Siftome Phase 3L

GSE32424

Identification of a Novel Angiogenesis and Tumor Suppressor Gene Rab25 in Esophageal Squamous Cell Carcinoma

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
2011-09-27
Last update
2019-05-15
Organization
University of Notre Dame
Department
Not available
Public date
2012-12-05
Experiment types
Expression profiling by high throughput sequencing
Platforms
GPL10999 Illumina Genome Analyzer IIx (Homo sapiens)
Series type
Series
SubSeries
Not available
BioProject
PRJNA147913
Supplementary files
TAR: GSE32424_RAW.tar; TXT: GSE32424_RPKM.txt.gz
Organism
Homo sapiens
Assay
bulk RNA-seq
Samples
12
Study design
Tumor vs unmatched normal
Specimen/source
Tissue
Scoring version
intent-aware-scoring-v15
Ranking batch
9c08145d0461e1fec7a4077ea17c91ea89b2eb7a2e58866d66ed05bdfdb1d938
Ranking created
2026-06-06T05:53:35.566009Z
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
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

No readiness blockers detected.

Next Steps

  • Review the sample grouping CSV and contrast CSV before running differential expression.
  • Confirm processed count files and sample identifiers match the exported metadata.

Analysis Preparation Checklist

5/6 ready

Group labels reviewed

Needs review

Siftome proposed case and control labels, but no reviewer confirmation is stored yet.

Open the sample grouping CSV and confirm group labels before analysis.

Minimum sample count met

Ready

Both groups meet the minimum of 2 samples.

Confirm whether the cohort is large enough for the intended statistical analysis.

Processed counts available

Ready

Processed data availability is marked true in the GEO index.

Verify that downloaded processed files contain usable count or expression identifiers.

Ambiguous samples handled

Ready

No review-needed or unassigned samples are present in the proposed grouping.

Still scan the grouping table for biology-specific ambiguity.

Exclusion decisions recorded

Ready

No hard-excluded samples were detected by the current rules.

Record any manual exclusions in the downstream analysis notes.

Source links preserved

Ready

The dataset and sample accessions can be linked back to GEO.

Keep GEO dataset and sample links with exported metadata.

Bioinformatician Review

Standard analyst review

Proceed only after the analyst confirms grouping, exclusions, and source files.

No expert-review triggers were detected by Siftome.

Why This Is Ranked Here

Patient tissue tumor-vs-normal
Not suitable Dataset does not meet the current suitability threshold.

Score Components

  • relevance 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 7 samples
  • Likely control group normal tissue 5 samples

Warnings

  • 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 2 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 2 warnings require review. Contributed to match or upgrade 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
GSE32424
Sample records
12 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
GSE32424
  • 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
GSE32424
  • 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
GSE32424
  • 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: GSE32424
dataset_title: Identification of a Novel Angiogenesis and Tumor Suppressor Gene   Rab25 in Esophageal Squamous Cell Carcinoma
organism: Homo sapiens
assay_type: bulk RNA-seq
processed_data_available: true
raw_data_available: true
submission_date: 2011-09-27
last_update_date: 2019-05-15
organization_name: University of Notre Dame
department: Not available
public_date: 2012-12-05
experiment_types: Expression profiling by high throughput sequencing
platforms: GPL10999 Illumina Genome Analyzer IIx (Homo sapiens)
sub_series: Not available
bioproject: PRJNA147913
supplementary_files: TAR: GSE32424_RAW.tar; TXT: GSE32424_RPKM.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.
  • 2 warnings require review.

Why It May Not Be Suitable

  • 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 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

