Siftome Phase 3L

GSE117627

Intrahepatic MAIT cell gene expression revealed by RNA-seq

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
2018-07-24
Last update
2019-03-21
Organization
Zhongshan Hospital
Department
Not available
Public date
2018-12-01
Experiment types
Expression profiling by high throughput sequencing
Platforms
GPL20301 Illumina HiSeq 4000 (Homo sapiens)
Series type
Series
SubSeries
Not available
BioProject
PRJNA482707
Supplementary files
TAR: GSE117627_RAW.tar; CSV: GSE117627_read_count_matrix.csv.gz
Organism
Homo sapiens
Assay
bulk RNA-seq
Samples
15
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
100% 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

10/10 pts

No dataset warnings are present.

Metadata normalization

10/10 pts

Metadata quality is high enough to support downstream handoff.

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
Not suitable Dataset does not meet the current suitability threshold.

Score Components

  • relevance 100% Disease or condition metadata normalized. Organism normalized. Assay type normalized. Tissue metadata 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 100% 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 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 10 samples
  • Likely control group normal tissue 5 samples

Warnings

No ranking warnings are active.

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 0 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.
  • 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: 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
GSE117627
Sample records
15 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
GSE117627
  • 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
GSE117627
  • 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
GSE117627
  • 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: GSE117627
dataset_title: Intrahepatic MAIT cell gene expression revealed by RNA-seq
organism: Homo sapiens
assay_type: bulk RNA-seq
processed_data_available: true
raw_data_available: true
submission_date: 2018-07-24
last_update_date: 2019-03-21
organization_name: Zhongshan Hospital
department: Not available
public_date: 2018-12-01
experiment_types: Expression profiling by high throughput sequencing
platforms: GPL20301 Illumina HiSeq 4000 (Homo sapiens)
sub_series: Not available
bioproject: PRJNA482707
supplementary_files: TAR: GSE117627_RAW.tar; CSV: GSE117627_read_count_matrix.csv.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.

Why It May Not Be Suitable

  • Non-colorectal cancer context downgraded for colorectal tumor-vs-normal tissue ranking.
  • 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

