Siftome Phase 3L

GSE315136

Comprehensive long-read transcriptome analysis uncovers alternative RNA processing feature and isoform diversity in ovarian cancer progression

Exploratory only Dataset can inform exploration but is not strong enough for primary analysis.
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
2025-12-29
Last update
2025-12-31
Organization
Nankai University
Department
Not available
Public date
2025-12-31
Experiment types
Expression profiling by high throughput sequencing
Platforms
GPL29480 DNBSEQ-T7 (Homo sapiens); GPL34382 Revio (Homo sapiens)
Series type
Series
SubSeries
Not available
BioProject
PRJNA1395038
Supplementary files
TXT: GSE315136_featurecounts_gene_counts.txt.gz; TXT: GSE315136_featurecounts_transcript_counts.txt.gz; TSV: GSE315136_iso.gene_counts.tsv.gz; GTF: GSE315136_iso.gtf.gz; TSV: GSE315136_iso.transcript_counts.tsv.gz
Organism
Homo sapiens
Assay
bulk RNA-seq
Samples
18
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
Exploratory only Dataset can inform exploration but is not strong enough for primary analysis.

Score Components

  • relevance 100% Disease or condition metadata normalized. Organism normalized. Assay type normalized. Tissue metadata normalized.
  • comparison suitability 35% 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. Multi-cancer tissue cohort with colorectal samples downgraded to secondary relevance.
  • 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 65% 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 the cohort mixes colorectal context with other cancer contexts.

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 12 samples
  • Likely control group normal tissue 6 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: multi-cancer cohort is only secondary for colorectal ranking. Derived from current-intent ranking reasons and warnings.

Applied Review Decisions

No active review decisions affect this ranking.

Ranking Facts

  • Recommendation Exploratory only Dataset can inform exploration but is not strong enough for primary analysis.
  • Supporting fact Tumor vs unmatched normal · Tissue · suitability 35%. 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: multi-cancer cohort is only secondary for colorectal ranking. Contributed to match or upgrade evidence.
  • Supporting fact Processed data is available for downstream review. Contributed to match or upgrade evidence.
  • Caution fact Multi-cancer tissue cohort with colorectal samples downgraded to secondary relevance. 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 the cohort mixes colorectal context with other cancer contexts. Contributed to downgrade or manual-review evidence.
  • Caution fact Downgraded disease context: multi-cancer cohort is only secondary for colorectal ranking. 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
GSE315136
Sample records
18 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
GSE315136
  • 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
GSE315136
  • 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
GSE315136
  • 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: GSE315136
dataset_title: Comprehensive long-read transcriptome analysis uncovers alternative RNA processing feature and isoform diversity in ovarian cancer progression
organism: Homo sapiens
assay_type: bulk RNA-seq
processed_data_available: true
raw_data_available: true
submission_date: 2025-12-29
last_update_date: 2025-12-31
organization_name: Nankai University
department: Not available
public_date: 2025-12-31
experiment_types: Expression profiling by high throughput sequencing
platforms: GPL29480 DNBSEQ-T7 (Homo sapiens); GPL34382 Revio (Homo sapiens)
sub_series: Not available
bioproject: PRJNA1395038
supplementary_files: TXT: GSE315136_featurecounts_gene_counts.txt.gz; TXT: GSE315136_featurecounts_transcript_counts.txt.gz; TSV: GSE315136_iso.gene_counts.tsv.gz; GTF: GSE315136_iso.gtf.gz; TSV: GSE315136_iso.transcript_counts.tsv.gz
series_type: Series

Why It Matched

  • Tumor vs unmatched normal · Tissue · suitability 35%.
  • Prioritized assay: bulk RNA-seq is the active assay expectation.
  • Downgraded disease context: multi-cancer cohort is only secondary for colorectal ranking.
  • Processed data is available for downstream review.

Why It May Not Be Suitable

  • Multi-cancer tissue cohort with colorectal samples downgraded to secondary relevance.
  • 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 the cohort mixes colorectal context with other cancer contexts.
  • Downgraded disease context: multi-cancer cohort is only secondary for colorectal ranking.
  • Comparison suitability score is below the Phase 1 recommended threshold.

