Siftome Phase 3L

GSE234304

Co-enrichment of cancer-associated bacterial taxa is correlated with immune cell infiltrates in esophageal tumor tissue

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
2023-06-06
Last update
2024-02-07
Organization
NIH
Department
Not available
Public date
2024-02-07
Experiment types
Expression profiling by high throughput sequencing
Platforms
GPL18573 Illumina NextSeq 500 (Homo sapiens)
Series type
Series
SubSeries
Not available
BioProject
PRJNA980719
Supplementary files
CSV: GSE234304_raw_counts.csv.gz
Organism
Homo sapiens
Assay
bulk RNA-seq
Samples
44
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

  • 6 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 6 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
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 17 samples
  • Likely control group normal tissue 21 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
GSE234304
Sample records
44 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
GSE234304
  • 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
GSE234304
  • 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
GSE234304
  • 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: GSE234304
dataset_title: Co-enrichment of cancer-associated bacterial taxa is correlated with immune cell infiltrates in esophageal tumor tissue
organism: Homo sapiens
assay_type: bulk RNA-seq
processed_data_available: true
raw_data_available: true
submission_date: 2023-06-06
last_update_date: 2024-02-07
organization_name: NIH
department: Not available
public_date: 2024-02-07
experiment_types: Expression profiling by high throughput sequencing
platforms: GPL18573 Illumina NextSeq 500 (Homo sapiens)
sub_series: Not available
bioproject: PRJNA980719
supplementary_files: CSV: GSE234304_raw_counts.csv.gz
series_type: Series

Why It Matched

  • Tumor vs unmatched normal · Tissue · suitability 5%.
  • Prioritized assay: bulk RNA-seq is the active assay expectation.
  • Downgraded disease context: colorectal/GI relevance is unclear.
  • Processed data is available for downstream review.
  • 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

