Siftome Phase 3L

GSE57401

Transcriptome analysis of human reninomas as an approach to understanding juxtaglomerular cell biology

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
2014-05-07
Last update
2019-05-15
Organization
IRCM
Department
Labo Dr Reudelhuber
Public date
2018-02-15
Experiment types
Expression profiling by high throughput sequencing
Platforms
GPL11154 Illumina HiSeq 2000 (Homo sapiens)
Series type
Series
SubSeries
Not available
BioProject
PRJNA246396
Supplementary files
TAR: GSE57401_RAW.tar
Organism
Homo sapiens
Assay
bulk RNA-seq
Samples
8
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
82% DE readiness

Contrast completeness

25/25 pts

Both case and control groups are present in the proposed grouping.

Minimum group size

8/20 pts

A contrast exists, but at least one group is below the minimum sample count.

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

  • At least one contrast group is below the minimum sample count.

Next Steps

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

Analysis Preparation Checklist

4/6 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

Blocked

At least one group has fewer than 2 samples.

Choose a larger dataset or merge only scientifically valid groups.

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.
  • Analysis preparation checklist contains blocked items.
  • At least one comparison group has fewer than two samples.

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 50% Organism normalized. Assay type normalized.
  • comparison suitability 5% 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. Missing colorectal disease context downgraded for 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 45% Weighted score: 30% relevance, 30% comparison suitability, 25% metadata quality, 15% data availability. Overall score capped because comparison suitability is weak for the selected search intent. Overall score capped because fewer than ten samples limit cohort confidence. Overall score capped because colorectal/CRC disease context is not explicit.

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 1 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: colorectal/GI relevance is unclear. 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 5%. 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: colorectal/GI relevance is unclear. 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 Missing colorectal disease context downgraded for tumor-vs-normal tissue ranking. Contributed to downgrade or manual-review evidence.
  • Caution fact Missing or unclear metadata: Missing colorectal disease context downgraded for 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 fewer than ten samples limit cohort confidence. Contributed to downgrade or manual-review evidence.
  • Caution fact Overall score capped because colorectal/CRC disease context is not explicit. Contributed to downgrade or manual-review evidence.
  • Caution fact Downgraded disease context: colorectal/GI relevance is unclear. Contributed to downgrade or manual-review evidence.
  • Caution fact Missing or unclear metadata: Downgraded disease context: colorectal/GI relevance is unclear. 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
GSE57401
Sample records
8 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
GSE57401
  • 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
GSE57401
  • 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
GSE57401
  • 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: GSE57401
dataset_title: Transcriptome analysis of human reninomas as an approach to understanding juxtaglomerular cell biology
organism: Homo sapiens
assay_type: bulk RNA-seq
processed_data_available: true
raw_data_available: true
submission_date: 2014-05-07
last_update_date: 2019-05-15
organization_name: IRCM
department: Labo Dr Reudelhuber
public_date: 2018-02-15
experiment_types: Expression profiling by high throughput sequencing
platforms: GPL11154 Illumina HiSeq 2000 (Homo sapiens)
sub_series: Not available
bioproject: PRJNA246396
supplementary_files: TAR: GSE57401_RAW.tar
series_type: Series

Why It Matched

  • Tumor vs unmatched normal · Tissue · suitability 5%.
  • Prioritized assay: bulk RNA-seq is the active assay expectation.
  • Downgraded disease context: colorectal/GI relevance is unclear.
  • 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.
  • Missing colorectal disease context downgraded for tumor-vs-normal tissue ranking.
  • Missing or unclear metadata: Missing colorectal disease context downgraded for 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 fewer than ten samples limit cohort confidence.
  • Overall score capped because colorectal/CRC disease context is not explicit.
  • Downgraded disease context: colorectal/GI relevance is unclear.
  • Missing or unclear metadata: Downgraded disease context: colorectal/GI relevance is unclear.
  • 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