No warnings

Normalized Fields

24 fields
Field Value Source Origin Confidence Evidence Reason
assay_type bulk RNA-seq dataset GSE117627 Runtime Siftome inference GEO:dataset:GSE117627:e2307093bd59eae6426b445ffca778ceb684dce5ac23df7fe1a859531171a85a high confidence bulk rna-seq dataset_accession: GSE117627 dataset_title: Intrahepatic MAIT cell gene expression revealed by RNA-seq organism: Homo sapiens assay_type: bulk RNA-seq processed_data_available: ... keyword match keyword match: bulk rna-seq
disease colorectal cancer dataset GSE117627 Runtime Siftome inference GEO:dataset:GSE117627:e2307093bd59eae6426b445ffca778ceb684dce5ac23df7fe1a859531171a85a medium confidence read dataset_accession: GSE117627 dataset_title: Intrahepatic MAIT cell gene expression revealed by RNA-seq organism: Homo sapiens assay_type: bulk RNA-seq processed_data_available: ... controlled vocabulary controlled vocabulary disease match: read
organism Homo sapiens dataset GSE117627 Runtime Siftome inference GEO:dataset:GSE117627:e2307093bd59eae6426b445ffca778ceb684dce5ac23df7fe1a859531171a85a high confidence homo sapiens dataset_accession: GSE117627 dataset_title: Intrahepatic MAIT cell gene expression revealed by RNA-seq organism: Homo sapiens assay_type: bulk RNA-seq processed_data_available: ... keyword match keyword match: homo sapiens
sample_type tumor sample sample GSM3305280 Runtime Siftome inference GEO:sample:GSM3305280:d8889d9b093484db26b817850719e30bfb7a04d929558ed97e8b761bda8d240d low confidence tumor sample_accession: GSM3305280 sample_title: 1P source_name: HCC peritumoral tissues characteristics: disease status: HCC; tissue source: Peritumor; cell type: Immune cells; cell ... controlled vocabulary controlled vocabulary sample type match: tumor
sample_type tumor sample sample GSM3305281 Runtime Siftome inference GEO:sample:GSM3305281:876e839b37a29c628255a9d21237e5c8966190b6e445605bc43c320b176db5b5 low confidence tumor sample_accession: GSM3305281 sample_title: 2P source_name: HCC peritumoral tissues characteristics: disease status: HCC; tissue source: Peritumor; cell type: Immune cells; cell ... controlled vocabulary controlled vocabulary sample type match: tumor
sample_type tumor sample sample GSM3305282 Runtime Siftome inference GEO:sample:GSM3305282:00c10c96b08f74946f9ac51c593edd96679b7edb99b2b1a8d8e64868f9e224b8 low confidence tumor sample_accession: GSM3305282 sample_title: 3P source_name: HCC peritumoral tissues characteristics: disease status: HCC; tissue source: Peritumor; cell type: Immune cells; cell ... controlled vocabulary controlled vocabulary sample type match: tumor
sample_type tumor sample sample GSM3305283 Runtime Siftome inference GEO:sample:GSM3305283:019bde2683a2e2e649abfc941d1d391026b4d06627bff6a04fc7bfc714f4e5c0 low confidence tumor sample_accession: GSM3305283 sample_title: 4P source_name: HCC peritumoral tissues characteristics: disease status: HCC; tissue source: Peritumor; cell type: Immune cells; cell ... controlled vocabulary controlled vocabulary sample type match: tumor
sample_type tumor sample sample GSM3305284 Runtime Siftome inference GEO:sample:GSM3305284:5ce833440300d21d7cd6f2cefaabbbd5dabb6ce4615e0a85bdeae9be5671b1a1 low confidence tumor sample_accession: GSM3305284 sample_title: 5P source_name: HCC peritumoral tissues characteristics: disease status: HCC; tissue source: Peritumor; cell type: Immune cells; cell ... controlled vocabulary controlled vocabulary sample type match: tumor
sample_type normal tissue sample GSM3305285 Runtime Siftome inference GEO:sample:GSM3305285:723f74a208579725224937f0a9d8b33434c53272371000c91c51595cead949bc low confidence normal sample_accession: GSM3305285 sample_title: HDL1 source_name: Normal liver tissues characteristics: disease status: Healthy; tissue source: Liver; cell type: Immune cells; cell s... controlled vocabulary controlled vocabulary sample type match: normal
sample_type normal tissue sample GSM3305286 Runtime Siftome inference GEO:sample:GSM3305286:c722752278dcbf81cccfd925b5802eecfb2c8fe6b3e102c548556ae57ec09d9e low confidence normal sample_accession: GSM3305286 sample_title: HDL2 source_name: Normal liver tissues characteristics: disease status: Healthy; tissue source: Liver; cell type: Immune cells; cell s... controlled vocabulary controlled vocabulary sample type match: normal
sample_type normal tissue sample GSM3305287 Runtime Siftome inference GEO:sample:GSM3305287:ab5ba51ca45b4f7654d8aaf31e80326779821ae3239d9fd3718158e37fd8f2f2 low confidence normal sample_accession: GSM3305287 sample_title: HDL3 source_name: Normal liver tissues characteristics: disease status: Healthy; tissue source: Liver; cell type: Immune cells; cell s... controlled vocabulary controlled vocabulary sample type match: normal
sample_type normal tissue sample GSM3305288 Runtime Siftome inference GEO:sample:GSM3305288:4a56224b2a1d67d081eb165694882a842dad1e9dbe8cde7a3068b62221c73864 low confidence normal sample_accession: GSM3305288 sample_title: HDL4 source_name: Normal liver tissues characteristics: disease status: Healthy; tissue source: Liver; cell type: Immune cells; cell s... controlled vocabulary controlled vocabulary sample type match: normal