Warnings

No warnings

Normalized Fields

41 fields
Field Value Source Origin Confidence Evidence Reason
assay_type bulk RNA-seq dataset GSE315136 Runtime Siftome inference GEO:dataset:GSE315136:ecccd51ae60cd8a85ad3dc0c499e1ccfa4cab6531a651f475747c561edffccf2 high confidence bulk rna-seq dataset_accession: GSE315136 dataset_title: Comprehensive long-read transcriptome analysis uncovers alternative RNA processing feature and isoform diversity in ovarian cancer pr... keyword match keyword match: bulk rna-seq
disease colorectal cancer dataset GSE315136 Runtime Siftome inference GEO:dataset:GSE315136:ecccd51ae60cd8a85ad3dc0c499e1ccfa4cab6531a651f475747c561edffccf2 medium confidence read dataset_accession: GSE315136 dataset_title: Comprehensive long-read transcriptome analysis uncovers alternative RNA processing feature and isoform diversity in ovarian cancer pr... controlled vocabulary controlled vocabulary disease match: read
disease ovarian cancer dataset GSE315136 Runtime Siftome inference GEO:dataset:GSE315136:ecccd51ae60cd8a85ad3dc0c499e1ccfa4cab6531a651f475747c561edffccf2 high confidence ovarian cancer dataset_accession: GSE315136 dataset_title: Comprehensive long-read transcriptome analysis uncovers alternative RNA processing feature and isoform diversity in ovarian cancer pr... controlled vocabulary controlled vocabulary disease match: ovarian cancer
organism Homo sapiens dataset GSE315136 Runtime Siftome inference GEO:dataset:GSE315136:ecccd51ae60cd8a85ad3dc0c499e1ccfa4cab6531a651f475747c561edffccf2 high confidence homo sapiens dataset_accession: GSE315136 dataset_title: Comprehensive long-read transcriptome analysis uncovers alternative RNA processing feature and isoform diversity in ovarian cancer pr... keyword match keyword match: homo sapiens
sample_type normal tissue sample GSM9421908 Runtime Siftome inference GEO:sample:GSM9421908:c374e6116361e683814f8fcaee06f998c37cdb586fb43a9e67278e20a24953b0 low confidence normal sample_accession: GSM9421908 sample_title: Patient_1_Normal_tissue_LRS source_name: ovary characteristics: tissue: ovary Patient_1_Normal_tissue_LRS controlled vocabulary controlled vocabulary sample type match: normal
sample_type normal tissue sample GSM9421909 Runtime Siftome inference GEO:sample:GSM9421909:9fc5d03ac6635dc96672e3a933f16dd8545ccfe3aa5bca5447651a8f5eeb2d91 low confidence normal sample_accession: GSM9421909 sample_title: Patient_2_Normal_tissue_LRS source_name: ovary characteristics: tissue: ovary Patient_2_Normal_tissue_LRS controlled vocabulary controlled vocabulary sample type match: normal
sample_type normal tissue sample GSM9421910 Runtime Siftome inference GEO:sample:GSM9421910:9903413c2290d8c792dc4171c7cf5798aa04c0486f0b789c849566b8f2af99da low confidence normal sample_accession: GSM9421910 sample_title: Patient_3_Normal_tissue_LRS source_name: ovary characteristics: tissue: ovary Patient_3_Normal_tissue_LRS controlled vocabulary controlled vocabulary sample type match: normal
sample_type tumor sample sample GSM9421911 Runtime Siftome inference GEO:sample:GSM9421911:b1ff5b250f1f1dd6936e9dd3d08fac91a5e18afa3687b16720cc30687f0103f1 low confidence tumor sample_accession: GSM9421911 sample_title: Patient_1_Primary_tumor _LRS source_name: ovary characteristics: tissue: ovary Patient_1_Primary_tumor _LRS controlled vocabulary controlled vocabulary sample type match: tumor