14 fields
Field Value Source Origin Confidence Evidence Reason
assay_type bulk RNA-seq dataset GSE32424 Runtime Siftome inference GEO:dataset:GSE32424:48f6f4bdd817415afd58e12cf9fafa3feb6865db0fb02243a69b32ef0f603c61 high confidence bulk rna-seq dataset_accession: GSE32424 dataset_title: Identification of a Novel Angiogenesis and Tumor Suppressor Gene Rab25 in Esophageal Squamous Cell Carcinoma organism: Homo sapiens as... keyword match keyword match: bulk rna-seq
organism Homo sapiens dataset GSE32424 Runtime Siftome inference GEO:dataset:GSE32424:48f6f4bdd817415afd58e12cf9fafa3feb6865db0fb02243a69b32ef0f603c61 high confidence homo sapiens dataset_accession: GSE32424 dataset_title: Identification of a Novel Angiogenesis and Tumor Suppressor Gene Rab25 in Esophageal Squamous Cell Carcinoma organism: Homo sapiens as... keyword match keyword match: homo sapiens
sample_type tumor sample sample GSM802457 Runtime Siftome inference GEO:sample:GSM802457:9f8ad6d395c322e4eb20d1219bb7a819bf3f871504a3f23c6da766553ca46bcb low confidence tumor sample_accession: GSM802457 sample_title: Tumor sample 1T source_name: esophageal cell type characteristics: tissue: tumor Tumor sample 1T controlled vocabulary controlled vocabulary sample type match: tumor
sample_type tumor sample sample GSM802458 Runtime Siftome inference GEO:sample:GSM802458:8180cb807000d2df84e76779bb95b62579c446e3cfbf39caaee34998cf9cc357 low confidence tumor sample_accession: GSM802458 sample_title: Tumor sample 2T source_name: esophageal cell type characteristics: tissue: tumor Tumor sample 2T controlled vocabulary controlled vocabulary sample type match: tumor
sample_type tumor sample sample GSM802459 Runtime Siftome inference GEO:sample:GSM802459:9c0cd79b80d1da28e2f2fb5690358143d8d370181334a586544a93bee1c64c0e low confidence tumor sample_accession: GSM802459 sample_title: Tumor sample 3T source_name: esophageal cell type characteristics: tissue: tumor Tumor sample 3T controlled vocabulary controlled vocabulary sample type match: tumor
sample_type tumor sample sample GSM802460 Runtime Siftome inference GEO:sample:GSM802460:59827e65a047964bbbf17002e248cfebab677cf1d9346d2bdba62f6e87238f79 low confidence tumor sample_accession: GSM802460 sample_title: Tumor sample 6T source_name: esophageal cell type characteristics: tissue: tumor Tumor sample 6T controlled vocabulary controlled vocabulary sample type match: tumor
sample_type tumor sample sample GSM802461 Runtime Siftome inference GEO:sample:GSM802461:f2e800cdb0938e789fa4d2b018bc32dd8802bebf51f2948bf49a287d54085575 low confidence tumor sample_accession: GSM802461 sample_title: Tumor sample 7T source_name: esophageal cell type characteristics: tissue: tumor Tumor sample 7T controlled vocabulary controlled vocabulary sample type match: tumor
sample_type tumor sample sample GSM802462 Runtime Siftome inference GEO:sample:GSM802462:b70d6f8fb2bb315cab050694f4761e59fce69b1d890f0cb3d71d979c77bc57b5 low confidence tumor sample_accession: GSM802462 sample_title: Tumor sample 8T source_name: esophageal cell type characteristics: tissue: tumor Tumor sample 8T controlled vocabulary controlled vocabulary sample type match: tumor
sample_type tumor sample sample GSM802463 Runtime Siftome inference GEO:sample:GSM802463:06d3aff904cfcae42ef616259f69f9c367085ed7d2a0938f9f25732b936b5901 low confidence tumor sample_accession: GSM802463 sample_title: Tumor sample 9T source_name: esophageal cell type characteristics: tissue: tumor Tumor sample 9T controlled vocabulary controlled vocabulary sample type match: tumor
sample_type normal tissue sample GSM802464 Runtime Siftome inference GEO:sample:GSM802464:4c649441a92b0ace7f5162ab29ea3e252f4c23008202142cfd1db4bc65c8883b medium confidence non-tumor sample_accession: GSM802464 sample_title: Non-tumor sample 4N source_name: esophageal cell type characteristics: tissue: non-tumor Non-tumor sample 4N controlled vocabulary controlled vocabulary sample type match: non-tumor
sample_type normal tissue sample GSM802465 Runtime Siftome inference GEO:sample:GSM802465:118cc09bc9e69c4a6790ade41863ce803e30f6efd42c3f0e32167614f023b38e medium confidence non-tumor sample_accession: GSM802465 sample_title: Non-tumor sample 5N source_name: esophageal cell type characteristics: tissue: non-tumor Non-tumor sample 5N controlled vocabulary controlled vocabulary sample type match: non-tumor
sample_type normal tissue sample GSM802466 Runtime Siftome inference GEO:sample:GSM802466:242d59bb970627df1411ac2d7e03023b0b5c52f74aa70390239a83b01aa89e7f medium confidence non-tumor sample_accession: GSM802466 sample_title: Non-tumor sample 6N source_name: esophageal cell type characteristics: tissue: non-tumor Non-tumor sample 6N controlled vocabulary controlled vocabulary sample type match: non-tumor
sample_type normal tissue sample GSM802467 Runtime Siftome inference GEO:sample:GSM802467:076f08e1f35a047e3540b6f483b891e7b05d4d74dfe800f87572c8598d372088 medium confidence non-tumor sample_accession: GSM802467 sample_title: Non-tumor sample 8N source_name: esophageal cell type characteristics: tissue: non-tumor Non-tumor sample 8N controlled vocabulary controlled vocabulary sample type match: non-tumor
sample_type normal tissue sample GSM802468 Runtime Siftome inference GEO:sample:GSM802468:423d632ceffae3d5cc68281a14f4ab9f6a23faac6052b29528d5ea4e1e217a48 medium confidence non-tumor sample_accession: GSM802468 sample_title: Non-tumor sample 9N source_name: esophageal cell type characteristics: tissue: non-tumor Non-tumor sample 9N controlled vocabulary controlled vocabulary sample type match: non-tumor

