Siftome Phase 3L

GSE230087

Identification of prognostic biomarkers in early stage squamous cell lung cancer (LUSC) by transcriptomic and miRNA profiling [sRNA-Seq]

Not suitable Dataset does not meet the current suitability threshold.
Sample grouping CSV Contrast CSV DESeq2 metadata CSV R handoff notes Handoff report Download instructions Open GEO dataset
Source
GEO
Search intent
Patient tissue tumor-vs-normal
Intent behavior
search-intent-behavior-v1
Submission date
2023-04-19
Last update
2024-03-01
Organization
Ruder Boskovic Institute
Department
Division of Molecular Medicine
Public date
2024-03-01
Experiment types
Non-coding RNA profiling by high throughput sequencing
Platforms
GPL16791 Illumina HiSeq 2500 (Homo sapiens)
Series type
SubSeries
SubSeries
Not available
BioProject
PRJNA957440
Supplementary files
CSV: GSE230087_mature_sense_minExpr1_RCadj_deseq2_RLEnormTable.csv.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

Review before analysis
97% 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

7/10 pts

Warnings are present, but none are critical blockers.

Metadata normalization

10/10 pts

Metadata quality is high enough to support downstream handoff.

Blockers

  • Secondary RNA assay context should be analyzed separately from ordinary bulk RNA-seq.

Next Steps

  • Review blockers and update sample grouping or dataset selection before analysis.

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

Bioinformatician review required

Ask a bioinformatician to review grouping, count availability, exclusions, and design before DE.

  • Analysis readiness has blockers that must be resolved before DE.
  • Assay context may require expert handling before DESeq2-style analysis.

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: lung cancer vs normal tissue. No excluded sample type flags detected. Control type metadata detected. Tumor/normal design boosted for colorectal tumor-vs-normal tissue triage. Patient tissue or biopsy specimens boosted for tissue comparison triage. Small RNA, miRNA, circRNA, or extracellular-vesicle RNA context downgraded for primary mRNA tissue ranking. 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 secondary RNA assays are not primary mRNA tissue RNA-seq. 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 lung cancer 14 samples
  • Likely control group normal tissue 4 samples

Warnings

  • SECONDARY_ASSAY_CONTEXT warning Secondary RNA assay context such as small RNA, miRNA, circRNA, or non-coding RNA was detected.

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 lung 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 1 active warning 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.
  • Supporting fact 1 warning require review. Contributed to match or upgrade evidence.
  • Caution fact Secondary RNA assay context such as small RNA, miRNA, circRNA, or non-coding RNA was detected. Contributed to downgrade or manual-review evidence.
  • Caution fact Small RNA, miRNA, circRNA, or extracellular-vesicle RNA context downgraded for primary mRNA tissue ranking. Contributed to downgrade or manual-review 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 secondary RNA assays are not primary mRNA tissue RNA-seq. 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
GSE230087
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
GSE230087
  • 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
GSE230087
  • 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
GSE230087
  • 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: GSE230087
dataset_title: Identification of prognostic biomarkers in early stage squamous cell lung cancer (LUSC) by transcriptomic and miRNA profiling [sRNA-Seq]
organism: Homo sapiens
assay_type: bulk RNA-seq
processed_data_available: true
raw_data_available: true
submission_date: 2023-04-19
last_update_date: 2024-03-01
organization_name: Ruder Boskovic Institute
department: Division of Molecular Medicine
public_date: 2024-03-01
experiment_types: Non-coding RNA profiling by high throughput sequencing
platforms: GPL16791 Illumina HiSeq 2500 (Homo sapiens)
sub_series: Not available
bioproject: PRJNA957440
supplementary_files: CSV: GSE230087_mature_sense_minExpr1_RCadj_deseq2_RLEnormTable.csv.gz
series_type: SubSeries

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.
  • 1 warning require review.

Why It May Not Be Suitable

  • Secondary RNA assay context such as small RNA, miRNA, circRNA, or non-coding RNA was detected.
  • Small RNA, miRNA, circRNA, or extracellular-vesicle RNA context downgraded for primary mRNA tissue ranking.
  • 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 secondary RNA assays are not primary mRNA tissue RNA-seq.
  • 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

  • warning SECONDARY_ASSAY_CONTEXT Secondary RNA assay context such as small RNA, miRNA, circRNA, or non-coding RNA was detected.