sample_type tumor sample sample GSM9421912 Runtime Siftome inference GEO:sample:GSM9421912:35be810c8908afeef42d58253e7414c4bcbd9d699728137d7aaaebad276662f9 low confidence tumor sample_accession: GSM9421912 sample_title: Patient_2_Primary_tumor _LRS source_name: ovary characteristics: tissue: ovary Patient_2_Primary_tumor _LRS controlled vocabulary controlled vocabulary sample type match: tumor
sample_type tumor sample sample GSM9421913 Runtime Siftome inference GEO:sample:GSM9421913:debaf2d1757a34b8b8a449949e5cd80c3f3791120cbc1f7d67e8a918ab55d844 low confidence tumor sample_accession: GSM9421913 sample_title: Patient_3_Primary_tumor _LRS source_name: ovary characteristics: tissue: ovary Patient_3_Primary_tumor _LRS controlled vocabulary controlled vocabulary sample type match: tumor
sample_type tumor sample sample GSM9421914 Runtime Siftome inference GEO:sample:GSM9421914:7456b09e7cae3b8607009b7ba193ff0b4aa764e3fbfa616a9b3cfccb65524c07 medium confidence metastasis sample_accession: GSM9421914 sample_title: Patient_1_Metastasis_LRS source_name: omentum characteristics: tissue: omentum Patient_1_Metastasis_LRS controlled vocabulary controlled vocabulary sample type match: metastasis
sample_type tumor sample sample GSM9421915 Runtime Siftome inference GEO:sample:GSM9421915:3b984caea51f4bf92a5d1032c25646fce8dbbf1a6718a8fe28cc1604b828feb1 medium confidence metastasis sample_accession: GSM9421915 sample_title: Patient_2_Metastasis_LRS source_name: omentum characteristics: tissue: omentum Patient_2_Metastasis_LRS controlled vocabulary controlled vocabulary sample type match: metastasis
sample_type tumor sample sample GSM9421916 Runtime Siftome inference GEO:sample:GSM9421916:37b0fe3404b974b50448fa73901c2d95c579c142714bad562f9bf849b3090c77 medium confidence metastasis sample_accession: GSM9421916 sample_title: Patient_3_Metastasis_LRS source_name: omentum characteristics: tissue: omentum Patient_3_Metastasis_LRS controlled vocabulary controlled vocabulary sample type match: metastasis
sample_type normal tissue sample GSM9421917 Runtime Siftome inference GEO:sample:GSM9421917:2587443395ddb0c185d3bb58769a46b4f03bc5b25b6925224d384fce7343c4c1 low confidence normal sample_accession: GSM9421917 sample_title: Patient_1_Normal_tissue_SRS source_name: ovary characteristics: tissue: ovary Patient_1_Normal_tissue_SRS controlled vocabulary controlled vocabulary sample type match: normal
sample_type normal tissue sample GSM9421918 Runtime Siftome inference GEO:sample:GSM9421918:6a932ae4df2eda58b26981fc5b6371ac2798494d7a3e9a9f2a01ddfb604a193b low confidence normal sample_accession: GSM9421918 sample_title: Patient_2_Normal_tissue_SRS source_name: ovary characteristics: tissue: ovary Patient_2_Normal_tissue_SRS controlled vocabulary controlled vocabulary sample type match: normal
sample_type normal tissue sample GSM9421919 Runtime Siftome inference GEO:sample:GSM9421919:4b559790aef88c2fe482e1cc6f626b4e4b4a41f3d73c0f833bf2e85094a521f3 low confidence normal sample_accession: GSM9421919 sample_title: Patient_3_Normal_tissue_SRS source_name: ovary characteristics: tissue: ovary Patient_3_Normal_tissue_SRS controlled vocabulary controlled vocabulary sample type match: normal
