Siftome Phase 3L

GSE190079

Noncoding RNA expression profiles in five pairs of bladder cancer tumor tissues and matched adjacent non-tumor tissues

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
2021-12-03
Last update
2023-01-04
Organization
The Second Hospital of Shandong University
Department
Not available
Public date
2023-01-04
Experiment types
Non-coding RNA profiling by high throughput sequencing
Platforms
GPL20301 Illumina HiSeq 4000 (Homo sapiens)
Series type
Series
SubSeries
Not available
BioProject
PRJNA785791
Supplementary files
XLSX: GSE190079_circRNA_expression.xlsx; TXT: GSE190079_isoforms_fpkm_expression.txt.gz
Organism
Homo sapiens
Assay
bulk RNA-seq
Samples
10
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
94% 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

7/10 pts

Metadata quality is usable, but still deserves review.

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 50% Organism normalized. Assay type 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 70% 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 was not normalized. Tissue clarity: Tissue metadata was not normalized. Treatment clarity: No unclear treatment split detected in the sample metadata. Replicate clarity: No pooled sample or technical replicate flags detected. Data availability clarity: Dataset-level processed or raw data availability is explicit.
  • data availability 100% Processed data available. Raw data available.
  • overall 34% Weighted score: 30% relevance, 30% comparison suitability, 25% metadata quality, 15% data availability. Overall score capped because comparison suitability is weak for the selected search intent. Overall score capped because tumor/normal grouping is from a non-colorectal cancer context.

Derived Classifications

  • Organism Homo sapiens Organism remains rule-derived: Homo sapiens.
  • Assay bulk RNA-seq Assay remains rule-derived: bulk RNA-seq.
  • Study design Tumor vs unmatched normal Study design remains rule-derived: Tumor vs unmatched normal.
  • Specimen/source Tissue Specimen/source remains rule-derived: Tissue.
  • Likely case group tumor sample 5 samples
  • Likely control group normal tissue 5 samples

Warnings

  • SECONDARY_ASSAY_CONTEXT warning Secondary RNA assay context such as small RNA, miRNA, circRNA, or non-coding RNA was detected.
  • DISEASE_LABEL_UNCLEAR warning Disease or condition label could not be normalized.
  • TISSUE_TYPE_MISSING warning Tissue or cell type could not be normalized.

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 3 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.
  • Supporting fact 3 warnings 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 Disease or condition label could not be normalized. Contributed to downgrade or manual-review evidence.
  • Caution fact Tissue or cell type could not be normalized. 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: Disease clarity: Disease or condition metadata was not normalized. Contributed to downgrade or manual-review evidence.
  • Caution fact Missing or unclear metadata: Tissue clarity: Tissue metadata was not normalized. Contributed to downgrade or manual-review evidence.
  • Caution fact Missing or unclear metadata: Treatment clarity: No unclear treatment split detected in the sample metadata. Contributed to downgrade or manual-review evidence.
  • Caution fact Overall score capped because comparison suitability is weak for the selected search intent. Contributed to downgrade or manual-review evidence.
  • Caution fact Overall score capped because tumor/normal grouping is from a non-colorectal cancer context. Contributed to downgrade or manual-review evidence.
  • Caution fact Downgraded disease context: not a colorectal/GI cancer cohort. Contributed to downgrade or manual-review evidence.
  • Caution fact Comparison suitability score is below the Phase 1 recommended threshold. Contributed to downgrade or manual-review evidence.