Normalized Fields

48 fields
Field Value Source Origin Confidence Evidence Reason
assay_type bulk RNA-seq dataset GSE230087 Runtime Siftome inference GEO:dataset:GSE230087:a398577256835b270eb66a6d1bf39b457ca24d679510b131e03df835c04b86e7 high confidence bulk rna-seq dataset_accession: GSE230087 dataset_title: Identification of prognostic biomarkers in early stage squamous cell lung cancer (LUSC) by transcriptomic and miRNA profiling [sRNA-S... keyword match keyword match: bulk rna-seq
control_type healthy control sample GSM7186754 Runtime Siftome inference GEO:sample:GSM7186754:226dff41feaf3c73a77379f608bb985d481c3ae5d669cdf336aba5928516d7f6 high confidence healthy control sample_accession: GSM7186754 sample_title: 2, healthy control, sRNA source_name: FFPE tissue characteristics: tissue: FFPE tissue; Sex: male; disease state: healthy control 2, h... controlled vocabulary controlled vocabulary control type match: healthy control
control_type healthy control sample GSM7186755 Runtime Siftome inference GEO:sample:GSM7186755:d2f30a8a7627cb68d47aa062337f3b02c55610c1bd9a175d501db27d6c23c0bd high confidence healthy control sample_accession: GSM7186755 sample_title: 28, healthy control, sRNA source_name: FFPE tissue characteristics: tissue: FFPE tissue; Sex: male; disease state: healthy control 28,... controlled vocabulary controlled vocabulary control type match: healthy control
control_type healthy control sample GSM7186756 Runtime Siftome inference GEO:sample:GSM7186756:f35037b219e68e4fec61d4c5340759790047e44bd694b7b8b232b638f09ee3f0 high confidence healthy control sample_accession: GSM7186756 sample_title: 44, healthy control, sRNA source_name: FFPE tissue characteristics: tissue: FFPE tissue; Sex: male; disease state: healthy control 44,... controlled vocabulary controlled vocabulary control type match: healthy control
control_type healthy control sample GSM7186757 Runtime Siftome inference GEO:sample:GSM7186757:78c24dda1e6674991ff84ba5badfc6f7bd7c5a57cdd6aaaf463dd43092b2d9d1 high confidence healthy control sample_accession: GSM7186757 sample_title: 55, healthy control, sRNA source_name: FFPE tissue characteristics: tissue: FFPE tissue; Sex: male; disease state: healthy control 55,... controlled vocabulary controlled vocabulary control type match: healthy control
disease lung cancer dataset GSE230087 Runtime Siftome inference GEO:dataset:GSE230087:a398577256835b270eb66a6d1bf39b457ca24d679510b131e03df835c04b86e7 high confidence lung cancer dataset_accession: GSE230087 dataset_title: Identification of prognostic biomarkers in early stage squamous cell lung cancer (LUSC) by transcriptomic and miRNA profiling [sRNA-S... controlled vocabulary controlled vocabulary disease match: lung cancer
disease lung cancer sample GSM7186758 Runtime Siftome inference GEO:sample:GSM7186758:24c293bb9f54e5b80174dd9aaf15038e5e7a9d693e82a6d4ebee6e7a49422dff medium confidence lusc sample_accession: GSM7186758 sample_title: 3260, LUSC, sRNA source_name: FFPE tissue characteristics: tissue: FFPE tissue; Sex: male; disease state: LUSC 3260, LUSC, sRNA controlled vocabulary controlled vocabulary disease match: lusc
disease lung cancer sample GSM7186759 Runtime Siftome inference GEO:sample:GSM7186759:2fc01192e29a3d25e0c0d371265ff074179d4274b5d8fb69ff7a2d14013f5237 medium confidence lusc sample_accession: GSM7186759 sample_title: 4613, LUSC, sRNA source_name: FFPE tissue characteristics: tissue: FFPE tissue; Sex: male; disease state: LUSC 4613, LUSC, sRNA controlled vocabulary controlled vocabulary disease match: lusc
disease lung cancer sample GSM7186760 Runtime Siftome inference GEO:sample:GSM7186760:2b013e49c05b5d90a365f604ba3988d945e162e0aea1f58e2aef3c07cb0b900f medium confidence lusc sample_accession: GSM7186760 sample_title: 4737, LUSC, sRNA source_name: FFPE tissue characteristics: tissue: FFPE tissue; Sex: male; disease state: LUSC 4737, LUSC, sRNA controlled vocabulary controlled vocabulary disease match: lusc
disease lung cancer sample GSM7186761 Runtime Siftome inference GEO:sample:GSM7186761:5f775f7edff86e163143424feea98b18de7b3294ee61624630a91fc5378200ff medium confidence lusc sample_accession: GSM7186761 sample_title: 7202, LUSC, sRNA source_name: FFPE tissue characteristics: tissue: FFPE tissue; Sex: male; disease state: LUSC 7202, LUSC, sRNA controlled vocabulary controlled vocabulary disease match: lusc