sample_type tumor sample sample GSM9421920 Runtime Siftome inference GEO:sample:GSM9421920:1c8f6c78ad0ad663e66a6cc8609fb37e5964a42f9e4762cddb4be59fb8f1b3d5 low confidence tumor sample_accession: GSM9421920 sample_title: Patient_1_Primary_tumor _SRS source_name: ovary characteristics: tissue: ovary Patient_1_Primary_tumor _SRS controlled vocabulary controlled vocabulary sample type match: tumor
sample_type tumor sample sample GSM9421921 Runtime Siftome inference GEO:sample:GSM9421921:f87cb84594da6c416d56d7d7c51597904b5bce49c1623c1f1c14f80e08325aea low confidence tumor sample_accession: GSM9421921 sample_title: Patient_2_Primary_tumor _SRS source_name: ovary characteristics: tissue: ovary Patient_2_Primary_tumor _SRS controlled vocabulary controlled vocabulary sample type match: tumor
sample_type tumor sample sample GSM9421922 Runtime Siftome inference GEO:sample:GSM9421922:121d0bebf6d3434f568e2ac916ba4fb62305592b38d45ce724346ca0d1da80d6 low confidence tumor sample_accession: GSM9421922 sample_title: Patient_3_Primary_tumor _SRS source_name: ovary characteristics: tissue: ovary Patient_3_Primary_tumor _SRS controlled vocabulary controlled vocabulary sample type match: tumor
sample_type tumor sample sample GSM9421923 Runtime Siftome inference GEO:sample:GSM9421923:1b3a650c1dde9f7aabe09e066a3fef477cdb4ffc6df92f784670241c622de6bc medium confidence metastasis sample_accession: GSM9421923 sample_title: Patient_1_Metastasis_SRS source_name: omentum characteristics: tissue: omentum Patient_1_Metastasis_SRS controlled vocabulary controlled vocabulary sample type match: metastasis
sample_type tumor sample sample GSM9421924 Runtime Siftome inference GEO:sample:GSM9421924:bd67de9843c03509c4ba336717c41ae0f25f94f64bb4e852751cc6cf650ac028 medium confidence metastasis sample_accession: GSM9421924 sample_title: Patient_2_Metastasis_SRS source_name: omentum characteristics: tissue: omentum Patient_2_Metastasis_SRS controlled vocabulary controlled vocabulary sample type match: metastasis
sample_type tumor sample sample GSM9421925 Runtime Siftome inference GEO:sample:GSM9421925:5144d43ba6cb5bd0beb76428ffad27df9e1229eccf9be00a23ddd4a78b170ab1 medium confidence metastasis sample_accession: GSM9421925 sample_title: Patient_3_Metastasis_SRS source_name: omentum characteristics: tissue: omentum Patient_3_Metastasis_SRS controlled vocabulary controlled vocabulary sample type match: metastasis
tissue ovary dataset GSE315136 Runtime Siftome inference GEO:dataset:GSE315136:ecccd51ae60cd8a85ad3dc0c499e1ccfa4cab6531a651f475747c561edffccf2 medium confidence ovarian dataset_accession: GSE315136 dataset_title: Comprehensive long-read transcriptome analysis uncovers alternative RNA processing feature and isoform diversity in ovarian cancer pr... controlled vocabulary controlled vocabulary tissue match: ovarian
tissue ovary sample GSM9421908 Runtime Siftome inference GEO:sample:GSM9421908:c374e6116361e683814f8fcaee06f998c37cdb586fb43a9e67278e20a24953b0 low confidence ovary sample_accession: GSM9421908 sample_title: Patient_1_Normal_tissue_LRS source_name: ovary characteristics: tissue: ovary Patient_1_Normal_tissue_LRS controlled vocabulary controlled vocabulary tissue match: ovary