11 fields
Field Value Source Origin Confidence Evidence Reason
assay_type bulk RNA-seq dataset GSE57401 Runtime Siftome inference GEO:dataset:GSE57401:fdc725e7406f230bb9bf2f7ffec826634d474e5efa9eee83fa4263284ebb5c89 high confidence bulk rna-seq dataset_accession: GSE57401 dataset_title: Transcriptome analysis of human reninomas as an approach to understanding juxtaglomerular cell biology organism: Homo sapiens assay_ty... keyword match keyword match: bulk rna-seq
organism Homo sapiens dataset GSE57401 Runtime Siftome inference GEO:dataset:GSE57401:fdc725e7406f230bb9bf2f7ffec826634d474e5efa9eee83fa4263284ebb5c89 high confidence homo sapiens dataset_accession: GSE57401 dataset_title: Transcriptome analysis of human reninomas as an approach to understanding juxtaglomerular cell biology organism: Homo sapiens assay_ty... keyword match keyword match: homo sapiens
sample_type tumor sample sample GSM1382083 Runtime Siftome inference GEO:sample:GSM1382083:78caf9a45129f8edbaa530b8e106549236b1b16981cd02f90c8e24a0ab784493 low confidence tumor sample_accession: GSM1382083 sample_title: Reninoma from Paris (Par1B1) source_name: Reninoma tumor characteristics: tissue: reninoma tumor; patient: Paris1 Reninoma from Paris ... controlled vocabulary controlled vocabulary sample type match: tumor
sample_type tumor sample sample GSM1382084 Runtime Siftome inference GEO:sample:GSM1382084:8bffeaa9269e72530a44f830f12efee3227f7dbeb8d72f5d3bfc546cbdeb695a low confidence tumor sample_accession: GSM1382084 sample_title: Reninoma from Paris (Par1B2 source_name: Reninoma tumor characteristics: tissue: reninoma tumor; patient: Paris1 Reninoma from Paris (... controlled vocabulary controlled vocabulary sample type match: tumor
sample_type tumor sample sample GSM1382085 Runtime Siftome inference GEO:sample:GSM1382085:990c6e995b3404fdf9667a8ecdd694db3b0cb9778705e92ae13739b5bd2b9ff6 low confidence tumor sample_accession: GSM1382085 sample_title: Reninoma from Paris (Par1B3) source_name: Reninoma tumor characteristics: tissue: reninoma tumor; patient: Paris1 Reninoma from Paris ... controlled vocabulary controlled vocabulary sample type match: tumor
sample_type tumor sample sample GSM1382086 Runtime Siftome inference GEO:sample:GSM1382086:55c9b4d1abfcfac37ac3b1dbb558a74fa1019f4fd4903dae9223591bfaa6ed35 low confidence tumor sample_accession: GSM1382086 sample_title: Reninoma from Montreal (Mon) source_name: Reninoma tumor characteristics: tissue: reninoma tumor; patient: Montreal Reninoma from Mont... controlled vocabulary controlled vocabulary sample type match: tumor
sample_type tumor sample sample GSM1382087 Runtime Siftome inference GEO:sample:GSM1382087:89d02ff8fa30ddfd74578975962547cfdddecb0687e931d260b6b0a73b899cae low confidence tumor sample_accession: GSM1382087 sample_title: Reninoma from Rotterdam (RotB1) source_name: Reninoma tumor characteristics: tissue: reninoma tumor; patient: Rotterdam Reninoma from ... controlled vocabulary controlled vocabulary sample type match: tumor
sample_type tumor sample sample GSM1382088 Runtime Siftome inference GEO:sample:GSM1382088:e3fae05acdce79b71e884f81a38fd9435ec94aefbe98111816c97bec0421acb7 low confidence tumor sample_accession: GSM1382088 sample_title: Reninoma from Rotterdam (RotB2) source_name: Reninoma tumor characteristics: tissue: reninoma tumor; patient: Rotterdam Reninoma from ... controlled vocabulary controlled vocabulary sample type match: tumor
sample_type tumor sample sample GSM1382089 Runtime Siftome inference GEO:sample:GSM1382089:474bf739e16a3b2fe5a738419900f128faf57fd8ec3db56dc20308b607d752ae low confidence tumor sample_accession: GSM1382089 sample_title: Reninoma from Paris (Par2) source_name: Reninoma tumor characteristics: tissue: reninoma tumor; patient: Paris2 Reninoma from Paris (P... controlled vocabulary controlled vocabulary sample type match: tumor
sample_type normal tissue sample GSM1382090 Runtime Siftome inference GEO:sample:GSM1382090:886fa3aad2638a2b5d83e4709693f88aae0fc4175c0490a57cb11f041a011644 low confidence normal sample_accession: GSM1382090 sample_title: Adjacent supposedly normal tissue (Par2N) source_name: Kidney tissue adjacent to reninoma tumor, supposedly normal characteristics: ti... controlled vocabulary controlled vocabulary sample type match: normal
sample_type tumor sample sample GSM1382090 Runtime Siftome inference GEO:sample:GSM1382090:886fa3aad2638a2b5d83e4709693f88aae0fc4175c0490a57cb11f041a011644 low confidence tumor sample_accession: GSM1382090 sample_title: Adjacent supposedly normal tissue (Par2N) source_name: Kidney tissue adjacent to reninoma tumor, supposedly normal characteristics: ti... controlled vocabulary controlled vocabulary sample type match: tumor