disease lung cancer sample GSM7186762 Runtime Siftome inference GEO:sample:GSM7186762:f0d41eb0c6b6631e3f83c1fa0d34be2f20f043703f604d18591a6d2f3834909d medium confidence lusc sample_accession: GSM7186762 sample_title: 8323, LUSC, sRNA source_name: FFPE tissue characteristics: tissue: FFPE tissue; Sex: male; disease state: LUSC 8323, LUSC, sRNA controlled vocabulary controlled vocabulary disease match: lusc
disease lung cancer sample GSM7186763 Runtime Siftome inference GEO:sample:GSM7186763:73f4a79f8f61d33e5cad47c6386ea89f932a6b88bb9a08612edfb423f7c4cb25 medium confidence lusc sample_accession: GSM7186763 sample_title: 12545, LUSC, sRNA source_name: FFPE tissue characteristics: tissue: FFPE tissue; Sex: female; disease state: LUSC 12545, LUSC, sRNA controlled vocabulary controlled vocabulary disease match: lusc
disease lung cancer sample GSM7186764 Runtime Siftome inference GEO:sample:GSM7186764:7eb45c781c8d6ffdb6a07195f88ffbfc6f49d878ef6793b5729d0b8ef3f59289 medium confidence lusc sample_accession: GSM7186764 sample_title: 16734, LUSC, sRNA source_name: FFPE tissue characteristics: tissue: FFPE tissue; Sex: female; disease state: LUSC 16734, LUSC, sRNA controlled vocabulary controlled vocabulary disease match: lusc
disease lung cancer sample GSM7186765 Runtime Siftome inference GEO:sample:GSM7186765:ef813400f2fa31ab81efb2bed1501a070a35896b66add85521f0de3ec7a9006c medium confidence lusc sample_accession: GSM7186765 sample_title: 17664, LUSC, sRNA source_name: FFPE tissue characteristics: tissue: FFPE tissue; Sex: male; disease state: LUSC 17664, LUSC, sRNA controlled vocabulary controlled vocabulary disease match: lusc
disease lung cancer sample GSM7186766 Runtime Siftome inference GEO:sample:GSM7186766:5a825505da661618155fba03b94d666ab0e50a96787b4c50293efaae4e2757b8 medium confidence lusc sample_accession: GSM7186766 sample_title: 19694, LUSC, sRNA source_name: FFPE tissue characteristics: tissue: FFPE tissue; Sex: male; disease state: LUSC 19694, LUSC, sRNA controlled vocabulary controlled vocabulary disease match: lusc
disease lung cancer sample GSM7186767 Runtime Siftome inference GEO:sample:GSM7186767:c329e36863eb1cbf2240e615ce53505c17448e58e5879de5352fa628907aac2c medium confidence lusc sample_accession: GSM7186767 sample_title: 20432, LUSC, sRNA source_name: FFPE tissue characteristics: tissue: FFPE tissue; Sex: male; disease state: LUSC 20432, LUSC, sRNA controlled vocabulary controlled vocabulary disease match: lusc
disease lung cancer sample GSM7186768 Runtime Siftome inference GEO:sample:GSM7186768:dade868c94584aceaff0399ae5ae6f0926a6dbc684d158f5767f24d614c2a9c7 medium confidence lusc sample_accession: GSM7186768 sample_title: 21671, LUSC, sRNA source_name: FFPE tissue characteristics: tissue: FFPE tissue; Sex: male; disease state: LUSC 21671, LUSC, sRNA controlled vocabulary controlled vocabulary disease match: lusc
disease lung cancer sample GSM7186769 Runtime Siftome inference GEO:sample:GSM7186769:4643b3aa7dd9fa9ae18421c3fe40fe0a6526601d4a6082d9dc84128da56808c5 medium confidence lusc sample_accession: GSM7186769 sample_title: 25486, LUSC, sRNA source_name: FFPE tissue characteristics: tissue: FFPE tissue; Sex: male; disease state: LUSC 25486, LUSC, sRNA controlled vocabulary controlled vocabulary disease match: lusc
disease lung cancer sample GSM7186770 Runtime Siftome inference GEO:sample:GSM7186770:ffc658b2162ff4e9fdaca3a2c42384b99770893aa08b314d977ed5d74b9c27c2 medium confidence lusc sample_accession: GSM7186770 sample_title: 25609, LUSC, sRNA source_name: FFPE tissue characteristics: tissue: FFPE tissue; Sex: male; disease state: LUSC 25609, LUSC, sRNA controlled vocabulary controlled vocabulary disease match: lusc
disease lung cancer sample GSM7186771 Runtime Siftome inference GEO:sample:GSM7186771:62400888377adffcacdb09d9bab66d5f1c1e1688faa4ce773d6119c6d2d54b9a medium confidence lusc sample_accession: GSM7186771 sample_title: 25850, LUSC, sRNA source_name: FFPE tissue characteristics: tissue: FFPE tissue; Sex: male; disease state: LUSC 25850, LUSC, sRNA controlled vocabulary controlled vocabulary disease match: lusc