tissue ovary sample GSM9421909 Runtime Siftome inference GEO:sample:GSM9421909:9fc5d03ac6635dc96672e3a933f16dd8545ccfe3aa5bca5447651a8f5eeb2d91 low confidence ovary sample_accession: GSM9421909 sample_title: Patient_2_Normal_tissue_LRS source_name: ovary characteristics: tissue: ovary Patient_2_Normal_tissue_LRS controlled vocabulary controlled vocabulary tissue match: ovary
tissue ovary sample GSM9421910 Runtime Siftome inference GEO:sample:GSM9421910:9903413c2290d8c792dc4171c7cf5798aa04c0486f0b789c849566b8f2af99da low confidence ovary sample_accession: GSM9421910 sample_title: Patient_3_Normal_tissue_LRS source_name: ovary characteristics: tissue: ovary Patient_3_Normal_tissue_LRS controlled vocabulary controlled vocabulary tissue match: ovary
tissue ovary sample GSM9421911 Runtime Siftome inference GEO:sample:GSM9421911:b1ff5b250f1f1dd6936e9dd3d08fac91a5e18afa3687b16720cc30687f0103f1 low confidence ovary sample_accession: GSM9421911 sample_title: Patient_1_Primary_tumor _LRS source_name: ovary characteristics: tissue: ovary Patient_1_Primary_tumor _LRS controlled vocabulary controlled vocabulary tissue match: ovary
tissue ovary sample GSM9421912 Runtime Siftome inference GEO:sample:GSM9421912:35be810c8908afeef42d58253e7414c4bcbd9d699728137d7aaaebad276662f9 low confidence ovary sample_accession: GSM9421912 sample_title: Patient_2_Primary_tumor _LRS source_name: ovary characteristics: tissue: ovary Patient_2_Primary_tumor _LRS controlled vocabulary controlled vocabulary tissue match: ovary
tissue ovary sample GSM9421913 Runtime Siftome inference GEO:sample:GSM9421913:debaf2d1757a34b8b8a449949e5cd80c3f3791120cbc1f7d67e8a918ab55d844 low confidence ovary sample_accession: GSM9421913 sample_title: Patient_3_Primary_tumor _LRS source_name: ovary characteristics: tissue: ovary Patient_3_Primary_tumor _LRS controlled vocabulary controlled vocabulary tissue match: ovary
tissue ovary sample GSM9421917 Runtime Siftome inference GEO:sample:GSM9421917:2587443395ddb0c185d3bb58769a46b4f03bc5b25b6925224d384fce7343c4c1 low confidence ovary sample_accession: GSM9421917 sample_title: Patient_1_Normal_tissue_SRS source_name: ovary characteristics: tissue: ovary Patient_1_Normal_tissue_SRS controlled vocabulary controlled vocabulary tissue match: ovary
tissue ovary sample GSM9421918 Runtime Siftome inference GEO:sample:GSM9421918:6a932ae4df2eda58b26981fc5b6371ac2798494d7a3e9a9f2a01ddfb604a193b low confidence ovary sample_accession: GSM9421918 sample_title: Patient_2_Normal_tissue_SRS source_name: ovary characteristics: tissue: ovary Patient_2_Normal_tissue_SRS controlled vocabulary controlled vocabulary tissue match: ovary
tissue ovary sample GSM9421919 Runtime Siftome inference GEO:sample:GSM9421919:4b559790aef88c2fe482e1cc6f626b4e4b4a41f3d73c0f833bf2e85094a521f3 low confidence ovary sample_accession: GSM9421919 sample_title: Patient_3_Normal_tissue_SRS source_name: ovary characteristics: tissue: ovary Patient_3_Normal_tissue_SRS controlled vocabulary controlled vocabulary tissue match: ovary
tissue ovary sample GSM9421920 Runtime Siftome inference GEO:sample:GSM9421920:1c8f6c78ad0ad663e66a6cc8609fb37e5964a42f9e4762cddb4be59fb8f1b3d5 low confidence ovary sample_accession: GSM9421920 sample_title: Patient_1_Primary_tumor _SRS source_name: ovary characteristics: tissue: ovary Patient_1_Primary_tumor _SRS controlled vocabulary controlled vocabulary tissue match: ovary
