Siftome Phase 3L

GSE223804

Changes in gene expression and mechanisms underlying activation of tumor invasion and spread at the early steps of squamous cervical carcinoma progression.

Not suitable Dataset does not meet the current suitability threshold.
Sample grouping CSV Contrast CSV DESeq2 metadata CSV R handoff notes Handoff report Download instructions Open GEO dataset
Source
GEO
Search intent
Patient tissue tumor-vs-normal
Intent behavior
search-intent-behavior-v1
Submission date
2023-01-26
Last update
2023-09-27
Organization
University of Houston
Department
Psychology
Public date
2023-04-01
Experiment types
Expression profiling by high throughput sequencing
Platforms
GPL16791 Illumina HiSeq 2500 (Homo sapiens)
Series type
Series
SubSeries
Not available
BioProject
PRJNA928409
Supplementary files
TXT: GSE223804_cpm_CIN_CR_Norm.txt.gz
Organism
Homo sapiens
Assay
bulk RNA-seq
Samples
16
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
85% 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

3/15 pts

Unassigned or review-needed samples remain before analysis.

Blocking warnings

7/10 pts

Warnings are present, but none are critical blockers.

Metadata normalization

10/10 pts

Metadata quality is high enough to support downstream handoff.

Blockers

  • 12 samples are still unassigned.

Next Steps

  • Resolve unassigned or review-needed samples in the grouping table.

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

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

Needs review

0 review-needed samples and 12 unassigned samples remain.

Resolve ambiguous and unassigned samples before finalizing the contrast.

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.
  • One or more samples are unassigned and need manual grouping decisions.

Why This Is Ranked Here

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

Score Components

  • relevance 90% Disease or condition metadata normalized. 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 85% Sample source clarity: All samples have source metadata and clear GSE/GSM accessions. Group clarity: Rule-based grouping found both case and control samples. Disease clarity: Disease or condition metadata normalized. Tissue clarity: Tissue metadata 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 2 samples
  • Likely control group normal tissue 2 samples

Warnings

  • 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 1 active warning missing or unclear control group, unclear disease context, unclear tissue source, mixed sample types, model-system markers, secondary assay context, missing processed data, or small cohort size
  • Downgrade or exclusion reason Downgraded disease context: 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 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: 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 1 warning require review. Contributed to match or upgrade 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: 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: 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
GSE223804
Sample records
16 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
GSE223804
  • 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
GSE223804
  • 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
GSE223804
  • 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: GSE223804
dataset_title: Changes in gene expression and mechanisms underlying activation of tumor invasion and spread at the early steps of squamous cervical carcinoma progression.
organism: Homo sapiens
assay_type: bulk RNA-seq
processed_data_available: true
raw_data_available: true
submission_date: 2023-01-26
last_update_date: 2023-09-27
organization_name: University of Houston
department: Psychology
public_date: 2023-04-01
experiment_types: Expression profiling by high throughput sequencing
platforms: GPL16791 Illumina HiSeq 2500 (Homo sapiens)
sub_series: Not available
bioproject: PRJNA928409
supplementary_files: TXT: GSE223804_cpm_CIN_CR_Norm.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: colorectal/GI relevance is unclear.
  • Processed data is available for downstream review.
  • 1 warning require review.