normal_tissue_type healthy donor tissue sample GSM7186754 Runtime Siftome inference GEO:sample:GSM7186754:226dff41feaf3c73a77379f608bb985d481c3ae5d669cdf336aba5928516d7f6 high confidence healthy control sample_accession: GSM7186754 sample_title: 2, healthy control, sRNA source_name: FFPE tissue characteristics: tissue: FFPE tissue; Sex: male; disease state: healthy control 2, h... controlled vocabulary controlled vocabulary normal tissue type match: healthy control
normal_tissue_type healthy donor tissue sample GSM7186755 Runtime Siftome inference GEO:sample:GSM7186755:d2f30a8a7627cb68d47aa062337f3b02c55610c1bd9a175d501db27d6c23c0bd high confidence healthy control sample_accession: GSM7186755 sample_title: 28, healthy control, sRNA source_name: FFPE tissue characteristics: tissue: FFPE tissue; Sex: male; disease state: healthy control 28,... controlled vocabulary controlled vocabulary normal tissue type match: healthy control
normal_tissue_type healthy donor tissue sample GSM7186756 Runtime Siftome inference GEO:sample:GSM7186756:f35037b219e68e4fec61d4c5340759790047e44bd694b7b8b232b638f09ee3f0 high confidence healthy control sample_accession: GSM7186756 sample_title: 44, healthy control, sRNA source_name: FFPE tissue characteristics: tissue: FFPE tissue; Sex: male; disease state: healthy control 44,... controlled vocabulary controlled vocabulary normal tissue type match: healthy control
normal_tissue_type healthy donor tissue sample GSM7186757 Runtime Siftome inference GEO:sample:GSM7186757:78c24dda1e6674991ff84ba5badfc6f7bd7c5a57cdd6aaaf463dd43092b2d9d1 high confidence healthy control sample_accession: GSM7186757 sample_title: 55, healthy control, sRNA source_name: FFPE tissue characteristics: tissue: FFPE tissue; Sex: male; disease state: healthy control 55,... controlled vocabulary controlled vocabulary normal tissue type match: healthy control
organism Homo sapiens dataset GSE230087 Runtime Siftome inference GEO:dataset:GSE230087:a398577256835b270eb66a6d1bf39b457ca24d679510b131e03df835c04b86e7 high confidence homo sapiens dataset_accession: GSE230087 dataset_title: Identification of prognostic biomarkers in early stage squamous cell lung cancer (LUSC) by transcriptomic and miRNA profiling [sRNA-S... keyword match keyword match: homo sapiens
primary_tissue primary tissue sample GSM7186754 Runtime Siftome inference GEO:sample:GSM7186754:226dff41feaf3c73a77379f608bb985d481c3ae5d669cdf336aba5928516d7f6 high confidence ffpe tissue sample_accession: GSM7186754 sample_title: 2, healthy control, sRNA source_name: FFPE tissue characteristics: tissue: FFPE tissue; Sex: male; disease state: healthy control 2, h... controlled vocabulary controlled vocabulary primary tissue match: ffpe tissue
primary_tissue primary tissue sample GSM7186755 Runtime Siftome inference GEO:sample:GSM7186755:d2f30a8a7627cb68d47aa062337f3b02c55610c1bd9a175d501db27d6c23c0bd high confidence ffpe tissue sample_accession: GSM7186755 sample_title: 28, healthy control, sRNA source_name: FFPE tissue characteristics: tissue: FFPE tissue; Sex: male; disease state: healthy control 28,... controlled vocabulary controlled vocabulary primary tissue match: ffpe tissue
primary_tissue primary tissue sample GSM7186756 Runtime Siftome inference GEO:sample:GSM7186756:f35037b219e68e4fec61d4c5340759790047e44bd694b7b8b232b638f09ee3f0 high confidence ffpe tissue sample_accession: GSM7186756 sample_title: 44, healthy control, sRNA source_name: FFPE tissue characteristics: tissue: FFPE tissue; Sex: male; disease state: healthy control 44,... controlled vocabulary controlled vocabulary primary tissue match: ffpe tissue
primary_tissue primary tissue sample GSM7186757 Runtime Siftome inference GEO:sample:GSM7186757:78c24dda1e6674991ff84ba5badfc6f7bd7c5a57cdd6aaaf463dd43092b2d9d1 high confidence ffpe tissue sample_accession: GSM7186757 sample_title: 55, healthy control, sRNA source_name: FFPE tissue characteristics: tissue: FFPE tissue; Sex: male; disease state: healthy control 55,... controlled vocabulary controlled vocabulary primary tissue match: ffpe tissue
