Siftome Phase 3L

GSE299125

Paracrine Signals from HIV-1 Infected Immune Cells Reprogram Cervical Cancer Pathways

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
2025-06-05
Last update
2026-05-04
Organization
West African Centre for Cell Biology of Infectious Pathogens
Department
Department of Biochemistry, Cell and Molecular Biology
Public date
2026-05-04
Experiment types
Expression profiling by high throughput sequencing
Platforms
GPL21697 NextSeq 550 (Homo sapiens)
Series type
Series
SubSeries
Not available
BioProject
PRJNA1272618
Supplementary files
TXT: GSE299125_raw_counts.txt.gz
Organism
Homo sapiens
Assay
bulk RNA-seq
Samples
35
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

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

7/10 pts

Metadata quality is usable, but still deserves review.

Blockers

  • 10 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 10 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 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 13 samples
  • Likely control group normal tissue 12 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 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 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: 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
GSE299125
Sample records
35 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
GSE299125
  • 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
GSE299125
  • 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
GSE299125
  • 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: GSE299125
dataset_title: Paracrine Signals from HIV-1 Infected Immune Cells Reprogram Cervical Cancer Pathways
organism: Homo sapiens
assay_type: bulk RNA-seq
processed_data_available: true
raw_data_available: true
submission_date: 2025-06-05
last_update_date: 2026-05-04
organization_name: West African Centre for Cell Biology of Infectious Pathogens
department: Department of Biochemistry, Cell and Molecular Biology
public_date: 2026-05-04
experiment_types: Expression profiling by high throughput sequencing
platforms: GPL21697 NextSeq 550 (Homo sapiens)
sub_series: Not available
bioproject: PRJNA1272618
supplementary_files: TXT: GSE299125_raw_counts.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.
  • 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: 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