40 fields
Field Value Source Origin Confidence Evidence Reason
assay_type bulk RNA-seq dataset GSE234304 Runtime Siftome inference GEO:dataset:GSE234304:1edb97f2702b9e1359c1708cc716832e41aaa7a6058342f790c8a3b8a35b91fe high confidence bulk rna-seq dataset_accession: GSE234304 dataset_title: Co-enrichment of cancer-associated bacterial taxa is correlated with immune cell infiltrates in esophageal tumor tissue organism: Hom... keyword match keyword match: bulk rna-seq
organism Homo sapiens dataset GSE234304 Runtime Siftome inference GEO:dataset:GSE234304:1edb97f2702b9e1359c1708cc716832e41aaa7a6058342f790c8a3b8a35b91fe high confidence homo sapiens dataset_accession: GSE234304 dataset_title: Co-enrichment of cancer-associated bacterial taxa is correlated with immune cell infiltrates in esophageal tumor tissue organism: Hom... keyword match keyword match: homo sapiens
sample_type normal tissue sample GSM7462006 Runtime Siftome inference GEO:sample:GSM7462006:372913350bd3f1c7651689997254fec1926005be6b97e6522e5ed5cabc7213ea medium confidence non-tumor sample_accession: GSM7462006 sample_title: 10153N source_name: esophageal tissue characteristics: tissue: Non-tumor 10153N controlled vocabulary controlled vocabulary sample type match: non-tumor
sample_type normal tissue sample GSM7462007 Runtime Siftome inference GEO:sample:GSM7462007:a538dc89b44508923c2bd85ef3e92806ff8bb6c07a09683bfedd520ab775693d medium confidence non-tumor sample_accession: GSM7462007 sample_title: 11267N source_name: esophageal tissue characteristics: tissue: Non-tumor 11267N controlled vocabulary controlled vocabulary sample type match: non-tumor
sample_type tumor sample sample GSM7462008 Runtime Siftome inference GEO:sample:GSM7462008:5ad9ecace2470ad937ad8b0669125ac203082f97da8bb5ed2fe92cfabceae0e5 low confidence tumor sample_accession: GSM7462008 sample_title: 11267T source_name: esophageal tumor characteristics: tissue: Tumor 11267T controlled vocabulary controlled vocabulary sample type match: tumor
sample_type normal tissue sample GSM7462009 Runtime Siftome inference GEO:sample:GSM7462009:bcfc2d91ec2ccc80c9ca210b609aa9e0ae03c75e52b3611195d5ff7a721b482d medium confidence non-tumor sample_accession: GSM7462009 sample_title: 11362N source_name: esophageal tissue characteristics: tissue: Non-tumor 11362N controlled vocabulary controlled vocabulary sample type match: non-tumor
sample_type tumor sample sample GSM7462010 Runtime Siftome inference GEO:sample:GSM7462010:e6b19fe8d0c2459ada034ab4d317b81f0aa372ad941bd204da2998c329f15ac3 low confidence tumor sample_accession: GSM7462010 sample_title: 11362T source_name: esophageal tumor characteristics: tissue: Tumor 11362T controlled vocabulary controlled vocabulary sample type match: tumor
sample_type tumor sample sample GSM7462011 Runtime Siftome inference GEO:sample:GSM7462011:cb2331479efcd283df9d18cd6b92e08c2790d42aa42ea33d979b7c1fe2da413c low confidence tumor sample_accession: GSM7462011 sample_title: 11455T source_name: esophageal tumor characteristics: tissue: Tumor 11455T controlled vocabulary controlled vocabulary sample type match: tumor
sample_type normal tissue sample GSM7462012 Runtime Siftome inference GEO:sample:GSM7462012:6ce08b55595df27a068767517227578d2c2bfd6b6eed4ad846e52af09c210646 medium confidence non-tumor sample_accession: GSM7462012 sample_title: 11738N source_name: esophageal tissue characteristics: tissue: Non-tumor 11738N controlled vocabulary controlled vocabulary sample type match: non-tumor
sample_type normal tissue sample GSM7462014 Runtime Siftome inference GEO:sample:GSM7462014:98a668e39c4ef13cfa0d8c6d4f2b920992727ab07c233deb9e389a0397499987 medium confidence non-tumor sample_accession: GSM7462014 sample_title: 11802N source_name: esophageal tissue characteristics: tissue: Non-tumor 11802N controlled vocabulary controlled vocabulary sample type match: non-tumor
sample_type tumor sample sample GSM7462015 Runtime Siftome inference GEO:sample:GSM7462015:68309184bf4c005ac0cb2d833ce9b01d63322f3df117141a8abb9076105b5142 low confidence tumor sample_accession: GSM7462015 sample_title: 12291T source_name: esophageal tumor characteristics: tissue: Tumor 12291T controlled vocabulary controlled vocabulary sample type match: tumor
sample_type normal tissue sample GSM7462016 Runtime Siftome inference GEO:sample:GSM7462016:9321caba349785a920cfb67422b7c5557f3792f27c980847e265bb3966483c18 medium confidence non-tumor sample_accession: GSM7462016 sample_title: 12306N source_name: esophageal tissue characteristics: tissue: Non-tumor 12306N controlled vocabulary controlled vocabulary sample type match: non-tumor
sample_type normal tissue sample GSM7462017 Runtime Siftome inference GEO:sample:GSM7462017:bdc08a9e29de8472ec063af66fdfe110b52d12aae07f6c1be9e4d627235b1c7d medium confidence non-tumor sample_accession: GSM7462017 sample_title: 12631N source_name: esophageal tissue characteristics: tissue: Non-tumor 12631N controlled vocabulary controlled vocabulary sample type match: non-tumor