primary_tissue primary tissue sample GSM7186758 Runtime Siftome inference GEO:sample:GSM7186758:24c293bb9f54e5b80174dd9aaf15038e5e7a9d693e82a6d4ebee6e7a49422dff high confidence ffpe tissue sample_accession: GSM7186758 sample_title: 3260, LUSC, sRNA source_name: FFPE tissue characteristics: tissue: FFPE tissue; Sex: male; disease state: LUSC 3260, LUSC, sRNA controlled vocabulary controlled vocabulary primary tissue match: ffpe tissue
primary_tissue primary tissue sample GSM7186759 Runtime Siftome inference GEO:sample:GSM7186759:2fc01192e29a3d25e0c0d371265ff074179d4274b5d8fb69ff7a2d14013f5237 high confidence ffpe tissue sample_accession: GSM7186759 sample_title: 4613, LUSC, sRNA source_name: FFPE tissue characteristics: tissue: FFPE tissue; Sex: male; disease state: LUSC 4613, LUSC, sRNA controlled vocabulary controlled vocabulary primary tissue match: ffpe tissue
primary_tissue primary tissue sample GSM7186760 Runtime Siftome inference GEO:sample:GSM7186760:2b013e49c05b5d90a365f604ba3988d945e162e0aea1f58e2aef3c07cb0b900f high confidence ffpe tissue sample_accession: GSM7186760 sample_title: 4737, LUSC, sRNA source_name: FFPE tissue characteristics: tissue: FFPE tissue; Sex: male; disease state: LUSC 4737, LUSC, sRNA controlled vocabulary controlled vocabulary primary tissue match: ffpe tissue
primary_tissue primary tissue sample GSM7186761 Runtime Siftome inference GEO:sample:GSM7186761:5f775f7edff86e163143424feea98b18de7b3294ee61624630a91fc5378200ff high confidence ffpe tissue sample_accession: GSM7186761 sample_title: 7202, LUSC, sRNA source_name: FFPE tissue characteristics: tissue: FFPE tissue; Sex: male; disease state: LUSC 7202, LUSC, sRNA controlled vocabulary controlled vocabulary primary tissue match: ffpe tissue
primary_tissue primary tissue sample GSM7186762 Runtime Siftome inference GEO:sample:GSM7186762:f0d41eb0c6b6631e3f83c1fa0d34be2f20f043703f604d18591a6d2f3834909d high confidence ffpe tissue sample_accession: GSM7186762 sample_title: 8323, LUSC, sRNA source_name: FFPE tissue characteristics: tissue: FFPE tissue; Sex: male; disease state: LUSC 8323, LUSC, sRNA controlled vocabulary controlled vocabulary primary tissue match: ffpe tissue
primary_tissue primary tissue sample GSM7186763 Runtime Siftome inference GEO:sample:GSM7186763:73f4a79f8f61d33e5cad47c6386ea89f932a6b88bb9a08612edfb423f7c4cb25 high confidence ffpe tissue sample_accession: GSM7186763 sample_title: 12545, LUSC, sRNA source_name: FFPE tissue characteristics: tissue: FFPE tissue; Sex: female; disease state: LUSC 12545, LUSC, sRNA controlled vocabulary controlled vocabulary primary tissue match: ffpe tissue
primary_tissue primary tissue sample GSM7186764 Runtime Siftome inference GEO:sample:GSM7186764:7eb45c781c8d6ffdb6a07195f88ffbfc6f49d878ef6793b5729d0b8ef3f59289 high confidence ffpe tissue sample_accession: GSM7186764 sample_title: 16734, LUSC, sRNA source_name: FFPE tissue characteristics: tissue: FFPE tissue; Sex: female; disease state: LUSC 16734, LUSC, sRNA controlled vocabulary controlled vocabulary primary tissue match: ffpe tissue
primary_tissue primary tissue sample GSM7186765 Runtime Siftome inference GEO:sample:GSM7186765:ef813400f2fa31ab81efb2bed1501a070a35896b66add85521f0de3ec7a9006c high confidence ffpe tissue sample_accession: GSM7186765 sample_title: 17664, LUSC, sRNA source_name: FFPE tissue characteristics: tissue: FFPE tissue; Sex: male; disease state: LUSC 17664, LUSC, sRNA controlled vocabulary controlled vocabulary primary tissue match: ffpe tissue
primary_tissue primary tissue sample GSM7186766 Runtime Siftome inference GEO:sample:GSM7186766:5a825505da661618155fba03b94d666ab0e50a96787b4c50293efaae4e2757b8 high confidence ffpe tissue sample_accession: GSM7186766 sample_title: 19694, LUSC, sRNA source_name: FFPE tissue characteristics: tissue: FFPE tissue; Sex: male; disease state: LUSC 19694, LUSC, sRNA controlled vocabulary controlled vocabulary primary tissue match: ffpe tissue
primary_tissue primary tissue sample GSM7186767 Runtime Siftome inference GEO:sample:GSM7186767:c329e36863eb1cbf2240e615ce53505c17448e58e5879de5352fa628907aac2c high confidence ffpe tissue sample_accession: GSM7186767 sample_title: 20432, LUSC, sRNA source_name: FFPE tissue characteristics: tissue: FFPE tissue; Sex: male; disease state: LUSC 20432, LUSC, sRNA controlled vocabulary controlled vocabulary primary tissue match: ffpe tissue