tissue ovary sample GSM9421921 Runtime Siftome inference GEO:sample:GSM9421921:f87cb84594da6c416d56d7d7c51597904b5bce49c1623c1f1c14f80e08325aea low confidence ovary sample_accession: GSM9421921 sample_title: Patient_2_Primary_tumor _SRS source_name: ovary characteristics: tissue: ovary Patient_2_Primary_tumor _SRS controlled vocabulary controlled vocabulary tissue match: ovary
tissue ovary sample GSM9421922 Runtime Siftome inference GEO:sample:GSM9421922:121d0bebf6d3434f568e2ac916ba4fb62305592b38d45ce724346ca0d1da80d6 low confidence ovary sample_accession: GSM9421922 sample_title: Patient_3_Primary_tumor _SRS source_name: ovary characteristics: tissue: ovary Patient_3_Primary_tumor _SRS controlled vocabulary controlled vocabulary tissue match: ovary
tumor_type metastatic tumor sample GSM9421914 Runtime Siftome inference GEO:sample:GSM9421914:7456b09e7cae3b8607009b7ba193ff0b4aa764e3fbfa616a9b3cfccb65524c07 medium confidence metastasis sample_accession: GSM9421914 sample_title: Patient_1_Metastasis_LRS source_name: omentum characteristics: tissue: omentum Patient_1_Metastasis_LRS controlled vocabulary controlled vocabulary tumor type match: metastasis
tumor_type metastatic tumor sample GSM9421915 Runtime Siftome inference GEO:sample:GSM9421915:3b984caea51f4bf92a5d1032c25646fce8dbbf1a6718a8fe28cc1604b828feb1 medium confidence metastasis sample_accession: GSM9421915 sample_title: Patient_2_Metastasis_LRS source_name: omentum characteristics: tissue: omentum Patient_2_Metastasis_LRS controlled vocabulary controlled vocabulary tumor type match: metastasis
tumor_type metastatic tumor sample GSM9421916 Runtime Siftome inference GEO:sample:GSM9421916:37b0fe3404b974b50448fa73901c2d95c579c142714bad562f9bf849b3090c77 medium confidence metastasis sample_accession: GSM9421916 sample_title: Patient_3_Metastasis_LRS source_name: omentum characteristics: tissue: omentum Patient_3_Metastasis_LRS controlled vocabulary controlled vocabulary tumor type match: metastasis
tumor_type metastatic tumor sample GSM9421923 Runtime Siftome inference GEO:sample:GSM9421923:1b3a650c1dde9f7aabe09e066a3fef477cdb4ffc6df92f784670241c622de6bc medium confidence metastasis sample_accession: GSM9421923 sample_title: Patient_1_Metastasis_SRS source_name: omentum characteristics: tissue: omentum Patient_1_Metastasis_SRS controlled vocabulary controlled vocabulary tumor type match: metastasis
tumor_type metastatic tumor sample GSM9421924 Runtime Siftome inference GEO:sample:GSM9421924:bd67de9843c03509c4ba336717c41ae0f25f94f64bb4e852751cc6cf650ac028 medium confidence metastasis sample_accession: GSM9421924 sample_title: Patient_2_Metastasis_SRS source_name: omentum characteristics: tissue: omentum Patient_2_Metastasis_SRS controlled vocabulary controlled vocabulary tumor type match: metastasis
tumor_type metastatic tumor sample GSM9421925 Runtime Siftome inference GEO:sample:GSM9421925:5144d43ba6cb5bd0beb76428ffad27df9e1229eccf9be00a23ddd4a78b170ab1 medium confidence metastasis sample_accession: GSM9421925 sample_title: Patient_3_Metastasis_SRS source_name: omentum characteristics: tissue: omentum Patient_3_Metastasis_SRS controlled vocabulary controlled vocabulary tumor type match: metastasis