sample_type tumor sample sample GSM7462018 Runtime Siftome inference GEO:sample:GSM7462018:24905af270bf52b7300743bb2a68632b1cf9bc93f0e721b951a924650c939ea1 low confidence tumor sample_accession: GSM7462018 sample_title: 12631T source_name: esophageal tumor characteristics: tissue: Tumor 12631T controlled vocabulary controlled vocabulary sample type match: tumor
sample_type normal tissue sample GSM7462019 Runtime Siftome inference GEO:sample:GSM7462019:f80e8d5b296ca0bfd42fb999bd062e5d0b4563e6df55ac173855d38880bca37e medium confidence non-tumor sample_accession: GSM7462019 sample_title: 12672N source_name: esophageal tissue characteristics: tissue: Non-tumor 12672N controlled vocabulary controlled vocabulary sample type match: non-tumor
sample_type tumor sample sample GSM7462020 Runtime Siftome inference GEO:sample:GSM7462020:65c5367f7c4166aa7d05a7234764002c4f2cf519960f1269faf02f5b79253c97 low confidence tumor sample_accession: GSM7462020 sample_title: 12672T source_name: esophageal tumor characteristics: tissue: Tumor 12672T controlled vocabulary controlled vocabulary sample type match: tumor
sample_type normal tissue sample GSM7462022 Runtime Siftome inference GEO:sample:GSM7462022:22bf565e6e98c57573097723603fdc2795ab17153ddcc95b07a65ec22ef76fe1 medium confidence non-tumor sample_accession: GSM7462022 sample_title: 12841N source_name: esophageal tissue characteristics: tissue: Non-tumor 12841N controlled vocabulary controlled vocabulary sample type match: non-tumor
sample_type normal tissue sample GSM7462023 Runtime Siftome inference GEO:sample:GSM7462023:ba8029ff9a4563c303115cb694ba556fbc861a3e470e265950bb8100d0ee97e6 medium confidence non-tumor sample_accession: GSM7462023 sample_title: 12943N source_name: esophageal tissue characteristics: tissue: Non-tumor 12943N controlled vocabulary controlled vocabulary sample type match: non-tumor
sample_type tumor sample sample GSM7462024 Runtime Siftome inference GEO:sample:GSM7462024:d8f19c62467e76f307f1ade45346a8f2953579358e6eb2050a49848cc265ad4a low confidence tumor sample_accession: GSM7462024 sample_title: 12943T source_name: esophageal tumor characteristics: tissue: Tumor 12943T controlled vocabulary controlled vocabulary sample type match: tumor
sample_type normal tissue sample GSM7462025 Runtime Siftome inference GEO:sample:GSM7462025:aef1531016e8350a33348a7bf4557afbb339ce05444d123442a28d4c24c2f1ca medium confidence non-tumor sample_accession: GSM7462025 sample_title: 12997N source_name: esophageal tissue characteristics: tissue: Non-tumor 12997N controlled vocabulary controlled vocabulary sample type match: non-tumor
sample_type tumor sample sample GSM7462026 Runtime Siftome inference GEO:sample:GSM7462026:66351d2215d261e4a3c8517a0ce0213f8b0b82c28db9e3da9a2a75f1261fe246 low confidence tumor sample_accession: GSM7462026 sample_title: 12997T source_name: esophageal tumor characteristics: tissue: Tumor 12997T controlled vocabulary controlled vocabulary sample type match: tumor
sample_type normal tissue sample GSM7462027 Runtime Siftome inference GEO:sample:GSM7462027:ed1ed1ecff31fdc1ff82f5a77ff9c405400ec17a8fb7ce57721a7a643afe9e0b medium confidence non-tumor sample_accession: GSM7462027 sample_title: 13008N source_name: esophageal tissue characteristics: tissue: Non-tumor 13008N controlled vocabulary controlled vocabulary sample type match: non-tumor
sample_type tumor sample sample GSM7462028 Runtime Siftome inference GEO:sample:GSM7462028:0c137eedfe1df8f4be54417da58d2deab7822e9ea376b9d9797ddffac8eacf27 low confidence tumor sample_accession: GSM7462028 sample_title: 13008T source_name: esophageal tumor characteristics: tissue: Tumor 13008T controlled vocabulary controlled vocabulary sample type match: tumor
sample_type tumor sample sample GSM7462029 Runtime Siftome inference GEO:sample:GSM7462029:f31795800ac6dc7e48db70b7dd14957bce0fa0e21e54a1f98f34c2fd1d102d68 low confidence tumor sample_accession: GSM7462029 sample_title: 13041T source_name: esophageal tumor characteristics: tissue: Tumor 13041T controlled vocabulary controlled vocabulary sample type match: tumor
sample_type normal tissue sample GSM7462030 Runtime Siftome inference GEO:sample:GSM7462030:7acf93d468b7add1be0336c7cd38ab7ceebda8a513ba0d2fd25fe23743dd3a24 medium confidence non-tumor sample_accession: GSM7462030 sample_title: 13367N source_name: esophageal tissue characteristics: tissue: Non-tumor 13367N controlled vocabulary controlled vocabulary sample type match: non-tumor
sample_type tumor sample sample GSM7462031 Runtime Siftome inference GEO:sample:GSM7462031:8945cf99220db01f495f42d41a3921876df591c90ab85768b94dfa257e95cff0 low confidence tumor sample_accession: GSM7462031 sample_title: 13367T source_name: esophageal tumor characteristics: tissue: Tumor 13367T controlled vocabulary controlled vocabulary sample type match: tumor
sample_type normal tissue sample GSM7462032 Runtime Siftome inference GEO:sample:GSM7462032:25a78cae24fc6b34dd509457f39a8b94aaf5f72a1db4c21ee29278225b535017 medium confidence non-tumor sample_accession: GSM7462032 sample_title: 13460N source_name: esophageal tissue characteristics: tissue: Non-tumor 13460N controlled vocabulary controlled vocabulary sample type match: non-tumor
