Siftome Phase 3L

GSE288097

Active DNA demethylation is upstream of rod photoreceptor fate determination and required for retinal development [Human RNA-Seq]

Exploratory only Dataset can inform exploration but is not strong enough for primary analysis.
Sample grouping CSV Contrast CSV DESeq2 metadata CSV R handoff notes Handoff report Download instructions Open GEO dataset
Source
GEO
Search intent
Patient tissue tumor-vs-normal
Intent behavior
search-intent-behavior-v1
Submission date
2025-01-27
Last update
2025-03-11
Organization
Washington University
Department
Ophthalmology and Visual Sciences
Public date
2025-03-01
Experiment types
Expression profiling by high throughput sequencing
Platforms
GPL20301 Illumina HiSeq 4000 (Homo sapiens)
Series type
Series
SubSeries
Not available
BioProject
PRJNA1216190
Supplementary files
CSV: GSE288097_Human_Normal_Tumor_RNAseq.csv.gz
Organism
Homo sapiens
Assay
bulk RNA-seq
Samples
5
Study design
Tumor vs unmatched normal
Specimen/source
Tissue
Scoring version
intent-aware-scoring-v15
Ranking batch
b69568dd1e4fe1b9ee2d880bf5495d748a7e4c5c11e4107f02528c3be0e76012
Ranking created
2026-06-05T20:20:27.088676Z
Warning version
intent-aware-warnings-v2

Current Intent Interpretation

Patient tissue tumor-vs-normal

Expectations

Organism
Homo sapiens
Assay
bulk RNA-seq
Specimen/source
patient tissue or biopsy
Controls
matched normal, adjacent normal, paired normal, healthy tissue control, or otherwise normal tissue control

Rules

Default filters
Human only; Bulk RNA-seq only; Tumor-normal only; Tissue or biopsy only; Hide biofluid/model systems
Warning rules
missing or unclear control group, unclear disease context, unclear tissue source, mixed sample types, model-system markers, secondary assay context, missing processed data, or small cohort size
Score caps
non-human datasets stay below the primary recommendation band, missing colorectal/colon/rectal/CRC context stays below the primary recommendation band, biofluid and model-system datasets cannot reach Recommended by default, microarray and secondary assays are capped unless explicitly enabled, or small cohorts are capped below high-confidence recommendations
Downgraded contexts
microarray unless explicitly enabled, biofluid-only datasets, cell-line datasets, organoid datasets, xenograft or PDX datasets, non-colorectal disease contexts, or treatment-only experiments

Study Classification

Tumor vs unmatched normal Tissue

Analysis Readiness

Ready after review
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

Bioinformatician review required

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

  • Small cohort warning is present.

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 six samples are too small for top-ranked 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 3 samples
  • Likely control group normal tissue 2 samples

Warnings

  • SMALL_COHORT_NEEDS_REVIEW warning Dataset has fewer than six samples and should not be treated as a high-confidence cohort without manual review.
  • 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: 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 3 warnings require review. Contributed to match or upgrade evidence.
  • Caution fact Dataset has fewer than six samples and should not be treated as a high-confidence cohort without manual review. 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 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 six samples are too small for top-ranked 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
GSE288097
Sample records
5 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
GSE288097
  • 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
GSE288097
  • 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
GSE288097
  • 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: GSE288097
dataset_title: Active DNA demethylation is upstream of rod photoreceptor fate determination and required for retinal development [Human RNA-Seq]
organism: Homo sapiens
assay_type: bulk RNA-seq
processed_data_available: true
raw_data_available: true
submission_date: 2025-01-27
last_update_date: 2025-03-11
organization_name: Washington University
department: Ophthalmology and Visual Sciences
public_date: 2025-03-01
experiment_types: Expression profiling by high throughput sequencing
platforms: GPL20301 Illumina HiSeq 4000 (Homo sapiens)
sub_series: Not available
bioproject: PRJNA1216190
supplementary_files: CSV: GSE288097_Human_Normal_Tumor_RNAseq.csv.gz
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.
  • 3 warnings require review.

Why It May Not Be Suitable

  • Dataset has fewer than six samples and should not be treated as a high-confidence cohort without manual review.
  • 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 six samples are too small for top-ranked 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 SMALL_COHORT_NEEDS_REVIEW Dataset has fewer than six samples and should not be treated as a high-confidence cohort without manual review.
  • 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

