Siftome Phase 3L

GSE308395

Identification of Differentially Expressed Genes and Associated Immune Cell Types In South African Gallbladder Cancer Patients

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
2025-09-17
Last update
2025-12-04
Organization
University of the Witwatersrand
Department
Surgery
Public date
2025-12-04
Experiment types
Expression profiling by high throughput sequencing
Platforms
GPL15520 Illumina MiSeq (Homo sapiens)
Series type
Series
SubSeries
Not available
BioProject
PRJNA1330335
Supplementary files
TXT: GSE308395_GB_RNASeq_Raw_Counts.txt.gz
Organism
Homo sapiens
Assay
bulk RNA-seq
Samples
10
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

Standard analyst review

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

No expert-review triggers were detected by Siftome.

Why This Is Ranked Here

Patient tissue tumor-vs-normal
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 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 8 samples
  • Likely control group normal tissue 2 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 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
GSE308395
Sample records
10 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
GSE308395
  • 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
GSE308395
  • 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
GSE308395
  • 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: GSE308395
dataset_title: Identification of Differentially Expressed Genes and Associated Immune Cell Types In South African Gallbladder Cancer Patients
organism: Homo sapiens
assay_type: bulk RNA-seq
processed_data_available: true
raw_data_available: true
submission_date: 2025-09-17
last_update_date: 2025-12-04
organization_name: University of the Witwatersrand
department: Surgery
public_date: 2025-12-04
experiment_types: Expression profiling by high throughput sequencing
platforms: GPL15520 Illumina MiSeq (Homo sapiens)
sub_series: Not available
bioproject: PRJNA1330335
supplementary_files: TXT: GSE308395_GB_RNASeq_Raw_Counts.txt.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.
  • 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 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

12 fields
Field Value Source Origin Confidence Evidence Reason
assay_type bulk RNA-seq dataset GSE308395 Runtime Siftome inference GEO:dataset:GSE308395:c0415748aab14b924c1fbb60bb9a0291ced589520ffffea0d97e4d8de2cb5e38 high confidence bulk rna-seq dataset_accession: GSE308395 dataset_title: Identification of Differentially Expressed Genes and Associated Immune Cell Types In South African Gallbladder Cancer Patients organi... keyword match keyword match: bulk rna-seq
organism Homo sapiens dataset GSE308395 Runtime Siftome inference GEO:dataset:GSE308395:c0415748aab14b924c1fbb60bb9a0291ced589520ffffea0d97e4d8de2cb5e38 high confidence homo sapiens dataset_accession: GSE308395 dataset_title: Identification of Differentially Expressed Genes and Associated Immune Cell Types In South African Gallbladder Cancer Patients organi... keyword match keyword match: homo sapiens
sample_type normal tissue sample GSM9244690 Runtime Siftome inference GEO:sample:GSM9244690:00227c0a906890a3905bad2fdd3afec826a83d21f29e130a307fe1fc8e01157d low confidence normal sample_accession: GSM9244690 sample_title: Normal Gallbladder tissue, patient 1 source_name: Gallbladder characteristics: tissue: Gallbladder Normal Gallbladder tissue, patient 1 controlled vocabulary controlled vocabulary sample type match: normal
sample_type normal tissue sample GSM9244691 Runtime Siftome inference GEO:sample:GSM9244691:8fae434a14454b648ba249b0376c6c25c37a549e183bc7cf530ba906d30a5cc9 low confidence normal sample_accession: GSM9244691 sample_title: Normal Gallbladder tissue, patient 2 source_name: Gallbladder characteristics: tissue: Gallbladder Normal Gallbladder tissue, patient 2 controlled vocabulary controlled vocabulary sample type match: normal
sample_type tumor sample sample GSM9244692 Runtime Siftome inference GEO:sample:GSM9244692:94db6ef5c6cb641769a4fd829fc0d214cb6a2299e3a5b5c7764e7c2c02e853e7 low confidence tumour sample_accession: GSM9244692 sample_title: Gallbladder tumour, patient 1 source_name: Gallbladder characteristics: tissue: Gallbladder Gallbladder tumour, patient 1 controlled vocabulary controlled vocabulary sample type match: tumour
sample_type tumor sample sample GSM9244693 Runtime Siftome inference GEO:sample:GSM9244693:d5aadf6e4d0ae83b9e4cb25c4bbcb076ef1a9f1f4610ff8382432e38d57b12d4 low confidence tumour sample_accession: GSM9244693 sample_title: Gallbladder tumour, patient 2 source_name: Gallbladder characteristics: tissue: Gallbladder Gallbladder tumour, patient 2 controlled vocabulary controlled vocabulary sample type match: tumour
sample_type tumor sample sample GSM9244694 Runtime Siftome inference GEO:sample:GSM9244694:d7883c9f71c9b9e57b6902abcb0ccd74a4549e4fb01cb5b482758c0082fbfbde low confidence tumour sample_accession: GSM9244694 sample_title: Gallbladder tumour, patient 3 source_name: Gallbladder characteristics: tissue: Gallbladder Gallbladder tumour, patient 3 controlled vocabulary controlled vocabulary sample type match: tumour
sample_type tumor sample sample GSM9244695 Runtime Siftome inference GEO:sample:GSM9244695:71917d6357534ea6461593329659bf53e68231eac7d6c7dec1be66b2db7a2ccb low confidence tumour sample_accession: GSM9244695 sample_title: Gallbladder tumour, patient 4 source_name: Gallbladder characteristics: tissue: Gallbladder Gallbladder tumour, patient 4 controlled vocabulary controlled vocabulary sample type match: tumour
sample_type tumor sample sample GSM9244696 Runtime Siftome inference GEO:sample:GSM9244696:8d543a3d5a4bef5822756a4972e2fce0f93f8250ab5e43ec22c2f25b4ea81dd9 low confidence tumour sample_accession: GSM9244696 sample_title: Gallbladder tumour, patient 5 source_name: Gallbladder characteristics: tissue: Gallbladder Gallbladder tumour, patient 5 controlled vocabulary controlled vocabulary sample type match: tumour
sample_type tumor sample sample GSM9244697 Runtime Siftome inference GEO:sample:GSM9244697:2e8738276a60a4e06b3f98cbaf4631bd935ff957fda93a2fb7136bf7c012d66e low confidence tumour sample_accession: GSM9244697 sample_title: Gallbladder tumour, patient 6 source_name: Gallbladder characteristics: tissue: Gallbladder Gallbladder tumour, patient 6 controlled vocabulary controlled vocabulary sample type match: tumour
sample_type tumor sample sample GSM9244698 Runtime Siftome inference GEO:sample:GSM9244698:c2c76e694e2b8425bd3ed1beafdf79dfcf6b736a011a5088a7839046d9466f75 low confidence tumour sample_accession: GSM9244698 sample_title: Gallbladder tumour, patient 7 source_name: Gallbladder characteristics: tissue: Gallbladder Gallbladder tumour, patient 7 controlled vocabulary controlled vocabulary sample type match: tumour
sample_type tumor sample sample GSM9244699 Runtime Siftome inference GEO:sample:GSM9244699:02eef29e69ac9f57ee926901222db1264afe429157611dee58d4933cbc4c9064 low confidence tumour sample_accession: GSM9244699 sample_title: Gallbladder tumour, patient 8 source_name: Gallbladder characteristics: tissue: Gallbladder Gallbladder tumour, patient 8 controlled vocabulary controlled vocabulary sample type match: tumour