sample_type tumor sample sample GSM7462033 Runtime Siftome inference GEO:sample:GSM7462033:7200348657187614cbe2d67daf44825b958ed48b4c2deb7d7672353c6062d115 low confidence tumor sample_accession: GSM7462033 sample_title: 13460T source_name: esophageal tumor characteristics: tissue: Tumor 13460T controlled vocabulary controlled vocabulary sample type match: tumor
sample_type tumor sample sample GSM7462036 Runtime Siftome inference GEO:sample:GSM7462036:05015dfcbf8b3ddf670c128cf089477159916849bf1bc36c1abd7a10bef611a9 low confidence tumor sample_accession: GSM7462036 sample_title: 13812T source_name: esophageal tumor characteristics: tissue: Tumor 13812T controlled vocabulary controlled vocabulary sample type match: tumor
sample_type normal tissue sample GSM7462037 Runtime Siftome inference GEO:sample:GSM7462037:7b1c90f7aa111fd671da326afc57ee3790a457ffd040d125f25b8e7bb24f8881 medium confidence non-tumor sample_accession: GSM7462037 sample_title: 13850N source_name: esophageal tissue characteristics: tissue: Non-tumor 13850N controlled vocabulary controlled vocabulary sample type match: non-tumor
sample_type normal tissue sample GSM7462039 Runtime Siftome inference GEO:sample:GSM7462039:aac84efbecd139b3e6349e98dcaf0294bfa9fbe4f03fd25819e0d3e5954a7710 medium confidence non-tumor sample_accession: GSM7462039 sample_title: 14303N source_name: esophageal tissue characteristics: tissue: Non-tumor 14303N controlled vocabulary controlled vocabulary sample type match: non-tumor
sample_type tumor sample sample GSM7462040 Runtime Siftome inference GEO:sample:GSM7462040:ec295725fb5db26ae04d7dcb61ad3f7117e216ef822e5b80c48d38f671995d30 low confidence tumor sample_accession: GSM7462040 sample_title: 14303T source_name: esophageal tumor characteristics: tissue: Tumor 14303T controlled vocabulary controlled vocabulary sample type match: tumor
sample_type normal tissue sample GSM7462041 Runtime Siftome inference GEO:sample:GSM7462041:7d2ba2fddca95bc1ab4d885566a13ce02c1c51a244f980d8ce4513a606ef39fe medium confidence non-tumor sample_accession: GSM7462041 sample_title: 15180N source_name: esophageal tissue characteristics: tissue: Non-tumor 15180N controlled vocabulary controlled vocabulary sample type match: non-tumor
sample_type tumor sample sample GSM7462042 Runtime Siftome inference GEO:sample:GSM7462042:77dcd71fe85177f14d76f13b6297753fc2fd9b80050cae15a276ff7c8b785f6a low confidence tumor sample_accession: GSM7462042 sample_title: 15752T source_name: esophageal tumor characteristics: tissue: Tumor 15752T controlled vocabulary controlled vocabulary sample type match: tumor
sample_type tumor sample sample GSM7462043 Runtime Siftome inference GEO:sample:GSM7462043:bd9761dd1525f459d9508daad13c9e73d98a301cb6c25b495ba35b9436599e21 low confidence tumor sample_accession: GSM7462043 sample_title: 16210T source_name: esophageal tumor characteristics: tissue: Tumor 16210T controlled vocabulary controlled vocabulary sample type match: tumor
sample_type tumor sample sample GSM7462045 Runtime Siftome inference GEO:sample:GSM7462045:f5cbc97afb3d5bb78d61fce639f1c332325368afd6012d19cacf8dc5193a038c low confidence tumor sample_accession: GSM7462045 sample_title: 17206T source_name: esophageal tumor characteristics: tissue: Tumor 17206T controlled vocabulary controlled vocabulary sample type match: tumor
sample_type normal tissue sample GSM7462046 Runtime Siftome inference GEO:sample:GSM7462046:49608ab9ac38a8451b8b7c7ded4b3f752833588b0369ecb1c5c850b84d172534 medium confidence non-tumor sample_accession: GSM7462046 sample_title: 17300N source_name: esophageal tissue characteristics: tissue: Non-tumor 17300N controlled vocabulary controlled vocabulary sample type match: non-tumor
sample_type normal tissue sample GSM7462047 Runtime Siftome inference GEO:sample:GSM7462047:e0362d92d6760625f5d56f43b52d9d98e84668daaf29353cd240e1c3e9f99e2f medium confidence non-tumor sample_accession: GSM7462047 sample_title: 17304N source_name: esophageal tissue characteristics: tissue: Non-tumor 17304N controlled vocabulary controlled vocabulary sample type match: non-tumor
sample_type normal tissue sample GSM7462048 Runtime Siftome inference GEO:sample:GSM7462048:26b883462aeeea63eca992d194029e586451ac0f5841924397ff467060f9ca7e medium confidence non-tumor sample_accession: GSM7462048 sample_title: 17525N source_name: esophageal tissue characteristics: tissue: Non-tumor 17525N controlled vocabulary controlled vocabulary sample type match: non-tumor
sample_type normal tissue sample GSM7462049 Runtime Siftome inference GEO:sample:GSM7462049:5ef51829100493035dbd1bfc26e4747dd1bb96d1ac7a6d329112d0ec12dc5969 medium confidence non-tumor sample_accession: GSM7462049 sample_title: 17823N source_name: esophageal tissue characteristics: tissue: Non-tumor 17823N controlled vocabulary controlled vocabulary sample type match: non-tumor