primary_tissue primary tissue sample GSM7186768 Runtime Siftome inference GEO:sample:GSM7186768:dade868c94584aceaff0399ae5ae6f0926a6dbc684d158f5767f24d614c2a9c7 high confidence ffpe tissue sample_accession: GSM7186768 sample_title: 21671, LUSC, sRNA source_name: FFPE tissue characteristics: tissue: FFPE tissue; Sex: male; disease state: LUSC 21671, LUSC, sRNA controlled vocabulary controlled vocabulary primary tissue match: ffpe tissue
primary_tissue primary tissue sample GSM7186769 Runtime Siftome inference GEO:sample:GSM7186769:4643b3aa7dd9fa9ae18421c3fe40fe0a6526601d4a6082d9dc84128da56808c5 high confidence ffpe tissue sample_accession: GSM7186769 sample_title: 25486, LUSC, sRNA source_name: FFPE tissue characteristics: tissue: FFPE tissue; Sex: male; disease state: LUSC 25486, LUSC, sRNA controlled vocabulary controlled vocabulary primary tissue match: ffpe tissue
primary_tissue primary tissue sample GSM7186770 Runtime Siftome inference GEO:sample:GSM7186770:ffc658b2162ff4e9fdaca3a2c42384b99770893aa08b314d977ed5d74b9c27c2 high confidence ffpe tissue sample_accession: GSM7186770 sample_title: 25609, LUSC, sRNA source_name: FFPE tissue characteristics: tissue: FFPE tissue; Sex: male; disease state: LUSC 25609, LUSC, sRNA controlled vocabulary controlled vocabulary primary tissue match: ffpe tissue
primary_tissue primary tissue sample GSM7186771 Runtime Siftome inference GEO:sample:GSM7186771:62400888377adffcacdb09d9bab66d5f1c1e1688faa4ce773d6119c6d2d54b9a high confidence ffpe tissue sample_accession: GSM7186771 sample_title: 25850, LUSC, sRNA source_name: FFPE tissue characteristics: tissue: FFPE tissue; Sex: male; disease state: LUSC 25850, LUSC, sRNA controlled vocabulary controlled vocabulary primary tissue match: ffpe tissue
sample_type normal tissue sample GSM7186754 Runtime Siftome inference GEO:sample:GSM7186754:226dff41feaf3c73a77379f608bb985d481c3ae5d669cdf336aba5928516d7f6 high confidence healthy control sample_accession: GSM7186754 sample_title: 2, healthy control, sRNA source_name: FFPE tissue characteristics: tissue: FFPE tissue; Sex: male; disease state: healthy control 2, h... controlled vocabulary controlled vocabulary sample type match: healthy control
sample_type normal tissue sample GSM7186755 Runtime Siftome inference GEO:sample:GSM7186755:d2f30a8a7627cb68d47aa062337f3b02c55610c1bd9a175d501db27d6c23c0bd high confidence healthy control sample_accession: GSM7186755 sample_title: 28, healthy control, sRNA source_name: FFPE tissue characteristics: tissue: FFPE tissue; Sex: male; disease state: healthy control 28,... controlled vocabulary controlled vocabulary sample type match: healthy control
sample_type normal tissue sample GSM7186756 Runtime Siftome inference GEO:sample:GSM7186756:f35037b219e68e4fec61d4c5340759790047e44bd694b7b8b232b638f09ee3f0 high confidence healthy control sample_accession: GSM7186756 sample_title: 44, healthy control, sRNA source_name: FFPE tissue characteristics: tissue: FFPE tissue; Sex: male; disease state: healthy control 44,... controlled vocabulary controlled vocabulary sample type match: healthy control
sample_type normal tissue sample GSM7186757 Runtime Siftome inference GEO:sample:GSM7186757:78c24dda1e6674991ff84ba5badfc6f7bd7c5a57cdd6aaaf463dd43092b2d9d1 high confidence healthy control sample_accession: GSM7186757 sample_title: 55, healthy control, sRNA source_name: FFPE tissue characteristics: tissue: FFPE tissue; Sex: male; disease state: healthy control 55,... controlled vocabulary controlled vocabulary sample type match: healthy control
tissue lung dataset GSE230087 Runtime Siftome inference GEO:dataset:GSE230087:a398577256835b270eb66a6d1bf39b457ca24d679510b131e03df835c04b86e7 low confidence lung dataset_accession: GSE230087 dataset_title: Identification of prognostic biomarkers in early stage squamous cell lung cancer (LUSC) by transcriptomic and miRNA profiling [sRNA-S... controlled vocabulary controlled vocabulary tissue match: lung