27 fields
Field Value Source Origin Confidence Evidence Reason
assay_type bulk RNA-seq dataset GSE299125 Runtime Siftome inference GEO:dataset:GSE299125:17fdf4e7e09712d85c1b63dac8aaf22e277b25c48667580d7a3a8ee99b8118ac high confidence bulk rna-seq dataset_accession: GSE299125 dataset_title: Paracrine Signals from HIV-1 Infected Immune Cells Reprogram Cervical Cancer Pathways organism: Homo sapiens assay_type: bulk RNA-seq... keyword match keyword match: bulk rna-seq
organism Homo sapiens dataset GSE299125 Runtime Siftome inference GEO:dataset:GSE299125:17fdf4e7e09712d85c1b63dac8aaf22e277b25c48667580d7a3a8ee99b8118ac high confidence homo sapiens dataset_accession: GSE299125 dataset_title: Paracrine Signals from HIV-1 Infected Immune Cells Reprogram Cervical Cancer Pathways organism: Homo sapiens assay_type: bulk RNA-seq... keyword match keyword match: homo sapiens
sample_type normal tissue sample GSM9033939 Runtime Siftome inference GEO:sample:GSM9033939:612eaa36c5bc8154fe1eb059d671c0b29ea849a3f8a5f8df1a0b98d67c471177 low confidence normal sample_accession: GSM9033939 sample_title: sample1, HIV positive, normal cervix source_name: Cervical characteristics: tissue: Cervical; cell type: Epithelial cells sample1, HIV... controlled vocabulary controlled vocabulary sample type match: normal
sample_type normal tissue sample GSM9033940 Runtime Siftome inference GEO:sample:GSM9033940:1c9588cbbf56a01293d603496786a9611c38b3060b758a268dfa517271dfc1a3 low confidence normal sample_accession: GSM9033940 sample_title: sample2, HIV positive, normal cervix source_name: Cervical characteristics: tissue: Cervical; cell type: Epithelial cells sample2, HIV... controlled vocabulary controlled vocabulary sample type match: normal
sample_type normal tissue sample GSM9033941 Runtime Siftome inference GEO:sample:GSM9033941:8e68cfe702a3811f27f916df7d5b504760bc0321779ad186b6f8017b215ff539 low confidence normal sample_accession: GSM9033941 sample_title: sample3, HIV negative, normal cervix source_name: Cervical characteristics: tissue: Cervical; cell type: Epithelial cells sample3, HIV... controlled vocabulary controlled vocabulary sample type match: normal
sample_type normal tissue sample GSM9033942 Runtime Siftome inference GEO:sample:GSM9033942:09d86069899cb71f38c933633d4e8672179aef8005cbb457b21fb57857a99178 low confidence normal sample_accession: GSM9033942 sample_title: sample4, HIV positive, normal cervix source_name: Cervical characteristics: tissue: Cervical; cell type: Epithelial cells sample4, HIV... controlled vocabulary controlled vocabulary sample type match: normal
sample_type normal tissue sample GSM9033943 Runtime Siftome inference GEO:sample:GSM9033943:1e8fee253faf4df497518498e6278e29d1f9537358f65056d54603c986408d98 low confidence normal sample_accession: GSM9033943 sample_title: sample5, HIV negative, normal cervix source_name: Cervical characteristics: tissue: Cervical; cell type: Epithelial cells sample5, HIV... controlled vocabulary controlled vocabulary sample type match: normal
sample_type normal tissue sample GSM9033944 Runtime Siftome inference GEO:sample:GSM9033944:6c064e8ef2c38c29a80e97c156bbb6ac5b7308ebb973e5b3aeafa066264c375e low confidence normal sample_accession: GSM9033944 sample_title: sample6, HIV negative, normal cervix source_name: Cervical characteristics: tissue: Cervical; cell type: Epithelial cells sample6, HIV... controlled vocabulary controlled vocabulary sample type match: normal
sample_type normal tissue sample GSM9033945 Runtime Siftome inference GEO:sample:GSM9033945:b83b89158346ac42120dea4d36aeb50f667c04466888c7d3edd0c8f0703df0a5 low confidence normal sample_accession: GSM9033945 sample_title: sample7, HIV negative, normal cervix source_name: Cervical characteristics: tissue: Cervical; cell type: Epithelial cells sample7, HIV... controlled vocabulary controlled vocabulary sample type match: normal
sample_type normal tissue sample GSM9033946 Runtime Siftome inference GEO:sample:GSM9033946:b5e5c7410f17ada80f1630e90ff9ae29419afcc5b605b94c9a8f355fd14b76ab low confidence normal sample_accession: GSM9033946 sample_title: sample8, HIV negative, normal cervix source_name: Cervical characteristics: tissue: Cervical; cell type: Epithelial cells sample8, HIV... controlled vocabulary controlled vocabulary sample type match: normal
sample_type normal tissue sample GSM9033947 Runtime Siftome inference GEO:sample:GSM9033947:1405fd087866dac67aea3c378d8a6bc2a090c8ec9566baf98a234ef24e4cba03 low confidence normal sample_accession: GSM9033947 sample_title: sample9, HIV negative, normal cervix source_name: Cervical characteristics: tissue: Cervical; cell type: Epithelial cells sample9, HIV... controlled vocabulary controlled vocabulary sample type match: normal
sample_type normal tissue sample GSM9033948 Runtime Siftome inference GEO:sample:GSM9033948:0ce20acdac273dbc135e4c2f070dc3ad400a110a6996fde515235cbff0c44b0a low confidence normal sample_accession: GSM9033948 sample_title: sample10, HIV positive, normal cervix source_name: Cervical characteristics: tissue: Cervical; cell type: Epithelial cells sample10, H... controlled vocabulary controlled vocabulary sample type match: normal
sample_type normal tissue sample GSM9033949 Runtime Siftome inference GEO:sample:GSM9033949:72ccb861bc8b3e8abc39cc8555eecd535da0fe54811fa0f994c73eb7bcb5b4b6 low confidence normal sample_accession: GSM9033949 sample_title: sample11, HIV positive, normal cervix source_name: Cervical characteristics: tissue: Cervical; cell type: Epithelial cells sample11, H... controlled vocabulary controlled vocabulary sample type match: normal
sample_type normal tissue sample GSM9033950 Runtime Siftome inference GEO:sample:GSM9033950:e84f060ce6e7b28b7cb089258d162efa5b2752a576fb6ac8eb3edb0ea3c31682 low confidence normal sample_accession: GSM9033950 sample_title: sample12, HIV positive, normal cervix source_name: Cervical characteristics: tissue: Cervical; cell type: Epithelial cells sample12, H... controlled vocabulary controlled vocabulary sample type match: normal
