Siftome Phase 3L

GSE119336

RNA over-editing leads to aggressiveness of intrahepatic cholangiocarcinoma [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
2018-08-31
Last update
2023-01-04
Organization
Beijing Institute of Radiation Medicine
Department
Not available
Public date
2018-12-12
Experiment types
Expression profiling by high throughput sequencing
Platforms
GPL11154 Illumina HiSeq 2000 (Homo sapiens)
Series type
SubSeries
SubSeries
Not available
BioProject
PRJNA488803
Supplementary files
TXT: GSE119336_RNAseq_processed_data.txt.gz
Organism
Homo sapiens
Assay
bulk RNA-seq
Samples
30
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
97% 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

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 60% 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 85% Sample source clarity: All samples have source metadata and clear GSE/GSM accessions. Group clarity: Rule-based grouping found both case and control samples. Disease clarity: Disease or condition metadata was not 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 15 samples
  • Likely control group normal tissue 15 samples

Warnings

  • DISEASE_LABEL_UNCLEAR warning Disease or condition label could not be normalized.

Intent Interpretation

  • Active intent Patient tissue tumor-vs-normal Ranks human colorectal tissue or biopsy cohorts where tumor samples can be compared with normal controls.
  • Organism expectation Homo sapiens Dataset organism is interpreted as Homo sapiens.
  • Assay expectation bulk RNA-seq Dataset assay is interpreted as bulk RNA-seq.
  • Specimen assumption patient tissue or biopsy Derived specimen/source is Tissue.
  • Control-group assumption matched normal, adjacent normal, paired normal, healthy tissue control, or otherwise normal tissue control Derived study design is Tumor vs unmatched normal; likely groups are tumor sample vs normal tissue.
  • Score caps Applied when matching conditions are present non-human datasets stay below the primary recommendation band, missing colorectal/colon/rectal/CRC context stays below the primary recommendation band, biofluid and model-system datasets cannot reach Recommended by default, microarray and secondary assays are capped unless explicitly enabled, or small cohorts are capped below high-confidence recommendations
  • Warning rules 1 active warning missing or unclear control group, unclear disease context, unclear tissue source, mixed sample types, model-system markers, secondary assay context, missing processed data, or small cohort size
  • Downgrade or exclusion reason Downgraded disease context: colorectal/GI relevance is unclear. Derived from current-intent ranking reasons and warnings.

Applied Review Decisions

No active review decisions affect this ranking.

Ranking Facts

  • Recommendation Not suitable Dataset does not meet the current suitability threshold.
  • Supporting fact Tumor vs unmatched normal · Tissue · suitability 0%. Contributed to match or upgrade evidence.
  • Supporting fact Prioritized assay: bulk RNA-seq is the active assay expectation. Contributed to match or upgrade evidence.
  • Supporting fact Downgraded disease context: colorectal/GI relevance is unclear. Contributed to match or upgrade evidence.
  • Supporting fact Processed data is available for downstream review. Contributed to match or upgrade evidence.
  • Supporting fact 1 warning require review. Contributed to match or upgrade evidence.
  • Caution fact Disease or condition label could not be normalized. Contributed to downgrade or manual-review evidence.
  • Caution fact Non-colorectal cancer context downgraded for colorectal tumor-vs-normal tissue ranking. Contributed to downgrade or manual-review evidence.
  • Caution fact Missing or unclear metadata: Disease clarity: Disease or condition metadata was not normalized. Contributed to downgrade or manual-review evidence.
  • Caution fact Missing or unclear metadata: 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
GSE119336
Sample records
30 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
GSE119336
  • 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
GSE119336
  • 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
GSE119336
  • 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: GSE119336
dataset_title: RNA over-editing leads to aggressiveness of intrahepatic cholangiocarcinoma [RNA-Seq]
organism: Homo sapiens
assay_type: bulk RNA-seq
processed_data_available: true
raw_data_available: true
submission_date: 2018-08-31
last_update_date: 2023-01-04
organization_name: Beijing Institute of Radiation Medicine
department: Not available
public_date: 2018-12-12
experiment_types: Expression profiling by high throughput sequencing
platforms: GPL11154 Illumina HiSeq 2000 (Homo sapiens)
sub_series: Not available
bioproject: PRJNA488803
supplementary_files: TXT: GSE119336_RNAseq_processed_data.txt.gz
series_type: SubSeries

Why It Matched

  • Tumor vs unmatched normal · Tissue · suitability 0%.
  • Prioritized assay: bulk RNA-seq is the active assay expectation.
  • Downgraded disease context: colorectal/GI relevance is unclear.
  • Processed data is available for downstream review.
  • 1 warning require review.

