Siftome Phase 3L

GSE212991

Genome-wide expression profiling reveals novel biomarkers in epithelial ovarian cancer

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
2022-09-09
Last update
2024-05-01
Organization
Motilal Nehru National Institute of Technology
Department
Biotechnology
Public date
2022-09-13
Experiment types
Expression profiling by high throughput sequencing
Platforms
GPL18573 Illumina NextSeq 500 (Homo sapiens)
Series type
Series
SubSeries
Not available
BioProject
PRJNA878688
Supplementary files
XLSX: GSE212991_Raw_counts.xlsx
Organism
Homo sapiens
Assay
bulk RNA-seq
Samples
6
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% Tumor and normal sample groups detected. No excluded sample type flags detected. Tumor/normal design boosted for colorectal tumor-vs-normal tissue triage. Patient tissue or biopsy specimens boosted for tissue comparison triage. Non-colorectal cancer context downgraded for colorectal tumor-vs-normal tissue ranking.
  • metadata quality 100% Sample source clarity: All samples have source metadata and clear GSE/GSM accessions. Group clarity: Rule-based grouping found both case and control samples. Disease clarity: Disease or condition metadata normalized. Tissue clarity: Tissue metadata normalized. Treatment clarity: No unclear treatment split detected in the sample metadata. Replicate clarity: No pooled sample or technical replicate flags detected. Data availability clarity: Dataset-level processed or raw data availability is explicit.
  • data availability 100% Processed data available. Raw data available.
  • overall 34% Weighted score: 30% relevance, 30% comparison suitability, 25% metadata quality, 15% data availability. Overall score capped because comparison suitability is weak for the selected search intent. Overall score capped because fewer than ten samples limit cohort confidence. Overall score capped because tumor/normal grouping is from a non-colorectal cancer context.

Derived Classifications

  • Organism Homo sapiens Organism remains rule-derived: Homo sapiens.
  • Assay bulk RNA-seq Assay remains rule-derived: bulk RNA-seq.
  • Study design Tumor vs unmatched normal Study design remains rule-derived: Tumor vs unmatched normal.
  • Specimen/source Tissue Specimen/source remains rule-derived: Tissue.
  • Likely case group tumor sample 4 samples
  • Likely control group normal tissue 2 samples

Warnings

No ranking warnings are active.

Intent Interpretation

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

Applied Review Decisions

No active review decisions affect this ranking.

Ranking Facts

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

Manual Corrections

0 active

Source Evidence

4 sources

GEO

Primary source

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

Dataset accession
GSE212991
Sample records
6 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
GSE212991
  • 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
GSE212991
  • 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
GSE212991
  • 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: GSE212991
dataset_title: Genome-wide expression profiling reveals novel biomarkers in epithelial ovarian cancer
organism: Homo sapiens
assay_type: bulk RNA-seq
processed_data_available: true
raw_data_available: true
submission_date: 2022-09-09
last_update_date: 2024-05-01
organization_name: Motilal Nehru National Institute of Technology
department: Biotechnology
public_date: 2022-09-13
experiment_types: Expression profiling by high throughput sequencing
platforms: GPL18573 Illumina NextSeq 500 (Homo sapiens)
sub_series: Not available
bioproject: PRJNA878688
supplementary_files: XLSX: GSE212991_Raw_counts.xlsx
series_type: Series