sample_type tumor sample sample GSM9033952 Runtime Siftome inference GEO:sample:GSM9033952:bea091233c99f46ca332cb58209f67db253f87953b3a108fad77a33a6a0b899d medium confidence carcinoma sample_accession: GSM9033952 sample_title: sample14, HIV positive, invasive cervical carcinoma source_name: Cervical characteristics: tissue: Cervical; cell type: Epithelial cel... controlled vocabulary controlled vocabulary sample type match: carcinoma
sample_type tumor sample sample GSM9033959 Runtime Siftome inference GEO:sample:GSM9033959:b3d6c93a22ba10be35357f755de3bf153087692018a2ccd1888c382dc20c09bc medium confidence carcinoma sample_accession: GSM9033959 sample_title: sample21, HIV positive, invasive cervical carcinoma source_name: Cervical characteristics: tissue: Cervical; cell type: Epithelial cel... controlled vocabulary controlled vocabulary sample type match: carcinoma
sample_type tumor sample sample GSM9033960 Runtime Siftome inference GEO:sample:GSM9033960:ce2fd9b145cae59db6960e7d2b86e9849bb1cb155ed7072abe32af302616cf6c medium confidence carcinoma sample_accession: GSM9033960 sample_title: sample22, HIV negative, invasive cervical carcinoma source_name: Cervical characteristics: tissue: Cervical; cell type: Epithelial cel... controlled vocabulary controlled vocabulary sample type match: carcinoma
sample_type tumor sample sample GSM9033961 Runtime Siftome inference GEO:sample:GSM9033961:fea8805296108db9e522abcd785dad78470368c0ecd8148803960fe7a6c0018f medium confidence carcinoma sample_accession: GSM9033961 sample_title: sample, 23, HIV negative, invasive cervical carcinoma source_name: Cervical characteristics: tissue: Cervical; cell type: Epithelial c... controlled vocabulary controlled vocabulary sample type match: carcinoma
sample_type tumor sample sample GSM9033962 Runtime Siftome inference GEO:sample:GSM9033962:ecc68e58cbcedd971b5ac828668e6464b8bd2a6b4961073227cd950e80aeee13 medium confidence carcinoma sample_accession: GSM9033962 sample_title: sample24, HIV negative, invasive cervical carcinoma source_name: Cervical characteristics: tissue: Cervical; cell type: Epithelial cel... controlled vocabulary controlled vocabulary sample type match: carcinoma
sample_type tumor sample sample GSM9033963 Runtime Siftome inference GEO:sample:GSM9033963:f8b66819ba9a45a7784a93f78a59c1bd17ce32363bb18f9ffca4cd64297e3053 medium confidence carcinoma sample_accession: GSM9033963 sample_title: sample25, HIV negative, invasive cervical carcinoma source_name: Cervical characteristics: tissue: Cervical; cell type: Epithelial cel... controlled vocabulary controlled vocabulary sample type match: carcinoma
sample_type tumor sample sample GSM9033965 Runtime Siftome inference GEO:sample:GSM9033965:b13b9c8b89d50cabe720be1e2e73255f0b2b6ed08f7d496402462f0cc1cc3584 medium confidence carcinoma sample_accession: GSM9033965 sample_title: sample27, HIV negative, invasive cervical carcinoma source_name: Cervical characteristics: tissue: Cervical; cell type: Epithelial cel... controlled vocabulary controlled vocabulary sample type match: carcinoma
sample_type tumor sample sample GSM9033966 Runtime Siftome inference GEO:sample:GSM9033966:f1dd370d10f064809d20fb3923b1bc044d8ffea1f7fff1bc5a331069c272b9b5 medium confidence carcinoma sample_accession: GSM9033966 sample_title: sample28, HIV positive, invasive cervical carcinoma source_name: Cervical characteristics: tissue: Cervical; cell type: Epithelial cel... controlled vocabulary controlled vocabulary sample type match: carcinoma
sample_type tumor sample sample GSM9033968 Runtime Siftome inference GEO:sample:GSM9033968:42c3467d9cf1e06d81661f364de3894418d4df54d2ec74ccb53b45621c9cd4d5 medium confidence carcinoma sample_accession: GSM9033968 sample_title: sample30, HIV negative, invasive cervical carcinoma source_name: Cervical characteristics: tissue: Cervical; cell type: Epithelial cel... controlled vocabulary controlled vocabulary sample type match: carcinoma
sample_type tumor sample sample GSM9033969 Runtime Siftome inference GEO:sample:GSM9033969:456e73405e3bd2e3e8029de58dba43f4b903d0f9071d9a0a41d989302b5fe396 medium confidence carcinoma sample_accession: GSM9033969 sample_title: sample31, HIV negative, invasive cervical carcinoma source_name: Cervical characteristics: tissue: Cervical; cell type: Epithelial cel... controlled vocabulary controlled vocabulary sample type match: carcinoma
sample_type tumor sample sample GSM9033971 Runtime Siftome inference GEO:sample:GSM9033971:abd962feb4982ff95eb5a3da5985f25180b14b8b29718fdefb45dbeaa78ebce9 medium confidence carcinoma sample_accession: GSM9033971 sample_title: sample33, HIV negative, invasive cervical carcinoma source_name: Cervical characteristics: tissue: Cervical; cell type: Epithelial cel... controlled vocabulary controlled vocabulary sample type match: carcinoma
sample_type tumor sample sample GSM9033972 Runtime Siftome inference GEO:sample:GSM9033972:be195ebc1f354807307c751e79e5b8f14f2d164ec5908597707ca431f46e7a22 medium confidence carcinoma sample_accession: GSM9033972 sample_title: sample34, HIV negative, invasive cervical carcinoma source_name: Cervical characteristics: tissue: Cervical; cell type: Epithelial cel... controlled vocabulary controlled vocabulary sample type match: carcinoma
sample_type tumor sample sample GSM9033973 Runtime Siftome inference GEO:sample:GSM9033973:a4c989559e81f94c0a3c9fcb53d12b0b0f3fc3c7f51e14a3cad50b9cf306a2ce medium confidence carcinoma sample_accession: GSM9033973 sample_title: sample35, HIV negative, invasive cervical carcinoma source_name: Cervical characteristics: tissue: Cervical; cell type: Epithelial cel... controlled vocabulary controlled vocabulary sample type match: carcinoma