Sample Group Preview

Possible case samples

Samples currently treated as the comparison case group.

17
  • GSM7462008 11267T tumor sample Case marker detected. esophageal tumor tissue: Tumor
  • GSM7462010 11362T tumor sample Case marker detected. esophageal tumor tissue: Tumor
  • GSM7462011 11455T tumor sample Case marker detected. esophageal tumor tissue: Tumor
  • GSM7462015 12291T tumor sample Case marker detected. esophageal tumor tissue: Tumor
  • GSM7462018 12631T tumor sample Case marker detected. esophageal tumor tissue: Tumor
  • GSM7462020 12672T tumor sample Case marker detected. esophageal tumor tissue: Tumor
  • GSM7462024 12943T tumor sample Case marker detected. esophageal tumor tissue: Tumor
  • GSM7462026 12997T tumor sample Case marker detected. esophageal tumor tissue: Tumor
  • GSM7462028 13008T tumor sample Case marker detected. esophageal tumor tissue: Tumor
  • GSM7462029 13041T tumor sample Case marker detected. esophageal tumor tissue: Tumor
  • GSM7462031 13367T tumor sample Case marker detected. esophageal tumor tissue: Tumor
  • GSM7462033 13460T tumor sample Case marker detected. esophageal tumor tissue: Tumor
  • GSM7462036 13812T tumor sample Case marker detected. esophageal tumor tissue: Tumor
  • GSM7462040 14303T tumor sample Case marker detected. esophageal tumor tissue: Tumor
  • GSM7462042 15752T tumor sample Case marker detected. esophageal tumor tissue: Tumor
  • GSM7462043 16210T tumor sample Case marker detected. esophageal tumor tissue: Tumor
  • GSM7462045 17206T tumor sample Case marker detected. esophageal tumor tissue: Tumor

Possible control samples

Samples currently treated as controls or baseline.