Why It May Not Be Suitable

  • Disease or condition label could not be normalized.
  • Non-colorectal cancer context downgraded for colorectal tumor-vs-normal tissue ranking.
  • Missing or unclear metadata: Disease clarity: Disease or condition metadata was not normalized.
  • Missing or unclear metadata: Treatment clarity: No unclear treatment split detected in the sample metadata.
  • Overall score capped because comparison suitability is weak for the selected search intent.
  • Overall score capped because tumor/normal grouping is from a non-colorectal cancer context.
  • Downgraded disease context: colorectal/GI relevance is unclear.
  • Missing or unclear metadata: Downgraded disease context: colorectal/GI relevance is unclear.
  • Comparison suitability score is below the Phase 1 recommended threshold.

Warnings

  • warning DISEASE_LABEL_UNCLEAR Disease or condition label could not be normalized.

Normalized Fields

63 fields
Field Value Source Origin Confidence Evidence Reason
assay_type bulk RNA-seq dataset GSE119336 Runtime Siftome inference GEO:dataset:GSE119336:5088d66d28efb5cc601e18a21d4891e24b78abf3183cd03e6edd27b237c42b23 high confidence bulk rna-seq dataset_accession: GSE119336 dataset_title: RNA over-editing leads to aggressiveness of intrahepatic cholangiocarcinoma [RNA-Seq] organism: Homo sapiens assay_type: bulk RNA-seq... keyword match keyword match: bulk rna-seq
organism Homo sapiens dataset GSE119336 Runtime Siftome inference GEO:dataset:GSE119336:5088d66d28efb5cc601e18a21d4891e24b78abf3183cd03e6edd27b237c42b23 high confidence homo sapiens dataset_accession: GSE119336 dataset_title: RNA over-editing leads to aggressiveness of intrahepatic cholangiocarcinoma [RNA-Seq] organism: Homo sapiens assay_type: bulk RNA-seq... keyword match keyword match: homo sapiens
sample_type normal tissue sample GSM3370133 Runtime Siftome inference GEO:sample:GSM3370133:715d8bc332df2d10c97cc5314cc83f5faa044bf8f47032dc67154b21c193e66b medium confidence non-tumor sample_accession: GSM3370133 sample_title: 090608N source_name: adjacent non-tumor tissue characteristics: gender: male; age: 72; tissue: adjacent non-tumor liver tissue 090608N controlled vocabulary controlled vocabulary sample type match: non-tumor
sample_type tumor sample sample GSM3370134 Runtime Siftome inference GEO:sample:GSM3370134:9e311c666bf76129ba2e97a4706ee589dbea4dd53b82d6ef0b95675c73db0021 low confidence tumor sample_accession: GSM3370134 sample_title: 090608T source_name: tumor tissue characteristics: gender: male; age: 72; tissue: Intrahepatic cholangiocarcinoma 090608T controlled vocabulary controlled vocabulary sample type match: tumor
sample_type normal tissue sample GSM3370135 Runtime Siftome inference GEO:sample:GSM3370135:e5e591a17a5ffa83eebcf1f10ed25d98ccec9247e0f3822f72525f582cfb6e48 medium confidence non-tumor sample_accession: GSM3370135 sample_title: 098699N source_name: adjacent non-tumor tissue characteristics: gender: male; age: 33; tissue: adjacent non-tumor liver tissue 098699N controlled vocabulary controlled vocabulary sample type match: non-tumor
sample_type tumor sample sample GSM3370136 Runtime Siftome inference GEO:sample:GSM3370136:a0c0df59778b9a2ba1e013bf322d63760277b66f3330f79161f07077af69ebe0 low confidence tumor sample_accession: GSM3370136 sample_title: 098699T source_name: tumor tissue characteristics: gender: male; age: 33; tissue: Intrahepatic cholangiocarcinoma 098699T controlled vocabulary controlled vocabulary sample type match: tumor
sample_type normal tissue sample GSM3370137 Runtime Siftome inference GEO:sample:GSM3370137:3d5ea51545aba9c061429dd9345a9cdfb64c66cbe664fa05a99e1fce2ac4bb74 medium confidence non-tumor sample_accession: GSM3370137 sample_title: 099535N source_name: adjacent non-tumor tissue characteristics: gender: female; age: 61; tissue: adjacent non-tumor liver tissue 099535N controlled vocabulary controlled vocabulary sample type match: non-tumor