Sample Group Preview

Possible case samples

Samples currently treated as the comparison case group.

7
  • GSM1382083 Reninoma from Paris (Par1B1) tumor sample Case marker detected. Reninoma tumor tissue: reninoma tumor; patient: Paris1
  • GSM1382084 Reninoma from Paris (Par1B2 tumor sample Case marker detected. Reninoma tumor tissue: reninoma tumor; patient: Paris1
  • GSM1382085 Reninoma from Paris (Par1B3) tumor sample Case marker detected. Reninoma tumor tissue: reninoma tumor; patient: Paris1
  • GSM1382086 Reninoma from Montreal (Mon) tumor sample Case marker detected. Reninoma tumor tissue: reninoma tumor; patient: Montreal
  • GSM1382087 Reninoma from Rotterdam (RotB1) tumor sample Case marker detected. Reninoma tumor tissue: reninoma tumor; patient: Rotterdam
  • GSM1382088 Reninoma from Rotterdam (RotB2) tumor sample Case marker detected. Reninoma tumor tissue: reninoma tumor; patient: Rotterdam
  • GSM1382089 Reninoma from Paris (Par2) tumor sample Case marker detected. Reninoma tumor tissue: reninoma tumor; patient: Paris2

Possible control samples

Samples currently treated as controls or baseline.

1
  • GSM1382090 Adjacent supposedly normal tissue (Par2N) normal tissue Control marker detected. Kidney tissue adjacent to reninoma tumor, supposedly normal tissue: supposedly normal kidney tissue adjacent to reninoma tumor; patient: Paris2

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
  • GSM1382083 Reninoma from Paris (Par1B1) Reninoma tumor tissue: reninoma tumor; patient: Paris1
  • GSM1382084 Reninoma from Paris (Par1B2 Reninoma tumor tissue: reninoma tumor; patient: Paris1
  • GSM1382085 Reninoma from Paris (Par1B3) Reninoma tumor tissue: reninoma tumor; patient: Paris1
  • GSM1382086 Reninoma from Montreal (Mon) Reninoma tumor tissue: reninoma tumor; patient: Montreal
  • GSM1382087 Reninoma from Rotterdam (RotB1) Reninoma tumor tissue: reninoma tumor; patient: Rotterdam
  • GSM1382088 Reninoma from Rotterdam (RotB2) Reninoma tumor tissue: reninoma tumor; patient: Rotterdam
  • GSM1382089 Reninoma from Paris (Par2) Reninoma tumor tissue: reninoma tumor; patient: Paris2

normal tissue

1 sample
  • GSM1382090 Adjacent supposedly normal tissue (Par2N) Kidney tissue adjacent to reninoma tumor, supposedly normal tissue: supposedly normal kidney tissue adjacent to reninoma tumor; patient: Paris2

Score Breakdown

50%

relevance

  • Organism normalized.
  • Assay type normalized.
5%

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.
  • Missing colorectal disease context downgraded for 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.
45%

overall

  • Weighted score: 30% relevance, 30% comparison suitability, 25% metadata quality, 15% data availability.
  • Overall score capped because comparison suitability is weak for the selected search intent.
  • Overall score capped because fewer than ten samples limit cohort confidence.
  • Overall score capped because colorectal/CRC disease context is not explicit.

Sample Links

8 samples

Review Audit Trail

0 decisions

No review decisions have been stored for this dataset.