Why It May Not Be Suitable

  • Tissue or cell type could not be normalized.
  • Non-colorectal cancer context downgraded for colorectal tumor-vs-normal tissue ranking.
  • 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: 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 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 GSE223804 Runtime Siftome inference GEO:dataset:GSE223804:d752dda852592b92a25c0bacb90df051d22a88fad9ac6d17104ad5e2c4c10882 high confidence bulk rna-seq dataset_accession: GSE223804 dataset_title: Changes in gene expression and mechanisms underlying activation of tumor invasion and spread at the early steps of squamous cervical ... keyword match keyword match: bulk rna-seq
disease colorectal cancer dataset GSE223804 Runtime Siftome inference GEO:dataset:GSE223804:d752dda852592b92a25c0bacb90df051d22a88fad9ac6d17104ad5e2c4c10882 medium confidence read dataset_accession: GSE223804 dataset_title: Changes in gene expression and mechanisms underlying activation of tumor invasion and spread at the early steps of squamous cervical ... controlled vocabulary controlled vocabulary disease match: read
organism Homo sapiens dataset GSE223804 Runtime Siftome inference GEO:dataset:GSE223804:d752dda852592b92a25c0bacb90df051d22a88fad9ac6d17104ad5e2c4c10882 high confidence homo sapiens dataset_accession: GSE223804 dataset_title: Changes in gene expression and mechanisms underlying activation of tumor invasion and spread at the early steps of squamous cervical ... keyword match keyword match: homo sapiens
sample_type normal tissue sample GSM6996083 Runtime Siftome inference GEO:sample:GSM6996083:dcc03fe3d86b55795f169c4cbb6848aec0b3b23cd016c92119ab6e232bea20ac low confidence normal sample_accession: GSM6996083 sample_title: morphologically normal cervical epithelium [Norm1] source_name: Cervical tissue characteristics: tissue: Cervical tissue; tissue type:... controlled vocabulary controlled vocabulary sample type match: normal
sample_type normal tissue sample GSM6996084 Runtime Siftome inference GEO:sample:GSM6996084:61ce361532f9407f3ee416f102c51982e964584ddbaf6c8fc352d603c5c3d7f1 low confidence normal sample_accession: GSM6996084 sample_title: morphologically normal cervical epithelium [Norm2] source_name: Cervical tissue characteristics: tissue: Cervical tissue; tissue type:... controlled vocabulary controlled vocabulary sample type match: normal
sample_type tumor sample sample GSM6996086 Runtime Siftome inference GEO:sample:GSM6996086:1963bdb1d8e327700df13decf69b761b6f173c533d2ad9497a981a8c7f30603f medium confidence carcinoma sample_accession: GSM6996086 sample_title: CIN3 (carcinoma in situ) [CIN_2] source_name: Cervical tissue characteristics: tissue: Cervical tissue; Stage: CIN3 (carcinoma in situ... controlled vocabulary controlled vocabulary sample type match: carcinoma
sample_type tumor sample sample GSM6996088 Runtime Siftome inference GEO:sample:GSM6996088:fd310c42d65013c322310f6eb937d41d9348055f94e5f005026fb5cd869e588f medium confidence carcinoma sample_accession: GSM6996088 sample_title: CIN3 (carcinoma in situ) [CIN_4] source_name: Cervical tissue characteristics: tissue: Cervical tissue; Stage: CIN3 (carcinoma in situ... controlled vocabulary controlled vocabulary sample type match: carcinoma

Sample Group Preview

Possible case samples

Samples currently treated as the comparison case group.

2
  • GSM6996086 CIN3 (carcinoma in situ) [CIN_2] tumor sample Case marker detected. Cervical tissue tissue: Cervical tissue; Stage: CIN3 (carcinoma in situ)
  • GSM6996088 CIN3 (carcinoma in situ) [CIN_4] tumor sample Case marker detected. Cervical tissue tissue: Cervical tissue; Stage: CIN3 (carcinoma in situ)

Possible control samples

Samples currently treated as controls or baseline.

2
  • GSM6996083 morphologically normal cervical epithelium [Norm1] normal tissue Control marker detected. Cervical tissue tissue: Cervical tissue; tissue type: morphologically normal cervical epithelium
  • GSM6996084 morphologically normal cervical epithelium [Norm2] normal tissue Control marker detected. Cervical tissue tissue: Cervical tissue; tissue type: morphologically normal cervical epithelium

Unassigned samples

Samples with no explicit case or control marker.

