker detected. Ovary tissue: Ovary; disease: Normal ovary; phenotype: NA
  • GSM4876141 Normal_02 normal tissue Control marker detected. Ovary tissue: Ovary; disease: Normal ovary; phenotype: NA
  • GSM4876142 Normal_03 normal tissue Control marker detected. Ovary tissue: Ovary; disease: Normal ovary; phenotype: NA
  • GSM4876143 Normal_05 normal tissue Control marker detected. Ovary tissue: Ovary; disease: Normal ovary; phenotype: NA
  • GSM4876144 Normal_06 normal tissue Control marker detected. Ovary tissue: Ovary; disease: Normal ovary; phenotype: NA
  • GSM4876145 Normal_07 normal tissue Control marker detected. Ovary tissue: Ovary; disease: Normal ovary; phenotype: NA
  • GSM4876146 Normal_08 normal tissue Control marker detected. Ovary tissue: Ovary; disease: Normal ovary; phenotype: NA

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

normal tissue

7 samples
  • GSM4876140 Normal_01 Ovary tissue: Ovary; disease: Normal ovary; phenotype: NA
  • GSM4876141 Normal_02 Ovary tissue: Ovary; disease: Normal ovary; phenotype: NA
  • GSM4876142 Normal_03 Ovary tissue: Ovary; disease: Normal ovary; phenotype: NA
  • GSM4876143 Normal_05 Ovary tissue: Ovary; disease: Normal ovary; phenotype: NA
  • GSM4876144 Normal_06 Ovary tissue: Ovary; disease: Normal ovary; phenotype: NA
  • GSM4876145 Normal_07 Ovary tissue: Ovary; disease: Normal ovary; phenotype: NA
  • GSM4876146 Normal_08 Ovary tissue: Ovary; disease: Normal ovary; phenotype: NA

ovarian cancer

18 samples
  • GSM4876147 Resistance_01 Ovary tissue: Ovary; disease: Ovarian cancer; phenotype: Platinum resistant patient
  • GSM4876148 Resistance_03 Ovary tissue: Ovary; disease: Ovarian cancer; phenotype: Platinum resistant patient
  • GSM4876149 Resistance_04 Ovary tissue: Ovary; disease: Ovarian cancer; phenotype: Platinum resistant patient
  • GSM4876150 Resistance_05 Ovary tissue: Ovary; disease: Ovarian cancer; phenotype: Platinum resistant patient
  • GSM4876151 Resistance_06 Ovary tissue: Ovary; disease: Ovarian cancer; phenotype: Platinum resistant patient
  • GSM4876152 Resistance_07 Ovary tissue: Ovary; disease: Ovarian cancer; phenotype: Platinum resistant patient
  • GSM4876153 Resistance_08 Ovary tissue: Ovary; disease: Ovarian cancer; phenotype: Platinum resistant patient
  • GSM4876154 Resistance_09 Ovary tissue: Ovary; disease: Ovarian cancer; phenotype: Platinum resistant patient
  • GSM4876155 Sensitive_01 Ovary tissue: Ovary; disease: Ovarian cancer; phenotype: Platinum sensitive patient
  • GSM4876156 Sensitive_02 Ovary tissue: Ovary; disease: Ovarian cancer; phenotype: Platinum sensitive patient
  • GSM4876157 Sensitive_03 Ovary tissue: Ovary; disease: Ovarian cancer; phenotype: Platinum sensitive patient
  • GSM4876158 Sensitive_04 Ovary tissue: Ovary; disease: Ovarian cancer; phenotype: Platinum sensitive patient
  • GSM4876159 Sensitive_05 Ovary tissue: Ovary; disease: Ovarian cancer; phenotype: Platinum sensitive patient
  • GSM4876160 Sensitive_06 Ovary tissue: Ovary; disease: Ovarian cancer; phenotype: Platinum sensitive patient
  • GSM4876161 Sensitive_07 Ovary tissue: Ovary; disease: Ovarian cancer; phenotype: Platinum sensitive patient
  • GSM4876162 Sensitive_08 Ovary tissue: Ovary; disease: Ovarian cancer; phenotype: Platinum sensitive patient
  • GSM4876163 Sensitive_09 Ovary tissue: Ovary; disease: Ovarian cancer; phenotype: Platinum sensitive patient
  • GSM4876164 Sensitive_10 Ovary tissue: Ovary; disease: Ovarian cancer; phenotype: Platinum sensitive patient

Score Breakdown

100%

relevance

  • Disease or condition metadata normalized.
  • Organism normalized.
  • Assay type normalized.
  • Tissue metadata normalized.
0%

comparison suitability

  • Case and control sample groups detected: ovarian cancer vs normal tissue.
  • 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

25 samples

Review Audit Trail

0 decisions

No review decisions have been stored for this dataset.