sample_type tumor sample sample GSM3370138 Runtime Siftome inference GEO:sample:GSM3370138:f8e09fedb8f87380f9ca0cdc79ae3f272f5e00eeb7a3d5cafc720ad96c296719 low confidence tumor sample_accession: GSM3370138 sample_title: 099535T source_name: tumor tissue characteristics: gender: female; age: 61; tissue: Intrahepatic cholangiocarcinoma 099535T controlled vocabulary controlled vocabulary sample type match: tumor
sample_type normal tissue sample GSM3370139 Runtime Siftome inference GEO:sample:GSM3370139:7fbf6599373966be0ee591a9cfea1339ff490dfd4ab6c1c9cdc5507c99aec098 medium confidence non-tumor sample_accession: GSM3370139 sample_title: 11770N source_name: adjacent non-tumor tissue characteristics: gender: male; age: 55; tissue: adjacent non-tumor liver tissue 11770N controlled vocabulary controlled vocabulary sample type match: non-tumor
sample_type tumor sample sample GSM3370140 Runtime Siftome inference GEO:sample:GSM3370140:60f66690ef72d2e88b806bd60359bc32d6d9e8b094c8a02afda98d1a37b22b04 low confidence tumor sample_accession: GSM3370140 sample_title: 11770T source_name: tumor tissue characteristics: gender: male; age: 55; tissue: Intrahepatic cholangiocarcinoma 11770T controlled vocabulary controlled vocabulary sample type match: tumor
sample_type normal tissue sample GSM3370141 Runtime Siftome inference GEO:sample:GSM3370141:6e47b8e7f1761f5f8157434d938adb26f449dcfcecaab1114609e8478a88b327 medium confidence non-tumor sample_accession: GSM3370141 sample_title: 81023N source_name: adjacent non-tumor tissue characteristics: gender: female; age: 49; tissue: adjacent non-tumor liver tissue 81023N controlled vocabulary controlled vocabulary sample type match: non-tumor
sample_type tumor sample sample GSM3370142 Runtime Siftome inference GEO:sample:GSM3370142:c2aa896c4b9af7de2cd20858a5bfe05a0aa62072e49b92e32f58a3af0fc79070 low confidence tumor sample_accession: GSM3370142 sample_title: 81023T source_name: tumor tissue characteristics: gender: female; age: 49; tissue: Intrahepatic cholangiocarcinoma 81023T controlled vocabulary controlled vocabulary sample type match: tumor
sample_type normal tissue sample GSM3370143 Runtime Siftome inference GEO:sample:GSM3370143:cff65e2665f36472dc9f616dac4f660246a928c44b852bbb484d0c1c234a7d93 medium confidence non-tumor sample_accession: GSM3370143 sample_title: 81032N source_name: adjacent non-tumor tissue characteristics: gender: male; age: 50; tissue: adjacent non-tumor liver tissue 81032N controlled vocabulary controlled vocabulary sample type match: non-tumor
sample_type tumor sample sample GSM3370144 Runtime Siftome inference GEO:sample:GSM3370144:c88c5297b79d75037476d4a84fcf5d44a9f03911855cda5c2376a60600f477ac low confidence tumor sample_accession: GSM3370144 sample_title: 81032T source_name: tumor tissue characteristics: gender: male; age: 50; tissue: Intrahepatic cholangiocarcinoma 81032T controlled vocabulary controlled vocabulary sample type match: tumor
sample_type normal tissue sample GSM3370145 Runtime Siftome inference GEO:sample:GSM3370145:93428a4dd3b96e400ec9ffb0cb59cf3c3cff84f53600794c0fac1da98a9b69b2 medium confidence non-tumor sample_accession: GSM3370145 sample_title: 85421N source_name: adjacent non-tumor tissue characteristics: gender: male; age: 53; tissue: adjacent non-tumor liver tissue 85421N controlled vocabulary controlled vocabulary sample type match: non-tumor
sample_type tumor sample sample GSM3370146 Runtime Siftome inference GEO:sample:GSM3370146:7210dbe72f1871da3f21301089e5e1550085482d33fc1b62dde3ecb7321acb56 low confidence tumor sample_accession: GSM3370146 sample_title: 85421T source_name: tumor tissue characteristics: gender: male; age: 53; tissue: Intrahepatic cholangiocarcinoma 85421T controlled vocabulary controlled vocabulary sample type match: tumor
sample_type normal tissue sample GSM3370147 Runtime Siftome inference GEO:sample:GSM3370147:23312ab27642bdcab67bd71cfaf13720745b4efab58f86e6031e57165a0f53a2 medium confidence non-tumor sample_accession: GSM3370147 sample_title: 86279N source_name: adjacent non-tumor tissue characteristics: gender: female; age: 65; tissue: adjacent non-tumor liver tissue 86279N controlled vocabulary controlled vocabulary sample type match: non-tumor