Sample Group Preview

Possible case samples

Samples currently treated as the comparison case group.

7
  • GSM802457 Tumor sample 1T tumor sample Case marker detected. esophageal cell type tissue: tumor
  • GSM802458 Tumor sample 2T tumor sample Case marker detected. esophageal cell type tissue: tumor
  • GSM802459 Tumor sample 3T tumor sample Case marker detected. esophageal cell type tissue: tumor
  • GSM802460 Tumor sample 6T tumor sample Case marker detected. esophageal cell type tissue: tumor
  • GSM802461 Tumor sample 7T tumor sample Case marker detected. esophageal cell type tissue: tumor
  • GSM802462 Tumor sample 8T tumor sample Case marker detected. esophageal cell type tissue: tumor
  • GSM802463 Tumor sample 9T tumor sample Case marker detected. esophageal cell type tissue: tumor

Possible control samples

Samples currently treated as controls or baseline.

5
  • GSM802464 Non-tumor sample 4N normal tissue Control marker detected. esophageal cell type tissue: non-tumor
  • GSM802465 Non-tumor sample 5N normal tissue Control marker detected. esophageal cell type tissue: non-tumor
  • GSM802466 Non-tumor sample 6N normal tissue Control marker detected. esophageal cell type tissue: non-tumor
  • GSM802467 Non-tumor sample 8N normal tissue Control marker detected. esophageal cell type tissue: non-tumor
  • GSM802468 Non-tumor sample 9N normal tissue Control marker detected. esophageal cell type tissue: 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

7 samples
  • GSM802457 Tumor sample 1T esophageal cell type tissue: tumor
  • GSM802458 Tumor sample 2T esophageal cell type tissue: tumor
  • GSM802459 Tumor sample 3T esophageal cell type tissue: tumor
  • GSM802460 Tumor sample 6T esophageal cell type tissue: tumor
  • GSM802461 Tumor sample 7T esophageal cell type tissue: tumor
  • GSM802462 Tumor sample 8T esophageal cell type tissue: tumor
  • GSM802463 Tumor sample 9T esophageal cell type tissue: tumor

normal tissue

5 samples
  • GSM802464 Non-tumor sample 4N esophageal cell type tissue: non-tumor
  • GSM802465 Non-tumor sample 5N esophageal cell type tissue: non-tumor
  • GSM802466 Non-tumor sample 6N esophageal cell type tissue: non-tumor
  • GSM802467 Non-tumor sample 8N esophageal cell type tissue: non-tumor
  • GSM802468 Non-tumor sample 9N esophageal cell type tissue: 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

12 samples

Review Audit Trail

0 decisions

No review decisions have been stored for this dataset.