Manual Corrections

0 active

Source Evidence

4 sources

GEO

Primary source

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

Dataset accession
GSE190079
Sample records
10 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
GSE190079
  • 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
GSE190079
  • 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
GSE190079
  • 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: GSE190079
dataset_title: Noncoding RNA expression profiles in five pairs of bladder cancer tumor tissues and matched adjacent non-tumor tissues
organism: Homo sapiens
assay_type: bulk RNA-seq
processed_data_available: true
raw_data_available: true
submission_date: 2021-12-03
last_update_date: 2023-01-04
organization_name: The Second Hospital of Shandong University
department: Not available
public_date: 2023-01-04
experiment_types: Non-coding RNA profiling by high throughput sequencing
platforms: GPL20301 Illumina HiSeq 4000 (Homo sapiens)
sub_series: Not available
bioproject: PRJNA785791
supplementary_files: XLSX: GSE190079_circRNA_expression.xlsx; TXT: GSE190079_isoforms_fpkm_expression.txt.gz
series_type: Series

Why It Matched

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

Why It May Not Be Suitable

  • Secondary RNA assay context such as small RNA, miRNA, circRNA, or non-coding RNA was detected.
  • Disease or condition label could not be normalized.
  • Tissue or cell type could not be normalized.
  • Non-colorectal cancer context downgraded for colorectal tumor-vs-normal tissue ranking.
  • Missing or unclear metadata: Disease clarity: Disease or condition metadata was not normalized.
  • Missing or unclear metadata: Tissue clarity: Tissue metadata was not normalized.
  • Missing or unclear metadata: Treatment clarity: No unclear treatment split detected in the sample metadata.
  • Overall score capped because comparison suitability is weak for the selected search intent.
  • Overall score capped because tumor/normal grouping is from a non-colorectal cancer context.
  • Downgraded disease context: not a colorectal/GI cancer cohort.
  • Comparison suitability score is below the Phase 1 recommended threshold.

Warnings

  • warning SECONDARY_ASSAY_CONTEXT Secondary RNA assay context such as small RNA, miRNA, circRNA, or non-coding RNA was detected.
  • warning DISEASE_LABEL_UNCLEAR Disease or condition label could not be normalized.
  • warning TISSUE_TYPE_MISSING Tissue or cell type could not be normalized.