7 fields
Field Value Source Origin Confidence Evidence Reason
assay_type bulk RNA-seq dataset GSE288097 Runtime Siftome inference GEO:dataset:GSE288097:1fe578d45df5abc2fa09bb6a9fe9b2903e250452f15d1a3c4af6e10992c62a05 high confidence bulk rna-seq dataset_accession: GSE288097 dataset_title: Active DNA demethylation is upstream of rod photoreceptor fate determination and required for retinal development [Human RNA-Seq] org... keyword match keyword match: bulk rna-seq
organism Homo sapiens dataset GSE288097 Runtime Siftome inference GEO:dataset:GSE288097:1fe578d45df5abc2fa09bb6a9fe9b2903e250452f15d1a3c4af6e10992c62a05 high confidence homo sapiens dataset_accession: GSE288097 dataset_title: Active DNA demethylation is upstream of rod photoreceptor fate determination and required for retinal development [Human RNA-Seq] org... keyword match keyword match: homo sapiens
sample_type normal tissue sample GSM8758970 Runtime Siftome inference GEO:sample:GSM8758970:4784a6351bf2ecaa9f9cb8ae0758ea32272ba015a7ce4aaba169e07a86a54336 low confidence normal sample_accession: GSM8758970 sample_title: Human Normal Retina RNA-seq Replicate 1 - Sample_83265 source_name: Retina characteristics: tissue: Retina; genotype: Control; treatme... controlled vocabulary controlled vocabulary sample type match: normal
sample_type normal tissue sample GSM8758971 Runtime Siftome inference GEO:sample:GSM8758971:22ecbbc5d6b406c7dd701590121b7683ac3eb8ae7eaa09c4d9df44ae07ecf050 low confidence normal sample_accession: GSM8758971 sample_title: Human Normal Retina RNA-seq Replicate 2 - Sample_83266 source_name: Retina characteristics: tissue: Retina; genotype: Control; treatme... controlled vocabulary controlled vocabulary sample type match: normal
sample_type tumor sample sample GSM8758972 Runtime Siftome inference GEO:sample:GSM8758972:ca1e0224c93b2ebfd939da87582fbe449c5659ffe7a758ea8d27df001ca8a98d low confidence tumor sample_accession: GSM8758972 sample_title: Human Retinoblastoma Tumor Replicate 1 - Sample_83267 source_name: Retina Tumor characteristics: tissue: Retina Tumor; genotype: Tumor... controlled vocabulary controlled vocabulary sample type match: tumor
sample_type tumor sample sample GSM8758973 Runtime Siftome inference GEO:sample:GSM8758973:0ca06359965f287343bc7a8de921e26e154f9052ad55f3e601bbbae7098747a7 low confidence tumor sample_accession: GSM8758973 sample_title: Human Retinoblastoma Tumor Replicate 2 - Sample_83268 source_name: Retina Tumor characteristics: tissue: Retina Tumor; genotype: Tumor... controlled vocabulary controlled vocabulary sample type match: tumor
sample_type tumor sample sample GSM8758974 Runtime Siftome inference GEO:sample:GSM8758974:85c059984af9f49ffbfece99b83cedd1d22a9dd77794cd8732f37805321fc06a low confidence tumor sample_accession: GSM8758974 sample_title: Human Retinoblastoma Tumor Replicate 3 - Sample_83269 source_name: Retina Tumor characteristics: tissue: Retina Tumor; genotype: Tumor... controlled vocabulary controlled vocabulary sample type match: tumor

Sample Group Preview

Possible case samples

Samples currently treated as the comparison case group.

3
  • GSM8758972 Human Retinoblastoma Tumor Replicate 1 - Sample_83267 tumor sample Case marker detected. Retina Tumor tissue: Retina Tumor; genotype: Tumor; treatment: FFPE
  • GSM8758973 Human Retinoblastoma Tumor Replicate 2 - Sample_83268 tumor sample Case marker detected. Retina Tumor tissue: Retina Tumor; genotype: Tumor; treatment: FFPE
  • GSM8758974 Human Retinoblastoma Tumor Replicate 3 - Sample_83269 tumor sample Case marker detected. Retina Tumor tissue: Retina Tumor; genotype: Tumor; treatment: FFPE

Possible control samples

Samples currently treated as controls or baseline.

2
  • GSM8758970 Human Normal Retina RNA-seq Replicate 1 - Sample_83265 normal tissue Control marker detected. Retina tissue: Retina; genotype: Control; treatment: FFPE
  • GSM8758971 Human Normal Retina RNA-seq Replicate 2 - Sample_83266 normal tissue Control marker detected. Retina tissue: Retina; genotype: Control; treatment: FFPE

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

normal tissue

2 samples
  • GSM8758970 Human Normal Retina RNA-seq Replicate 1 - Sample_83265 Retina tissue: Retina; genotype: Control; treatment: FFPE
  • GSM8758971 Human Normal Retina RNA-seq Replicate 2 - Sample_83266 Retina tissue: Retina; genotype: Control; treatment: FFPE

tumor sample

3 samples
  • GSM8758972 Human Retinoblastoma Tumor Replicate 1 - Sample_83267 Retina Tumor tissue: Retina Tumor; genotype: Tumor; treatment: FFPE
  • GSM8758973 Human Retinoblastoma Tumor Replicate 2 - Sample_83268 Retina Tumor tissue: Retina Tumor; genotype: Tumor; treatment: FFPE
  • GSM8758974 Human Retinoblastoma Tumor Replicate 3 - Sample_83269 Retina Tumor tissue: Retina Tumor; genotype: Tumor; treatment: FFPE

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 six samples are too small for top-ranked cohort confidence.
  • Overall score capped because colorectal/CRC disease context is not explicit.

Sample Links

5 samples

Review Audit Trail

0 decisions

No review decisions have been stored for this dataset.