12
  • GSM6996085 Cervical intraepithelial neoplasia grade 3 (CIN3) [CIN_1] unassigned No explicit case or control marker detected. Cervical tissue tissue: Cervical tissue; Stage: Cervical intraepithelial neoplasia grade 3 (CIN3)
  • GSM6996087 CIN2/3 [CIN_3] unassigned No explicit case or control marker detected. Cervical tissue tissue: Cervical tissue; Stage: CIN2/3
  • GSM6996089 CIN1 [CIN_5] unassigned No explicit case or control marker detected. Cervical tissue tissue: Cervical tissue; Stage: CIN1
  • GSM6996090 cancer stage IA1 [CR_1] unassigned No explicit case or control marker detected. Cervical tissue tissue: Cervical tissue; Stage: cancer stage IA1
  • GSM6996091 cancer stage IB1 [CR_2] unassigned No explicit case or control marker detected. Cervical tissue tissue: Cervical tissue; Stage: cancer stage IB1
  • GSM6996092 cancer stage IA1 [CR_3] unassigned No explicit case or control marker detected. Cervical tissue tissue: Cervical tissue; Stage: cancer stage IA1
  • GSM6996093 cancer stage IA1 [CR_4] unassigned No explicit case or control marker detected. Cervical tissue tissue: Cervical tissue; Stage: cancer stage IA1
  • GSM6996094 cancer stage IB1 [CR_5] unassigned No explicit case or control marker detected. Cervical tissue tissue: Cervical tissue; Stage: cancer stage IB1
  • GSM6996095 cancer stage IB2/IIA1 [CR_6] unassigned No explicit case or control marker detected. Cervical tissue tissue: Cervical tissue; Stage: cancer stage IB2/IIA1
  • GSM6996096 cancer stage IIB [CR_7] unassigned No explicit case or control marker detected. Cervical tissue tissue: Cervical tissue; Stage: cancer stage IIB
  • GSM6996097 cancer stage IA1 [CR_8] unassigned No explicit case or control marker detected. Cervical tissue tissue: Cervical tissue; Stage: cancer stage IA1
  • GSM6996098 cancer stage IA2 [CR_9] unassigned No explicit case or control marker detected. Cervical tissue tissue: Cervical tissue; Stage: cancer stage IA2

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

85 pts
Clarity
85%
Weight
100 pts

Sample source clarity: All samples have source metadata and clear GSE/GSM accessions. Group clarity: Rule-based grouping found both case and control samples. Disease clarity: Disease or condition metadata normalized. Tissue clarity: Tissue metadata 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
  • GSM6996083 morphologically normal cervical epithelium [Norm1] Cervical tissue tissue: Cervical tissue; tissue type: morphologically normal cervical epithelium
  • GSM6996084 morphologically normal cervical epithelium [Norm2] Cervical tissue tissue: Cervical tissue; tissue type: morphologically normal cervical epithelium

unassigned

12 samples
  • GSM6996085 Cervical intraepithelial neoplasia grade 3 (CIN3) [CIN_1] Cervical tissue tissue: Cervical tissue; Stage: Cervical intraepithelial neoplasia grade 3 (CIN3)
  • GSM6996087 CIN2/3 [CIN_3] Cervical tissue tissue: Cervical tissue; Stage: CIN2/3
  • GSM6996089 CIN1 [CIN_5] Cervical tissue tissue: Cervical tissue; Stage: CIN1
  • GSM6996090 cancer stage IA1 [CR_1] Cervical tissue tissue: Cervical tissue; Stage: cancer stage IA1
  • GSM6996091 cancer stage IB1 [CR_2] Cervical tissue tissue: Cervical tissue; Stage: cancer stage IB1
  • GSM6996092 cancer stage IA1 [CR_3] Cervical tissue tissue: Cervical tissue; Stage: cancer stage IA1
  • GSM6996093 cancer stage IA1 [CR_4] Cervical tissue tissue: Cervical tissue; Stage: cancer stage IA1
  • GSM6996094 cancer stage IB1 [CR_5] Cervical tissue tissue: Cervical tissue; Stage: cancer stage IB1
  • GSM6996095 cancer stage IB2/IIA1 [CR_6] Cervical tissue tissue: Cervical tissue; Stage: cancer stage IB2/IIA1
  • GSM6996096 cancer stage IIB [CR_7] Cervical tissue tissue: Cervical tissue; Stage: cancer stage IIB
  • GSM6996097 cancer stage IA1 [CR_8] Cervical tissue tissue: Cervical tissue; Stage: cancer stage IA1
  • GSM6996098 cancer stage IA2 [CR_9] Cervical tissue tissue: Cervical tissue; Stage: cancer stage IA2

tumor sample

2 samples
  • GSM6996086 CIN3 (carcinoma in situ) [CIN_2] Cervical tissue tissue: Cervical tissue; Stage: CIN3 (carcinoma in situ)
  • GSM6996088 CIN3 (carcinoma in situ) [CIN_4] Cervical tissue tissue: Cervical tissue; Stage: CIN3 (carcinoma in situ)

Score Breakdown

90%

relevance

  • Disease or condition metadata normalized.
  • 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.
85%

metadata quality

  • Sample source clarity: All samples have source metadata and clear GSE/GSM accessions.
  • Group clarity: Rule-based grouping found both case and control samples.
  • Disease clarity: Disease or condition metadata normalized.
  • Tissue clarity: Tissue metadata 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

16 samples

Review Audit Trail

0 decisions

No review decisions have been stored for this dataset.