Sample Group Preview

Possible case samples

Samples currently treated as the comparison case group.

14
  • GSM7186758 3260, LUSC, sRNA lung cancer Case marker detected. FFPE tissue tissue: FFPE tissue; Sex: male; disease state: LUSC
  • GSM7186759 4613, LUSC, sRNA lung cancer Case marker detected. FFPE tissue tissue: FFPE tissue; Sex: male; disease state: LUSC
  • GSM7186760 4737, LUSC, sRNA lung cancer Case marker detected. FFPE tissue tissue: FFPE tissue; Sex: male; disease state: LUSC
  • GSM7186761 7202, LUSC, sRNA lung cancer Case marker detected. FFPE tissue tissue: FFPE tissue; Sex: male; disease state: LUSC
  • GSM7186762 8323, LUSC, sRNA lung cancer Case marker detected. FFPE tissue tissue: FFPE tissue; Sex: male; disease state: LUSC
  • GSM7186763 12545, LUSC, sRNA lung cancer Case marker detected. FFPE tissue tissue: FFPE tissue; Sex: female; disease state: LUSC
  • GSM7186764 16734, LUSC, sRNA lung cancer Case marker detected. FFPE tissue tissue: FFPE tissue; Sex: female; disease state: LUSC
  • GSM7186765 17664, LUSC, sRNA lung cancer Case marker detected. FFPE tissue tissue: FFPE tissue; Sex: male; disease state: LUSC
  • GSM7186766 19694, LUSC, sRNA lung cancer Case marker detected. FFPE tissue tissue: FFPE tissue; Sex: male; disease state: LUSC
  • GSM7186767 20432, LUSC, sRNA lung cancer Case marker detected. FFPE tissue tissue: FFPE tissue; Sex: male; disease state: LUSC
  • GSM7186768 21671, LUSC, sRNA lung cancer Case marker detected. FFPE tissue tissue: FFPE tissue; Sex: male; disease state: LUSC
  • GSM7186769 25486, LUSC, sRNA lung cancer Case marker detected. FFPE tissue tissue: FFPE tissue; Sex: male; disease state: LUSC
  • GSM7186770 25609, LUSC, sRNA lung cancer Case marker detected. FFPE tissue tissue: FFPE tissue; Sex: male; disease state: LUSC
  • GSM7186771 25850, LUSC, sRNA lung cancer Case marker detected. FFPE tissue tissue: FFPE tissue; Sex: male; disease state: LUSC

Possible control samples

Samples currently treated as controls or baseline.