Sample Group Preview

Possible case samples

Samples currently treated as the comparison case group.

13
  • GSM9033952 sample14, HIV positive, invasive cervical carcinoma tumor sample Case marker detected. Cervical tissue: Cervical; cell type: Epithelial cells
  • GSM9033959 sample21, HIV positive, invasive cervical carcinoma tumor sample Case marker detected. Cervical tissue: Cervical; cell type: Epithelial cells
  • GSM9033960 sample22, HIV negative, invasive cervical carcinoma tumor sample Case marker detected. Cervical tissue: Cervical; cell type: Epithelial cells
  • GSM9033961 sample, 23, HIV negative, invasive cervical carcinoma tumor sample Case marker detected. Cervical tissue: Cervical; cell type: Epithelial cells
  • GSM9033962 sample24, HIV negative, invasive cervical carcinoma tumor sample Case marker detected. Cervical tissue: Cervical; cell type: Epithelial cells
  • GSM9033963 sample25, HIV negative, invasive cervical carcinoma tumor sample Case marker detected. Cervical tissue: Cervical; cell type: Epithelial cells
  • GSM9033965 sample27, HIV negative, invasive cervical carcinoma tumor sample Case marker detected. Cervical tissue: Cervical; cell type: Epithelial cells
  • GSM9033966 sample28, HIV positive, invasive cervical carcinoma tumor sample Case marker detected. Cervical tissue: Cervical; cell type: Epithelial cells
  • GSM9033968 sample30, HIV negative, invasive cervical carcinoma tumor sample Case marker detected. Cervical tissue: Cervical; cell type: Epithelial cells
  • GSM9033969 sample31, HIV negative, invasive cervical carcinoma tumor sample Case marker detected. Cervical tissue: Cervical; cell type: Epithelial cells
  • GSM9033971 sample33, HIV negative, invasive cervical carcinoma tumor sample Case marker detected. Cervical tissue: Cervical; cell type: Epithelial cells
  • GSM9033972 sample34, HIV negative, invasive cervical carcinoma tumor sample Case marker detected. Cervical tissue: Cervical; cell type: Epithelial cells
  • GSM9033973 sample35, HIV negative, invasive cervical carcinoma tumor sample Case marker detected. Cervical tissue: Cervical; cell type: Epithelial cells

Possible control samples

Samples currently treated as controls or baseline.