sample_type normal tissue sample GSM3305289 Runtime Siftome inference GEO:sample:GSM3305289:fe572dc44005751c79860e55474348371a273ca67a33fa844054fb12d9f1fbaf low confidence normal sample_accession: GSM3305289 sample_title: HDL5 source_name: Normal liver tissues characteristics: disease status: Healthy; tissue source: Liver; cell type: Immune cells; cell s... controlled vocabulary controlled vocabulary sample type match: normal
sample_type tumor sample sample GSM3305290 Runtime Siftome inference GEO:sample:GSM3305290:ade4b18478b11a1931de78da30d6377aa8f9fba039b22da4908766d3c48a32dc low confidence tumor sample_accession: GSM3305290 sample_title: 1T source_name: HCC tumoral tissues characteristics: disease status: HCC; tissue source: Tumor; cell type: Immune cells; cell subset: ... controlled vocabulary controlled vocabulary sample type match: tumor
sample_type tumor sample sample GSM3305291 Runtime Siftome inference GEO:sample:GSM3305291:c743090d7d0580da2686143c8ee27987d967a28bb0507c5a372eeb6f647864d2 low confidence tumor sample_accession: GSM3305291 sample_title: 2T source_name: HCC tumoral tissues characteristics: disease status: HCC; tissue source: Tumor; cell type: Immune cells; cell subset: ... controlled vocabulary controlled vocabulary sample type match: tumor
sample_type tumor sample sample GSM3305292 Runtime Siftome inference GEO:sample:GSM3305292:dfc12d8a0622e53af2a71faf4a2a72573fe0417ef867097e3e085d8d1fd02b4c low confidence tumor sample_accession: GSM3305292 sample_title: 3T source_name: HCC tumoral tissues characteristics: disease status: HCC; tissue source: Tumor; cell type: Immune cells; cell subset: ... controlled vocabulary controlled vocabulary sample type match: tumor
sample_type tumor sample sample GSM3305293 Runtime Siftome inference GEO:sample:GSM3305293:6a8d5ea9aef3cbcbf675c3412d4dacad3818dfaba7635d14d041d4836e065f0c low confidence tumor sample_accession: GSM3305293 sample_title: 4T source_name: HCC tumoral tissues characteristics: disease status: HCC; tissue source: Tumor; cell type: Immune cells; cell subset: ... controlled vocabulary controlled vocabulary sample type match: tumor
sample_type tumor sample sample GSM3305294 Runtime Siftome inference GEO:sample:GSM3305294:53eb9292f393f88bf8b44107524d30a63bfaf6b80d1bd5a13d1bd431deb43e48 low confidence tumor sample_accession: GSM3305294 sample_title: 5T source_name: HCC tumoral tissues characteristics: disease status: HCC; tissue source: Tumor; cell type: Immune cells; cell subset: ... controlled vocabulary controlled vocabulary sample type match: tumor
tissue liver dataset GSE117627 Runtime Siftome inference GEO:dataset:GSE117627:e2307093bd59eae6426b445ffca778ceb684dce5ac23df7fe1a859531171a85a medium confidence hepatic dataset_accession: GSE117627 dataset_title: Intrahepatic MAIT cell gene expression revealed by RNA-seq organism: Homo sapiens assay_type: bulk RNA-seq processed_data_available: ... controlled vocabulary controlled vocabulary tissue match: hepatic
tissue liver sample GSM3305285 Runtime Siftome inference GEO:sample:GSM3305285:723f74a208579725224937f0a9d8b33434c53272371000c91c51595cead949bc low confidence liver sample_accession: GSM3305285 sample_title: HDL1 source_name: Normal liver tissues characteristics: disease status: Healthy; tissue source: Liver; cell type: Immune cells; cell s... controlled vocabulary controlled vocabulary tissue match: liver
tissue liver sample GSM3305286 Runtime Siftome inference GEO:sample:GSM3305286:c722752278dcbf81cccfd925b5802eecfb2c8fe6b3e102c548556ae57ec09d9e low confidence liver sample_accession: GSM3305286 sample_title: HDL2 source_name: Normal liver tissues characteristics: disease status: Healthy; tissue source: Liver; cell type: Immune cells; cell s... controlled vocabulary controlled vocabulary tissue match: liver
tissue liver sample GSM3305287 Runtime Siftome inference GEO:sample:GSM3305287:ab5ba51ca45b4f7654d8aaf31e80326779821ae3239d9fd3718158e37fd8f2f2 low confidence liver sample_accession: GSM3305287 sample_title: HDL3 source_name: Normal liver tissues characteristics: disease status: Healthy; tissue source: Liver; cell type: Immune cells; cell s... controlled vocabulary controlled vocabulary tissue match: liver
tissue liver sample GSM3305288 Runtime Siftome inference GEO:sample:GSM3305288:4a56224b2a1d67d081eb165694882a842dad1e9dbe8cde7a3068b62221c73864 low confidence liver sample_accession: GSM3305288 sample_title: HDL4 source_name: Normal liver tissues characteristics: disease status: Healthy; tissue source: Liver; cell type: Immune cells; cell s... controlled vocabulary controlled vocabulary tissue match: liver
tissue liver sample GSM3305289 Runtime Siftome inference GEO:sample:GSM3305289:fe572dc44005751c79860e55474348371a273ca67a33fa844054fb12d9f1fbaf low confidence liver sample_accession: GSM3305289 sample_title: HDL5 source_name: Normal liver tissues characteristics: disease status: Healthy; tissue source: Liver; cell type: Immune cells; cell s... controlled vocabulary controlled vocabulary tissue match: liver