Normalized Fields

12 fields
Field Value Source Origin Confidence Evidence Reason
assay_type bulk RNA-seq dataset GSE190079 Runtime Siftome inference GEO:dataset:GSE190079:b2398a343108523934c5d1f5eb0519aa7fd337b09b8d2abda94265f312e4e358 high confidence bulk rna-seq dataset_accession: GSE190079 dataset_title: Noncoding RNA expression profiles in five pairs of bladder cancer tumor tissues and matched adjacent non-tumor tissues organism: Homo... keyword match keyword match: bulk rna-seq
organism Homo sapiens dataset GSE190079 Runtime Siftome inference GEO:dataset:GSE190079:b2398a343108523934c5d1f5eb0519aa7fd337b09b8d2abda94265f312e4e358 high confidence homo sapiens dataset_accession: GSE190079 dataset_title: Noncoding RNA expression profiles in five pairs of bladder cancer tumor tissues and matched adjacent non-tumor tissues organism: Homo... keyword match keyword match: homo sapiens
sample_type tumor sample sample GSM5712881 Runtime Siftome inference GEO:sample:GSM5712881:c00c734c24e38ecf3e10b8b0031688be64aeca3b17464f6a04f1479c6957f4c8 low confidence tumor sample_accession: GSM5712881 sample_title: Bladder cancer tumor tissue-BC_35 source_name: bladder cancer tissue characteristics: tissue: bladder cancer Bladder cancer tumor tiss... controlled vocabulary controlled vocabulary sample type match: tumor
sample_type tumor sample sample GSM5712882 Runtime Siftome inference GEO:sample:GSM5712882:13109421715e7ab62c3fd97b48a247a42c3fffd22b7576e6fcdc2e0efec5be57 low confidence tumor sample_accession: GSM5712882 sample_title: Bladder cancer tumor tissue-BC_36 source_name: bladder cancer tissue characteristics: tissue: bladder cancer Bladder cancer tumor tiss... controlled vocabulary controlled vocabulary sample type match: tumor
sample_type tumor sample sample GSM5712883 Runtime Siftome inference GEO:sample:GSM5712883:a9e39114db6cf69bdb723ffee4609fb20965aedf44c29b7b9050a58c8802eba5 low confidence tumor sample_accession: GSM5712883 sample_title: Bladder cancer tumor tissue-BC_40 source_name: bladder cancer tissue characteristics: tissue: bladder cancer Bladder cancer tumor tiss... controlled vocabulary controlled vocabulary sample type match: tumor
sample_type tumor sample sample GSM5712884 Runtime Siftome inference GEO:sample:GSM5712884:a97410e381087d5b813e0247a1343b7252cfb6dedcd154407baa60f59f12d3f3 low confidence tumor sample_accession: GSM5712884 sample_title: Bladder cancer tumor tissue-BC_42 source_name: bladder cancer tissue characteristics: tissue: bladder cancer Bladder cancer tumor tiss... controlled vocabulary controlled vocabulary sample type match: tumor
sample_type tumor sample sample GSM5712885 Runtime Siftome inference GEO:sample:GSM5712885:a7801f1c6dc89ed31ce2c5699fe0d585b0c87b4d31d7dd4dc8faabacce6fe137 low confidence tumor sample_accession: GSM5712885 sample_title: Bladder cancer tumor tissue-BC_43 source_name: bladder cancer tissue characteristics: tissue: bladder cancer Bladder cancer tumor tiss... controlled vocabulary controlled vocabulary sample type match: tumor
sample_type normal tissue sample GSM5712886 Runtime Siftome inference GEO:sample:GSM5712886:1967fc9978f94ca8c215d09c43717b67520ff53066f3e4191864926fd2f77393 medium confidence non-tumor sample_accession: GSM5712886 sample_title: Adjacant non-tumor tissue-Ctrl_35 source_name: adjacent non-tumor tissue characteristics: tissue: adjacent non-tumor Adjacant non-tumo... controlled vocabulary controlled vocabulary sample type match: non-tumor
sample_type normal tissue sample GSM5712887 Runtime Siftome inference GEO:sample:GSM5712887:0b080b81fa46ce8bbdf9e91a59bfc4fb5b179d3a57ca45f25c91e2b3d96a0ea5 medium confidence non-tumor sample_accession: GSM5712887 sample_title: Adjacant non-tumor tissue-Ctrl_36 source_name: adjacent non-tumor tissue characteristics: tissue: adjacent non-tumor Adjacant non-tumo... controlled vocabulary controlled vocabulary sample type match: non-tumor
sample_type normal tissue sample GSM5712888 Runtime Siftome inference GEO:sample:GSM5712888:94184782169385c056ffc23b8b4515191622950c827ffeb2411c71f245d195d3 medium confidence non-tumor sample_accession: GSM5712888 sample_title: Adjacant non-tumor tissue-Ctrl_40 source_name: adjacent non-tumor tissue characteristics: tissue: adjacent non-tumor Adjacant non-tumo... controlled vocabulary controlled vocabulary sample type match: non-tumor
sample_type normal tissue sample GSM5712889 Runtime Siftome inference GEO:sample:GSM5712889:1bbe0a54859c47e80bc749e82fd7b20a63d77931d69d1187a75d4ba5df6cc93b medium confidence non-tumor sample_accession: GSM5712889 sample_title: Adjacant non-tumor tissue-Ctrl_42 source_name: adjacent non-tumor tissue characteristics: tissue: adjacent non-tumor Adjacant non-tumo... controlled vocabulary controlled vocabulary sample type match: non-tumor
sample_type normal tissue sample GSM5712890 Runtime Siftome inference GEO:sample:GSM5712890:66fd424a9c850424b112adfb981399ce4bfd704a393f268301747a2c99982323 medium confidence non-tumor sample_accession: GSM5712890 sample_title: Adjacant non-tumor tissue-Ctrl_43 source_name: adjacent non-tumor tissue characteristics: tissue: adjacent non-tumor Adjacant non-tumo... controlled vocabulary controlled vocabulary sample type match: non-tumor

Sample Group Preview

Possible case samples

Samples currently treated as the comparison case group.