Why It Matched

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

Why It May Not Be Suitable

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

Warnings

No warnings

Normalized Fields

18 fields
Field Value Source Origin Confidence Evidence Reason
assay_type bulk RNA-seq dataset GSE212991 Runtime Siftome inference GEO:dataset:GSE212991:9041cbfec7fd66f7d409acd94751ea0c6872a4cadf031f0826da66b449cc0e97 high confidence bulk rna-seq dataset_accession: GSE212991 dataset_title: Genome-wide expression profiling reveals novel biomarkers in epithelial ovarian cancer organism: Homo sapiens assay_type: bulk RNA-se... keyword match keyword match: bulk rna-seq
disease ovarian cancer dataset GSE212991 Runtime Siftome inference GEO:dataset:GSE212991:9041cbfec7fd66f7d409acd94751ea0c6872a4cadf031f0826da66b449cc0e97 high confidence ovarian cancer dataset_accession: GSE212991 dataset_title: Genome-wide expression profiling reveals novel biomarkers in epithelial ovarian cancer organism: Homo sapiens assay_type: bulk RNA-se... controlled vocabulary controlled vocabulary disease match: ovarian cancer
organism Homo sapiens dataset GSE212991 Runtime Siftome inference GEO:dataset:GSE212991:9041cbfec7fd66f7d409acd94751ea0c6872a4cadf031f0826da66b449cc0e97 high confidence homo sapiens dataset_accession: GSE212991 dataset_title: Genome-wide expression profiling reveals novel biomarkers in epithelial ovarian cancer organism: Homo sapiens assay_type: bulk RNA-se... keyword match keyword match: homo sapiens
sample_type tumor sample sample GSM6568182 Runtime Siftome inference GEO:sample:GSM6568182:157cd0d109365c64eb78e395a7a5b381eaaaac52741fd971d80afd06a73f67b4 low confidence tumor sample_accession: GSM6568182 sample_title: Tumor Sample 1 source_name: Cancerous Ovarian Tissue characteristics: tissue: Cancerous Ovarian Tissue; tumor stage: IIIC; age: 25; hi... controlled vocabulary controlled vocabulary sample type match: tumor
sample_type normal tissue sample GSM6568183 Runtime Siftome inference GEO:sample:GSM6568183:9885a8f6119a7a2a2f58cf6b4fac699b78accb334921c56dd068b8d5c57b8fc4 low confidence normal sample_accession: GSM6568183 sample_title: Normal Sample 1 source_name: Normal Ovary Tissue characteristics: tissue: Normal Ovary Tissue; tumor stage: N/A; age: 54; histology: N... controlled vocabulary controlled vocabulary sample type match: normal
sample_type tumor sample sample GSM6568183 Runtime Siftome inference GEO:sample:GSM6568183:9885a8f6119a7a2a2f58cf6b4fac699b78accb334921c56dd068b8d5c57b8fc4 low confidence tumor sample_accession: GSM6568183 sample_title: Normal Sample 1 source_name: Normal Ovary Tissue characteristics: tissue: Normal Ovary Tissue; tumor stage: N/A; age: 54; histology: N... controlled vocabulary controlled vocabulary sample type match: tumor
sample_type tumor sample sample GSM6568184 Runtime Siftome inference GEO:sample:GSM6568184:ce7f169d0c305f8614b980faeae24d7953a69392fdc98b5f9ca020add9ef83a4 low confidence tumor sample_accession: GSM6568184 sample_title: Tumor Sample 2 source_name: Cancerous Ovarian Tissue characteristics: tissue: Cancerous Ovarian Tissue; tumor stage: III; age: 47; his... controlled vocabulary controlled vocabulary sample type match: tumor
sample_type tumor sample sample GSM6568185 Runtime Siftome inference GEO:sample:GSM6568185:62328f0b73a3b578ffe3826516c586f5267d9e982533c08178c58283c76d69f5 low confidence tumor sample_accession: GSM6568185 sample_title: Tumor Sample 3 source_name: Cancerous Ovarian Tissue characteristics: tissue: Cancerous Ovarian Tissue; tumor stage: IV; age: 45; hist... controlled vocabulary controlled vocabulary sample type match: tumor
sample_type normal tissue sample GSM6568186 Runtime Siftome inference GEO:sample:GSM6568186:996fbeb2a3ea7a6f47bbd71a79573214ca90630c667d1b8c146be67b742ebd6f low confidence normal sample_accession: GSM6568186 sample_title: Normal Sample 2 source_name: Normal Ovary Tissue characteristics: tissue: Normal Ovary Tissue; tumor stage: N/A; age: 57; histology: N... controlled vocabulary controlled vocabulary sample type match: normal