Sample Group Preview

Possible case samples

Samples currently treated as the comparison case group.

12
  • GSM9421911 Patient_1_Primary_tumor _LRS tumor sample Case marker detected. ovary tissue: ovary
  • GSM9421912 Patient_2_Primary_tumor _LRS tumor sample Case marker detected. ovary tissue: ovary
  • GSM9421913 Patient_3_Primary_tumor _LRS tumor sample Case marker detected. ovary tissue: ovary
  • GSM9421914 Patient_1_Metastasis_LRS tumor sample Case marker detected. omentum tissue: omentum
  • GSM9421915 Patient_2_Metastasis_LRS tumor sample Case marker detected. omentum tissue: omentum
  • GSM9421916 Patient_3_Metastasis_LRS tumor sample Case marker detected. omentum tissue: omentum
  • GSM9421920 Patient_1_Primary_tumor _SRS tumor sample Case marker detected. ovary tissue: ovary
  • GSM9421921 Patient_2_Primary_tumor _SRS tumor sample Case marker detected. ovary tissue: ovary
  • GSM9421922 Patient_3_Primary_tumor _SRS tumor sample Case marker detected. ovary tissue: ovary
  • GSM9421923 Patient_1_Metastasis_SRS tumor sample Case marker detected. omentum tissue: omentum
  • GSM9421924 Patient_2_Metastasis_SRS tumor sample Case marker detected. omentum tissue: omentum
  • GSM9421925 Patient_3_Metastasis_SRS tumor sample Case marker detected. omentum tissue: omentum

Possible control samples

Samples currently treated as controls or baseline.

6
  • GSM9421908 Patient_1_Normal_tissue_LRS normal tissue Control marker detected. ovary tissue: ovary
  • GSM9421909 Patient_2_Normal_tissue_LRS normal tissue Control marker detected. ovary tissue: ovary
  • GSM9421910 Patient_3_Normal_tissue_LRS normal tissue Control marker detected. ovary tissue: ovary
  • GSM9421917 Patient_1_Normal_tissue_SRS normal tissue Control marker detected. ovary tissue: ovary
  • GSM9421918 Patient_2_Normal_tissue_SRS normal tissue Control marker detected. ovary tissue: ovary
  • GSM9421919 Patient_3_Normal_tissue_SRS normal tissue Control marker detected. ovary tissue: ovary

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

6 samples
  • GSM9421908 Patient_1_Normal_tissue_LRS ovary tissue: ovary
  • GSM9421909 Patient_2_Normal_tissue_LRS ovary tissue: ovary
  • GSM9421910 Patient_3_Normal_tissue_LRS ovary tissue: ovary
  • GSM9421917 Patient_1_Normal_tissue_SRS ovary tissue: ovary
  • GSM9421918 Patient_2_Normal_tissue_SRS ovary tissue: ovary
  • GSM9421919 Patient_3_Normal_tissue_SRS ovary tissue: ovary

tumor sample

12 samples
  • GSM9421911 Patient_1_Primary_tumor _LRS ovary tissue: ovary
  • GSM9421912 Patient_2_Primary_tumor _LRS ovary tissue: ovary
  • GSM9421913 Patient_3_Primary_tumor _LRS ovary tissue: ovary
  • GSM9421914 Patient_1_Metastasis_LRS omentum tissue: omentum
  • GSM9421915 Patient_2_Metastasis_LRS omentum tissue: omentum
  • GSM9421916 Patient_3_Metastasis_LRS omentum tissue: omentum
  • GSM9421920 Patient_1_Primary_tumor _SRS ovary tissue: ovary
  • GSM9421921 Patient_2_Primary_tumor _SRS ovary tissue: ovary
  • GSM9421922 Patient_3_Primary_tumor _SRS ovary tissue: ovary
  • GSM9421923 Patient_1_Metastasis_SRS omentum tissue: omentum
  • GSM9421924 Patient_2_Metastasis_SRS omentum tissue: omentum
  • GSM9421925 Patient_3_Metastasis_SRS omentum tissue: omentum

Score Breakdown

100%

relevance

  • Disease or condition metadata normalized.
  • Organism normalized.
  • Assay type normalized.
  • Tissue metadata normalized.
35%

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.
  • Multi-cancer tissue cohort with colorectal samples downgraded to secondary relevance.
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.
65%

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 the cohort mixes colorectal context with other cancer contexts.

Sample Links

18 samples

Review Audit Trail

0 decisions

No review decisions have been stored for this dataset.