5
  • GSM5712881 Bladder cancer tumor tissue-BC_35 tumor sample Case marker detected. bladder cancer tissue tissue: bladder cancer
  • GSM5712882 Bladder cancer tumor tissue-BC_36 tumor sample Case marker detected. bladder cancer tissue tissue: bladder cancer
  • GSM5712883 Bladder cancer tumor tissue-BC_40 tumor sample Case marker detected. bladder cancer tissue tissue: bladder cancer
  • GSM5712884 Bladder cancer tumor tissue-BC_42 tumor sample Case marker detected. bladder cancer tissue tissue: bladder cancer
  • GSM5712885 Bladder cancer tumor tissue-BC_43 tumor sample Case marker detected. bladder cancer tissue tissue: bladder cancer

Possible control samples

Samples currently treated as controls or baseline.

5
  • GSM5712886 Adjacant non-tumor tissue-Ctrl_35 normal tissue Control marker detected. adjacent non-tumor tissue tissue: adjacent non-tumor
  • GSM5712887 Adjacant non-tumor tissue-Ctrl_36 normal tissue Control marker detected. adjacent non-tumor tissue tissue: adjacent non-tumor
  • GSM5712888 Adjacant non-tumor tissue-Ctrl_40 normal tissue Control marker detected. adjacent non-tumor tissue tissue: adjacent non-tumor
  • GSM5712889 Adjacant non-tumor tissue-Ctrl_42 normal tissue Control marker detected. adjacent non-tumor tissue tissue: adjacent non-tumor
  • GSM5712890 Adjacant non-tumor tissue-Ctrl_43 normal tissue Control marker detected. adjacent non-tumor tissue tissue: adjacent non-tumor

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

70 pts
Clarity
70%
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 was not normalized. Tissue clarity: Tissue metadata was not normalized. Treatment clarity: No unclear treatment split detected in the sample metadata. Replicate clarity: No pooled sample or technical replicate flags detected. Data availability clarity: Dataset-level processed or raw data availability is explicit.

Detected Sample Groups

tumor sample

5 samples
  • GSM5712881 Bladder cancer tumor tissue-BC_35 bladder cancer tissue tissue: bladder cancer
  • GSM5712882 Bladder cancer tumor tissue-BC_36 bladder cancer tissue tissue: bladder cancer
  • GSM5712883 Bladder cancer tumor tissue-BC_40 bladder cancer tissue tissue: bladder cancer
  • GSM5712884 Bladder cancer tumor tissue-BC_42 bladder cancer tissue tissue: bladder cancer
  • GSM5712885 Bladder cancer tumor tissue-BC_43 bladder cancer tissue tissue: bladder cancer

normal tissue

5 samples
  • GSM5712886 Adjacant non-tumor tissue-Ctrl_35 adjacent non-tumor tissue tissue: adjacent non-tumor
  • GSM5712887 Adjacant non-tumor tissue-Ctrl_36 adjacent non-tumor tissue tissue: adjacent non-tumor
  • GSM5712888 Adjacant non-tumor tissue-Ctrl_40 adjacent non-tumor tissue tissue: adjacent non-tumor
  • GSM5712889 Adjacant non-tumor tissue-Ctrl_42 adjacent non-tumor tissue tissue: adjacent non-tumor
  • GSM5712890 Adjacant non-tumor tissue-Ctrl_43 adjacent non-tumor tissue tissue: adjacent non-tumor

Score Breakdown

50%

relevance

  • Organism normalized.
  • Assay type 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.
70%

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 was not normalized.
  • Tissue clarity: Tissue metadata was not normalized.
  • Treatment clarity: No unclear treatment split detected in the sample metadata.
  • Replicate clarity: No pooled sample or technical replicate flags detected.
  • Data availability clarity: Dataset-level processed or raw data availability is explicit.
100%

data availability

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

overall

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

Sample Links

10 samples

Review Audit Trail

0 decisions

No review decisions have been stored for this dataset.