Sample Group Preview

Possible case samples

Samples currently treated as the comparison case group.

8
  • GSM9244692 Gallbladder tumour, patient 1 tumor sample Case marker detected. Gallbladder tissue: Gallbladder
  • GSM9244693 Gallbladder tumour, patient 2 tumor sample Case marker detected. Gallbladder tissue: Gallbladder
  • GSM9244694 Gallbladder tumour, patient 3 tumor sample Case marker detected. Gallbladder tissue: Gallbladder
  • GSM9244695 Gallbladder tumour, patient 4 tumor sample Case marker detected. Gallbladder tissue: Gallbladder
  • GSM9244696 Gallbladder tumour, patient 5 tumor sample Case marker detected. Gallbladder tissue: Gallbladder
  • GSM9244697 Gallbladder tumour, patient 6 tumor sample Case marker detected. Gallbladder tissue: Gallbladder
  • GSM9244698 Gallbladder tumour, patient 7 tumor sample Case marker detected. Gallbladder tissue: Gallbladder
  • GSM9244699 Gallbladder tumour, patient 8 tumor sample Case marker detected. Gallbladder tissue: Gallbladder

Possible control samples

Samples currently treated as controls or baseline.

2
  • GSM9244690 Normal Gallbladder tissue, patient 1 normal tissue Control marker detected. Gallbladder tissue: Gallbladder
  • GSM9244691 Normal Gallbladder tissue, patient 2 normal tissue Control marker detected. Gallbladder tissue: Gallbladder

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
  • GSM9244690 Normal Gallbladder tissue, patient 1 Gallbladder tissue: Gallbladder
  • GSM9244691 Normal Gallbladder tissue, patient 2 Gallbladder tissue: Gallbladder

tumor sample

8 samples
  • GSM9244692 Gallbladder tumour, patient 1 Gallbladder tissue: Gallbladder
  • GSM9244693 Gallbladder tumour, patient 2 Gallbladder tissue: Gallbladder
  • GSM9244694 Gallbladder tumour, patient 3 Gallbladder tissue: Gallbladder
  • GSM9244695 Gallbladder tumour, patient 4 Gallbladder tissue: Gallbladder
  • GSM9244696 Gallbladder tumour, patient 5 Gallbladder tissue: Gallbladder
  • GSM9244697 Gallbladder tumour, patient 6 Gallbladder tissue: Gallbladder
  • GSM9244698 Gallbladder tumour, patient 7 Gallbladder tissue: Gallbladder
  • GSM9244699 Gallbladder tumour, patient 8 Gallbladder tissue: Gallbladder

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 colorectal/CRC disease context is not explicit.

Sample Links

10 samples

Review Audit Trail

0 decisions

No review decisions have been stored for this dataset.