4
  • GSM7186754 2, healthy control, sRNA normal tissue Control marker detected. FFPE tissue tissue: FFPE tissue; Sex: male; disease state: healthy control
  • GSM7186755 28, healthy control, sRNA normal tissue Control marker detected. FFPE tissue tissue: FFPE tissue; Sex: male; disease state: healthy control
  • GSM7186756 44, healthy control, sRNA normal tissue Control marker detected. FFPE tissue tissue: FFPE tissue; Sex: male; disease state: healthy control
  • GSM7186757 55, healthy control, sRNA normal tissue Control marker detected. FFPE tissue tissue: FFPE tissue; Sex: male; disease state: healthy control

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

4 samples
  • GSM7186754 2, healthy control, sRNA FFPE tissue tissue: FFPE tissue; Sex: male; disease state: healthy control
  • GSM7186755 28, healthy control, sRNA FFPE tissue tissue: FFPE tissue; Sex: male; disease state: healthy control
  • GSM7186756 44, healthy control, sRNA FFPE tissue tissue: FFPE tissue; Sex: male; disease state: healthy control
  • GSM7186757 55, healthy control, sRNA FFPE tissue tissue: FFPE tissue; Sex: male; disease state: healthy control

lung cancer

14 samples
  • GSM7186758 3260, LUSC, sRNA FFPE tissue tissue: FFPE tissue; Sex: male; disease state: LUSC
  • GSM7186759 4613, LUSC, sRNA FFPE tissue tissue: FFPE tissue; Sex: male; disease state: LUSC
  • GSM7186760 4737, LUSC, sRNA FFPE tissue tissue: FFPE tissue; Sex: male; disease state: LUSC
  • GSM7186761 7202, LUSC, sRNA FFPE tissue tissue: FFPE tissue; Sex: male; disease state: LUSC
  • GSM7186762 8323, LUSC, sRNA FFPE tissue tissue: FFPE tissue; Sex: male; disease state: LUSC
  • GSM7186763 12545, LUSC, sRNA FFPE tissue tissue: FFPE tissue; Sex: female; disease state: LUSC
  • GSM7186764 16734, LUSC, sRNA FFPE tissue tissue: FFPE tissue; Sex: female; disease state: LUSC
  • GSM7186765 17664, LUSC, sRNA FFPE tissue tissue: FFPE tissue; Sex: male; disease state: LUSC
  • GSM7186766 19694, LUSC, sRNA FFPE tissue tissue: FFPE tissue; Sex: male; disease state: LUSC
  • GSM7186767 20432, LUSC, sRNA FFPE tissue tissue: FFPE tissue; Sex: male; disease state: LUSC
  • GSM7186768 21671, LUSC, sRNA FFPE tissue tissue: FFPE tissue; Sex: male; disease state: LUSC
  • GSM7186769 25486, LUSC, sRNA FFPE tissue tissue: FFPE tissue; Sex: male; disease state: LUSC
  • GSM7186770 25609, LUSC, sRNA FFPE tissue tissue: FFPE tissue; Sex: male; disease state: LUSC
  • GSM7186771 25850, LUSC, sRNA FFPE tissue tissue: FFPE tissue; Sex: male; disease state: LUSC

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: lung cancer vs normal tissue.
  • No excluded sample type flags detected.
  • Control type metadata detected.
  • Tumor/normal design boosted for colorectal tumor-vs-normal tissue triage.
  • Patient tissue or biopsy specimens boosted for tissue comparison triage.
  • Small RNA, miRNA, circRNA, or extracellular-vesicle RNA context downgraded for primary mRNA tissue ranking.
  • 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 secondary RNA assays are not primary mRNA tissue RNA-seq.
  • Overall score capped because tumor/normal grouping is from a non-colorectal cancer context.

Sample Links

18 samples

Review Audit Trail

0 decisions

No review decisions have been stored for this dataset.