Sample Group Preview

Possible case samples

Samples currently treated as the comparison case group.

10
  • GSM3305280 1P tumor sample Case marker detected. HCC peritumoral tissues disease status: HCC; tissue source: Peritumor; cell type: Immune cells; cell subset: CD4- MAIT cells; subset definition: CD3+CD4-CD161+TCRva7.2+
  • GSM3305281 2P tumor sample Case marker detected. HCC peritumoral tissues disease status: HCC; tissue source: Peritumor; cell type: Immune cells; cell subset: CD4- MAIT cells; subset definition: CD3+CD4-CD161+TCRva7.2+
  • GSM3305282 3P tumor sample Case marker detected. HCC peritumoral tissues disease status: HCC; tissue source: Peritumor; cell type: Immune cells; cell subset: CD4- MAIT cells; subset definition: CD3+CD4-CD161+TCRva7.2+
  • GSM3305283 4P tumor sample Case marker detected. HCC peritumoral tissues disease status: HCC; tissue source: Peritumor; cell type: Immune cells; cell subset: CD4- MAIT cells; subset definition: CD3+CD4-CD161+TCRva7.2+
  • GSM3305284 5P tumor sample Case marker detected. HCC peritumoral tissues disease status: HCC; tissue source: Peritumor; cell type: Immune cells; cell subset: CD4- MAIT cells; subset definition: CD3+CD4-CD161+TCRva7.2+
  • GSM3305290 1T tumor sample Case marker detected. HCC tumoral tissues disease status: HCC; tissue source: Tumor; cell type: Immune cells; cell subset: CD4- MAIT cells; subset definition: CD3+CD4-CD161+TCRva7.2+
  • GSM3305291 2T tumor sample Case marker detected. HCC tumoral tissues disease status: HCC; tissue source: Tumor; cell type: Immune cells; cell subset: CD4- MAIT cells; subset definition: CD3+CD4-CD161+TCRva7.2+
  • GSM3305292 3T tumor sample Case marker detected. HCC tumoral tissues disease status: HCC; tissue source: Tumor; cell type: Immune cells; cell subset: CD4- MAIT cells; subset definition: CD3+CD4-CD161+TCRva7.2+
  • GSM3305293 4T tumor sample Case marker detected. HCC tumoral tissues disease status: HCC; tissue source: Tumor; cell type: Immune cells; cell subset: CD4- MAIT cells; subset definition: CD3+CD4-CD161+TCRva7.2+
  • GSM3305294 5T tumor sample Case marker detected. HCC tumoral tissues disease status: HCC; tissue source: Tumor; cell type: Immune cells; cell subset: CD4- MAIT cells; subset definition: CD3+CD4-CD161+TCRva7.2+

Possible control samples

Samples currently treated as controls or baseline.

5
  • GSM3305285 HDL1 normal tissue Control marker detected. Normal liver tissues disease status: Healthy; tissue source: Liver; cell type: Immune cells; cell subset: CD4- MAIT cells; subset definition: CD3+CD4-CD161+TCRva7.2+
  • GSM3305286 HDL2 normal tissue Control marker detected. Normal liver tissues disease status: Healthy; tissue source: Liver; cell type: Immune cells; cell subset: CD4- MAIT cells; subset definition: CD3+CD4-CD161+TCRva7.2+
  • GSM3305287 HDL3 normal tissue Control marker detected. Normal liver tissues disease status: Healthy; tissue source: Liver; cell type: Immune cells; cell subset: CD4- MAIT cells; subset definition: CD3+CD4-CD161+TCRva7.2+
  • GSM3305288 HDL4 normal tissue Control marker detected. Normal liver tissues disease status: Healthy; tissue source: Liver; cell type: Immune cells; cell subset: CD4- MAIT cells; subset definition: CD3+CD4-CD161+TCRva7.2+
  • GSM3305289 HDL5 normal tissue Control marker detected. Normal liver tissues disease status: Healthy; tissue source: Liver; cell type: Immune cells; cell subset: CD4- MAIT cells; subset definition: CD3+CD4-CD161+TCRva7.2+

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

100 pts
Clarity
100%
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 normalized. Treatment clarity: No unclear treatment split detected in the sample metadata. Replicate clarity: No pooled sample or technical replicate flags detected. Data availability clarity: Dataset-level processed or raw data availability is explicit.