12
  • GSM9033939 sample1, HIV positive, normal cervix normal tissue Control marker detected. Cervical tissue: Cervical; cell type: Epithelial cells
  • GSM9033940 sample2, HIV positive, normal cervix normal tissue Control marker detected. Cervical tissue: Cervical; cell type: Epithelial cells
  • GSM9033941 sample3, HIV negative, normal cervix normal tissue Control marker detected. Cervical tissue: Cervical; cell type: Epithelial cells
  • GSM9033942 sample4, HIV positive, normal cervix normal tissue Control marker detected. Cervical tissue: Cervical; cell type: Epithelial cells
  • GSM9033943 sample5, HIV negative, normal cervix normal tissue Control marker detected. Cervical tissue: Cervical; cell type: Epithelial cells
  • GSM9033944 sample6, HIV negative, normal cervix normal tissue Control marker detected. Cervical tissue: Cervical; cell type: Epithelial cells
  • GSM9033945 sample7, HIV negative, normal cervix normal tissue Control marker detected. Cervical tissue: Cervical; cell type: Epithelial cells
  • GSM9033946 sample8, HIV negative, normal cervix normal tissue Control marker detected. Cervical tissue: Cervical; cell type: Epithelial cells
  • GSM9033947 sample9, HIV negative, normal cervix normal tissue Control marker detected. Cervical tissue: Cervical; cell type: Epithelial cells
  • GSM9033948 sample10, HIV positive, normal cervix normal tissue Control marker detected. Cervical tissue: Cervical; cell type: Epithelial cells
  • GSM9033949 sample11, HIV positive, normal cervix normal tissue Control marker detected. Cervical tissue: Cervical; cell type: Epithelial cells
  • GSM9033950 sample12, HIV positive, normal cervix normal tissue Control marker detected. Cervical tissue: Cervical; cell type: Epithelial cells

Unassigned samples

Samples with no explicit case or control marker.

10
  • GSM9033951 sample13, HIV positive, precancerous cervical lesion unassigned No explicit case or control marker detected. Cervical tissue: Cervical; cell type: Epithelial cells
  • GSM9033953 sample15, HIV positive, precancerous cervical lesion unassigned No explicit case or control marker detected. Cervical tissue: Cervical; cell type: Epithelial cells
  • GSM9033954 sample16, HIV positive, precancerous cervical lesion unassigned No explicit case or control marker detected. Cervical tissue: Cervical; cell type: Epithelial cells
  • GSM9033955 sample17, HIV positive, precancerous cervical lesion unassigned No explicit case or control marker detected. Cervical tissue: Cervical; cell type: Epithelial cells
  • GSM9033956 sample18, HIV positive, precancerous cervical lesion unassigned No explicit case or control marker detected. Cervical tissue: Cervical; cell type: Epithelial cells
  • GSM9033957 sample19, HIV positive, precancerous cervical lesion unassigned No explicit case or control marker detected. Cervical tissue: Cervical; cell type: Epithelial cells
  • GSM9033958 sample20, HIV positive, precancerous cervical lesion unassigned No explicit case or control marker detected. Cervical tissue: Cervical; cell type: Epithelial cells
  • GSM9033964 sample26, HIV negative, precancerous cervical lesion unassigned No explicit case or control marker detected. Cervical tissue: Cervical; cell type: Epithelial cells
  • GSM9033967 sample29, HIV negative, precancerous cervical lesion unassigned No explicit case or control marker detected. Cervical tissue: Cervical; cell type: Epithelial cells
  • GSM9033970 sample32, HIV negative, precancerous cervical lesion unassigned No explicit case or control marker detected. Cervical tissue: Cervical; cell type: Epithelial cells