sample_type tumor sample sample GSM6568186 Runtime Siftome inference GEO:sample:GSM6568186:996fbeb2a3ea7a6f47bbd71a79573214ca90630c667d1b8c146be67b742ebd6f low confidence tumor sample_accession: GSM6568186 sample_title: Normal Sample 2 source_name: Normal Ovary Tissue characteristics: tissue: Normal Ovary Tissue; tumor stage: N/A; age: 57; histology: N... controlled vocabulary controlled vocabulary sample type match: tumor
sample_type tumor sample sample GSM6568187 Runtime Siftome inference GEO:sample:GSM6568187:2e59dbb75a450749678561785cc611a5f0075d72ccc36e78bc4df85e18c89882 low confidence tumor sample_accession: GSM6568187 sample_title: Tumor Sample 4 source_name: Cancerous Ovarian Tissue characteristics: tissue: Cancerous Ovarian Tissue; tumor stage: IV; age: 55; hist... controlled vocabulary controlled vocabulary sample type match: tumor
tissue ovary dataset GSE212991 Runtime Siftome inference GEO:dataset:GSE212991:9041cbfec7fd66f7d409acd94751ea0c6872a4cadf031f0826da66b449cc0e97 medium confidence ovarian dataset_accession: GSE212991 dataset_title: Genome-wide expression profiling reveals novel biomarkers in epithelial ovarian cancer organism: Homo sapiens assay_type: bulk RNA-se... controlled vocabulary controlled vocabulary tissue match: ovarian
tissue ovary sample GSM6568182 Runtime Siftome inference GEO:sample:GSM6568182:157cd0d109365c64eb78e395a7a5b381eaaaac52741fd971d80afd06a73f67b4 medium confidence ovarian sample_accession: GSM6568182 sample_title: Tumor Sample 1 source_name: Cancerous Ovarian Tissue characteristics: tissue: Cancerous Ovarian Tissue; tumor stage: IIIC; age: 25; hi... controlled vocabulary controlled vocabulary tissue match: ovarian
tissue ovary sample GSM6568183 Runtime Siftome inference GEO:sample:GSM6568183:9885a8f6119a7a2a2f58cf6b4fac699b78accb334921c56dd068b8d5c57b8fc4 low confidence ovary sample_accession: GSM6568183 sample_title: Normal Sample 1 source_name: Normal Ovary Tissue characteristics: tissue: Normal Ovary Tissue; tumor stage: N/A; age: 54; histology: N... controlled vocabulary controlled vocabulary tissue match: ovary
tissue ovary sample GSM6568184 Runtime Siftome inference GEO:sample:GSM6568184:ce7f169d0c305f8614b980faeae24d7953a69392fdc98b5f9ca020add9ef83a4 medium confidence ovarian sample_accession: GSM6568184 sample_title: Tumor Sample 2 source_name: Cancerous Ovarian Tissue characteristics: tissue: Cancerous Ovarian Tissue; tumor stage: III; age: 47; his... controlled vocabulary controlled vocabulary tissue match: ovarian
tissue ovary sample GSM6568185 Runtime Siftome inference GEO:sample:GSM6568185:62328f0b73a3b578ffe3826516c586f5267d9e982533c08178c58283c76d69f5 medium confidence ovarian sample_accession: GSM6568185 sample_title: Tumor Sample 3 source_name: Cancerous Ovarian Tissue characteristics: tissue: Cancerous Ovarian Tissue; tumor stage: IV; age: 45; hist... controlled vocabulary controlled vocabulary tissue match: ovarian
tissue ovary sample GSM6568186 Runtime Siftome inference GEO:sample:GSM6568186:996fbeb2a3ea7a6f47bbd71a79573214ca90630c667d1b8c146be67b742ebd6f low confidence ovary sample_accession: GSM6568186 sample_title: Normal Sample 2 source_name: Normal Ovary Tissue characteristics: tissue: Normal Ovary Tissue; tumor stage: N/A; age: 57; histology: N... controlled vocabulary controlled vocabulary tissue match: ovary
tissue ovary sample GSM6568187 Runtime Siftome inference GEO:sample:GSM6568187:2e59dbb75a450749678561785cc611a5f0075d72ccc36e78bc4df85e18c89882 medium confidence ovarian sample_accession: GSM6568187 sample_title: Tumor Sample 4 source_name: Cancerous Ovarian Tissue characteristics: tissue: Cancerous Ovarian Tissue; tumor stage: IV; age: 55; hist... controlled vocabulary controlled vocabulary tissue match: ovarian