Detected Sample Groups

tumor sample

10 samples
  • GSM3305280 1P HCC peritumoral tissues disease status: HCC; tissue source: Peritumor; cell type: Immune cells; cell subset: CD4- MAIT cells; subset definition: CD3+CD4-CD161+TCRva7.2+
  • GSM3305281 2P HCC peritumoral tissues disease status: HCC; tissue source: Peritumor; cell type: Immune cells; cell subset: CD4- MAIT cells; subset definition: CD3+CD4-CD161+TCRva7.2+
  • GSM3305282 3P HCC peritumoral tissues disease status: HCC; tissue source: Peritumor; cell type: Immune cells; cell subset: CD4- MAIT cells; subset definition: CD3+CD4-CD161+TCRva7.2+
  • GSM3305283 4P HCC peritumoral tissues disease status: HCC; tissue source: Peritumor; cell type: Immune cells; cell subset: CD4- MAIT cells; subset definition: CD3+CD4-CD161+TCRva7.2+
  • GSM3305284 5P HCC peritumoral tissues disease status: HCC; tissue source: Peritumor; cell type: Immune cells; cell subset: CD4- MAIT cells; subset definition: CD3+CD4-CD161+TCRva7.2+
  • GSM3305290 1T HCC tumoral tissues disease status: HCC; tissue source: Tumor; cell type: Immune cells; cell subset: CD4- MAIT cells; subset definition: CD3+CD4-CD161+TCRva7.2+
  • GSM3305291 2T HCC tumoral tissues disease status: HCC; tissue source: Tumor; cell type: Immune cells; cell subset: CD4- MAIT cells; subset definition: CD3+CD4-CD161+TCRva7.2+
  • GSM3305292 3T HCC tumoral tissues disease status: HCC; tissue source: Tumor; cell type: Immune cells; cell subset: CD4- MAIT cells; subset definition: CD3+CD4-CD161+TCRva7.2+
  • GSM3305293 4T HCC tumoral tissues disease status: HCC; tissue source: Tumor; cell type: Immune cells; cell subset: CD4- MAIT cells; subset definition: CD3+CD4-CD161+TCRva7.2+
  • GSM3305294 5T HCC tumoral tissues disease status: HCC; tissue source: Tumor; cell type: Immune cells; cell subset: CD4- MAIT cells; subset definition: CD3+CD4-CD161+TCRva7.2+

normal tissue

5 samples
  • GSM3305285 HDL1 Normal liver tissues disease status: Healthy; tissue source: Liver; cell type: Immune cells; cell subset: CD4- MAIT cells; subset definition: CD3+CD4-CD161+TCRva7.2+
  • GSM3305286 HDL2 Normal liver tissues disease status: Healthy; tissue source: Liver; cell type: Immune cells; cell subset: CD4- MAIT cells; subset definition: CD3+CD4-CD161+TCRva7.2+
  • GSM3305287 HDL3 Normal liver tissues disease status: Healthy; tissue source: Liver; cell type: Immune cells; cell subset: CD4- MAIT cells; subset definition: CD3+CD4-CD161+TCRva7.2+
  • GSM3305288 HDL4 Normal liver tissues disease status: Healthy; tissue source: Liver; cell type: Immune cells; cell subset: CD4- MAIT cells; subset definition: CD3+CD4-CD161+TCRva7.2+
  • GSM3305289 HDL5 Normal liver tissues disease status: Healthy; tissue source: Liver; cell type: Immune cells; cell subset: CD4- MAIT cells; subset definition: CD3+CD4-CD161+TCRva7.2+

Score Breakdown

100%

relevance

  • Disease or condition metadata normalized.
  • Organism normalized.
  • Assay type normalized.
  • Tissue metadata 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.
100%

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 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

15 samples

Review Audit Trail

0 decisions

No review decisions have been stored for this dataset.