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

12 samples
  • GSM9033939 sample1, HIV positive, normal cervix Cervical tissue: Cervical; cell type: Epithelial cells
  • GSM9033940 sample2, HIV positive, normal cervix Cervical tissue: Cervical; cell type: Epithelial cells
  • GSM9033941 sample3, HIV negative, normal cervix Cervical tissue: Cervical; cell type: Epithelial cells
  • GSM9033942 sample4, HIV positive, normal cervix Cervical tissue: Cervical; cell type: Epithelial cells
  • GSM9033943 sample5, HIV negative, normal cervix Cervical tissue: Cervical; cell type: Epithelial cells
  • GSM9033944 sample6, HIV negative, normal cervix Cervical tissue: Cervical; cell type: Epithelial cells
  • GSM9033945 sample7, HIV negative, normal cervix Cervical tissue: Cervical; cell type: Epithelial cells
  • GSM9033946 sample8, HIV negative, normal cervix Cervical tissue: Cervical; cell type: Epithelial cells
  • GSM9033947 sample9, HIV negative, normal cervix Cervical tissue: Cervical; cell type: Epithelial cells
  • GSM9033948 sample10, HIV positive, normal cervix Cervical tissue: Cervical; cell type: Epithelial cells
  • GSM9033949 sample11, HIV positive, normal cervix Cervical tissue: Cervical; cell type: Epithelial cells
  • GSM9033950 sample12, HIV positive, normal cervix Cervical tissue: Cervical; cell type: Epithelial cells

unassigned

10 samples
  • GSM9033951 sample13, HIV positive, precancerous cervical lesion Cervical tissue: Cervical; cell type: Epithelial cells
  • GSM9033953 sample15, HIV positive, precancerous cervical lesion Cervical tissue: Cervical; cell type: Epithelial cells
  • GSM9033954 sample16, HIV positive, precancerous cervical lesion Cervical tissue: Cervical; cell type: Epithelial cells
  • GSM9033955 sample17, HIV positive, precancerous cervical lesion Cervical tissue: Cervical; cell type: Epithelial cells
  • GSM9033956 sample18, HIV positive, precancerous cervical lesion Cervical tissue: Cervical; cell type: Epithelial cells
  • GSM9033957 sample19, HIV positive, precancerous cervical lesion Cervical tissue: Cervical; cell type: Epithelial cells
  • GSM9033958 sample20, HIV positive, precancerous cervical lesion Cervical tissue: Cervical; cell type: Epithelial cells
  • GSM9033964 sample26, HIV negative, precancerous cervical lesion Cervical tissue: Cervical; cell type: Epithelial cells
  • GSM9033967 sample29, HIV negative, precancerous cervical lesion Cervical tissue: Cervical; cell type: Epithelial cells
  • GSM9033970 sample32, HIV negative, precancerous cervical lesion Cervical tissue: Cervical; cell type: Epithelial cells

tumor sample

13 samples
  • GSM9033952 sample14, HIV positive, invasive cervical carcinoma Cervical tissue: Cervical; cell type: Epithelial cells
  • GSM9033959 sample21, HIV positive, invasive cervical carcinoma Cervical tissue: Cervical; cell type: Epithelial cells
  • GSM9033960 sample22, HIV negative, invasive cervical carcinoma Cervical tissue: Cervical; cell type: Epithelial cells
  • GSM9033961 sample, 23, HIV negative, invasive cervical carcinoma Cervical tissue: Cervical; cell type: Epithelial cells
  • GSM9033962 sample24, HIV negative, invasive cervical carcinoma Cervical tissue: Cervical; cell type: Epithelial cells
  • GSM9033963 sample25, HIV negative, invasive cervical carcinoma Cervical tissue: Cervical; cell type: Epithelial cells
  • GSM9033965 sample27, HIV negative, invasive cervical carcinoma Cervical tissue: Cervical; cell type: Epithelial cells
  • GSM9033966 sample28, HIV positive, invasive cervical carcinoma Cervical tissue: Cervical; cell type: Epithelial cells
  • GSM9033968 sample30, HIV negative, invasive cervical carcinoma Cervical tissue: Cervical; cell type: Epithelial cells
  • GSM9033969 sample31, HIV negative, invasive cervical carcinoma Cervical tissue: Cervical; cell type: Epithelial cells
  • GSM9033971 sample33, HIV negative, invasive cervical carcinoma Cervical tissue: Cervical; cell type: Epithelial cells
  • GSM9033972 sample34, HIV negative, invasive cervical carcinoma Cervical tissue: Cervical; cell type: Epithelial cells
  • GSM9033973 sample35, HIV negative, invasive cervical carcinoma Cervical tissue: Cervical; cell type: Epithelial cells

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

35 samples

Review Audit Trail

0 decisions

No review decisions have been stored for this dataset.