21
  • GSM7462006 10153N normal tissue Control marker detected. esophageal tissue tissue: Non-tumor
  • GSM7462007 11267N normal tissue Control marker detected. esophageal tissue tissue: Non-tumor
  • GSM7462009 11362N normal tissue Control marker detected. esophageal tissue tissue: Non-tumor
  • GSM7462012 11738N normal tissue Control marker detected. esophageal tissue tissue: Non-tumor
  • GSM7462014 11802N normal tissue Control marker detected. esophageal tissue tissue: Non-tumor
  • GSM7462016 12306N normal tissue Control marker detected. esophageal tissue tissue: Non-tumor
  • GSM7462017 12631N normal tissue Control marker detected. esophageal tissue tissue: Non-tumor
  • GSM7462019 12672N normal tissue Control marker detected. esophageal tissue tissue: Non-tumor
  • GSM7462022 12841N normal tissue Control marker detected. esophageal tissue tissue: Non-tumor
  • GSM7462023 12943N normal tissue Control marker detected. esophageal tissue tissue: Non-tumor
  • GSM7462025 12997N normal tissue Control marker detected. esophageal tissue tissue: Non-tumor
  • GSM7462027 13008N normal tissue Control marker detected. esophageal tissue tissue: Non-tumor
  • GSM7462030 13367N normal tissue Control marker detected. esophageal tissue tissue: Non-tumor
  • GSM7462032 13460N normal tissue Control marker detected. esophageal tissue tissue: Non-tumor
  • GSM7462037 13850N normal tissue Control marker detected. esophageal tissue tissue: Non-tumor
  • GSM7462039 14303N normal tissue Control marker detected. esophageal tissue tissue: Non-tumor
  • GSM7462041 15180N normal tissue Control marker detected. esophageal tissue tissue: Non-tumor
  • GSM7462046 17300N normal tissue Control marker detected. esophageal tissue tissue: Non-tumor
  • GSM7462047 17304N normal tissue Control marker detected. esophageal tissue tissue: Non-tumor
  • GSM7462048 17525N normal tissue Control marker detected. esophageal tissue tissue: Non-tumor
  • GSM7462049 17823N normal tissue Control marker detected. esophageal tissue tissue: Non-tumor

Unassigned samples

Samples with no explicit case or control marker.

6
  • GSM7462013 11802BO unassigned No explicit case or control marker detected. esophageal tissue tissue: Barretts esophagus
  • GSM7462021 12767BO unassigned No explicit case or control marker detected. esophageal tissue tissue: Barretts esophagus
  • GSM7462034 13622BO unassigned No explicit case or control marker detected. esophageal tissue tissue: Barretts esophagus
  • GSM7462035 13732BO unassigned No explicit case or control marker detected. esophageal tissue tissue: Barretts esophagus
  • GSM7462038 13922BO unassigned No explicit case or control marker detected. esophageal tissue tissue: Barretts esophagus
  • GSM7462044 16592BF unassigned No explicit case or control marker detected. esophageal tissue tissue: Barretts esophagus

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

21 samples
  • GSM7462006 10153N esophageal tissue tissue: Non-tumor
  • GSM7462007 11267N esophageal tissue tissue: Non-tumor
  • GSM7462009 11362N esophageal tissue tissue: Non-tumor
  • GSM7462012 11738N esophageal tissue tissue: Non-tumor
  • GSM7462014 11802N esophageal tissue tissue: Non-tumor
  • GSM7462016 12306N esophageal tissue tissue: Non-tumor
  • GSM7462017 12631N esophageal tissue tissue: Non-tumor
  • GSM7462019 12672N esophageal tissue tissue: Non-tumor
  • GSM7462022 12841N esophageal tissue tissue: Non-tumor
  • GSM7462023 12943N esophageal tissue tissue: Non-tumor
  • GSM7462025 12997N esophageal tissue tissue: Non-tumor
  • GSM7462027 13008N esophageal tissue tissue: Non-tumor
  • GSM7462030 13367N esophageal tissue tissue: Non-tumor
  • GSM7462032 13460N esophageal tissue tissue: Non-tumor
  • GSM7462037 13850N esophageal tissue tissue: Non-tumor
  • GSM7462039 14303N esophageal tissue tissue: Non-tumor
  • GSM7462041 15180N esophageal tissue tissue: Non-tumor
  • GSM7462046 17300N esophageal tissue tissue: Non-tumor
  • GSM7462047 17304N esophageal tissue tissue: Non-tumor
  • GSM7462048 17525N esophageal tissue tissue: Non-tumor
  • GSM7462049 17823N esophageal tissue tissue: Non-tumor

tumor sample

17 samples

unassigned

6 samples
  • GSM7462013 11802BO esophageal tissue tissue: Barretts esophagus
  • GSM7462021 12767BO esophageal tissue tissue: Barretts esophagus
  • GSM7462034 13622BO esophageal tissue tissue: Barretts esophagus
  • GSM7462035 13732BO esophageal tissue tissue: Barretts esophagus
  • GSM7462038 13922BO esophageal tissue tissue: Barretts esophagus
  • GSM7462044 16592BF esophageal tissue tissue: Barretts esophagus

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

44 samples

Review Audit Trail

0 decisions

No review decisions have been stored for this dataset.