Sample Group Preview

Possible case samples

Samples currently treated as the comparison case group.

4
  • GSM6568182 Tumor Sample 1 tumor sample Case marker detected. Cancerous Ovarian Tissue tissue: Cancerous Ovarian Tissue; tumor stage: IIIC; age: 25; histology: Adeocarcioma
  • GSM6568184 Tumor Sample 2 tumor sample Case marker detected. Cancerous Ovarian Tissue tissue: Cancerous Ovarian Tissue; tumor stage: III; age: 47; histology: Adeocarcioma
  • GSM6568185 Tumor Sample 3 tumor sample Case marker detected. Cancerous Ovarian Tissue tissue: Cancerous Ovarian Tissue; tumor stage: IV; age: 45; histology: Adeocarcioma
  • GSM6568187 Tumor Sample 4 tumor sample Case marker detected. Cancerous Ovarian Tissue tissue: Cancerous Ovarian Tissue; tumor stage: IV; age: 55; histology: Adeocarcioma

Possible control samples

Samples currently treated as controls or baseline.

2
  • GSM6568183 Normal Sample 1 normal tissue Control marker detected. Normal Ovary Tissue tissue: Normal Ovary Tissue; tumor stage: N/A; age: 54; histology: Normal
  • GSM6568186 Normal Sample 2 normal tissue Control marker detected. Normal Ovary Tissue tissue: Normal Ovary Tissue; tumor stage: N/A; age: 57; histology: Normal

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

Detected Sample Groups

tumor sample

4 samples
  • GSM6568182 Tumor Sample 1 Cancerous Ovarian Tissue tissue: Cancerous Ovarian Tissue; tumor stage: IIIC; age: 25; histology: Adeocarcioma
  • GSM6568184 Tumor Sample 2 Cancerous Ovarian Tissue tissue: Cancerous Ovarian Tissue; tumor stage: III; age: 47; histology: Adeocarcioma
  • GSM6568185 Tumor Sample 3 Cancerous Ovarian Tissue tissue: Cancerous Ovarian Tissue; tumor stage: IV; age: 45; histology: Adeocarcioma
  • GSM6568187 Tumor Sample 4 Cancerous Ovarian Tissue tissue: Cancerous Ovarian Tissue; tumor stage: IV; age: 55; histology: Adeocarcioma

normal tissue

2 samples
  • GSM6568183 Normal Sample 1 Normal Ovary Tissue tissue: Normal Ovary Tissue; tumor stage: N/A; age: 54; histology: Normal
  • GSM6568186 Normal Sample 2 Normal Ovary Tissue tissue: Normal Ovary Tissue; tumor stage: N/A; age: 57; histology: Normal

Score Breakdown

100%

relevance

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

comparison suitability

  • Tumor and normal sample groups detected.
  • No excluded sample type flags detected.
  • Tumor/normal design boosted for colorectal tumor-vs-normal tissue triage.
  • Patient tissue or biopsy specimens boosted for tissue comparison triage.
  • Non-colorectal cancer context downgraded for colorectal tumor-vs-normal tissue ranking.
100%

metadata quality

  • Sample source clarity: All samples have source metadata and clear GSE/GSM accessions.
  • Group clarity: Rule-based grouping found both case and control samples.
  • Disease clarity: Disease or condition metadata normalized.
  • Tissue clarity: Tissue metadata normalized.
  • Treatment clarity: No unclear treatment split detected in the sample metadata.
  • Replicate clarity: No pooled sample or technical replicate flags detected.
  • Data availability clarity: Dataset-level processed or raw data availability is explicit.
100%

data availability

  • Processed data available.
  • Raw data available.
34%

overall

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

Sample Links

6 samples

Review Audit Trail

0 decisions

No review decisions have been stored for this dataset.