sample_type tumor sample sample GSM3370148 Runtime Siftome inference GEO:sample:GSM3370148:36c531cb5b3a947eb9272c39b273fe0f3a486428bf527d60baca633149d9b78d low confidence tumor sample_accession: GSM3370148 sample_title: 86279T source_name: tumor tissue characteristics: gender: female; age: 65; tissue: Intrahepatic cholangiocarcinoma 86279T controlled vocabulary controlled vocabulary sample type match: tumor
sample_type normal tissue sample GSM3370149 Runtime Siftome inference GEO:sample:GSM3370149:d5d8fed84dd505c70ee812e84f4a32ff93efe92c5ac5c3bce18765b3dd0f9419 medium confidence non-tumor sample_accession: GSM3370149 sample_title: 86960N source_name: adjacent non-tumor tissue characteristics: gender: male; age: 60; tissue: adjacent non-tumor liver tissue 86960N controlled vocabulary controlled vocabulary sample type match: non-tumor
sample_type tumor sample sample GSM3370150 Runtime Siftome inference GEO:sample:GSM3370150:72e5ebdf717aa477958d48e170a8052be9ed926c5720ca5619888bc03f4da90b low confidence tumor sample_accession: GSM3370150 sample_title: 86960T source_name: tumor tissue characteristics: gender: male; age: 60; tissue: Intrahepatic cholangiocarcinoma 86960T controlled vocabulary controlled vocabulary sample type match: tumor
sample_type normal tissue sample GSM3370151 Runtime Siftome inference GEO:sample:GSM3370151:6768302b1acf5a345d550536142537d3959b0cc18653c9a1ec5303cc74d3c71f medium confidence non-tumor sample_accession: GSM3370151 sample_title: 87823N source_name: adjacent non-tumor tissue characteristics: gender: male; age: 48; tissue: adjacent non-tumor liver tissue 87823N controlled vocabulary controlled vocabulary sample type match: non-tumor
sample_type tumor sample sample GSM3370152 Runtime Siftome inference GEO:sample:GSM3370152:c2504e1618613f6a69b6f8cca3affccc10745cef7ac9f22aec5bd02002816995 low confidence tumor sample_accession: GSM3370152 sample_title: 87823T source_name: tumor tissue characteristics: gender: male; age: 48; tissue: Intrahepatic cholangiocarcinoma 87823T controlled vocabulary controlled vocabulary sample type match: tumor
sample_type normal tissue sample GSM3370153 Runtime Siftome inference GEO:sample:GSM3370153:00e0b2afb6791527cb816bea459f7d6e3eaac691529bdabfde664cb41528b811 medium confidence non-tumor sample_accession: GSM3370153 sample_title: 88659N source_name: adjacent non-tumor tissue characteristics: gender: male; age: 47; tissue: adjacent non-tumor liver tissue 88659N controlled vocabulary controlled vocabulary sample type match: non-tumor
sample_type tumor sample sample GSM3370154 Runtime Siftome inference GEO:sample:GSM3370154:65026e89243759dc1f50b230cc0507c2da43b7ea5d12ac4ad40522fbce95ccaa low confidence tumor sample_accession: GSM3370154 sample_title: 88659T source_name: tumor tissue characteristics: gender: male; age: 47; tissue: Intrahepatic cholangiocarcinoma 88659T controlled vocabulary controlled vocabulary sample type match: tumor
sample_type normal tissue sample GSM3370155 Runtime Siftome inference GEO:sample:GSM3370155:d40d81d03c5ff917795537285f12faa4c97a54730ecd7e674587240ce8609187 medium confidence non-tumor sample_accession: GSM3370155 sample_title: 88674N source_name: adjacent non-tumor tissue characteristics: gender: male; age: 44; tissue: adjacent non-tumor liver tissue 88674N controlled vocabulary controlled vocabulary sample type match: non-tumor
sample_type tumor sample sample GSM3370156 Runtime Siftome inference GEO:sample:GSM3370156:8e66072aee12f60fe5c20a99a2f48db5bdf3ea5c834d54ffdcf556ba6d10844a low confidence tumor sample_accession: GSM3370156 sample_title: 88674T source_name: tumor tissue characteristics: gender: male; age: 44; tissue: Intrahepatic cholangiocarcinoma 88674T controlled vocabulary controlled vocabulary sample type match: tumor
sample_type normal tissue sample GSM3370157 Runtime Siftome inference GEO:sample:GSM3370157:e5968800dda7267401445dcbf8f855cde428a00308543fec9b73bec8c19c9773 medium confidence non-tumor sample_accession: GSM3370157 sample_title: 88724N source_name: adjacent non-tumor tissue characteristics: gender: male; age: 26; tissue: adjacent non-tumor liver tissue 88724N controlled vocabulary controlled vocabulary sample type match: non-tumor
sample_type tumor sample sample GSM3370158 Runtime Siftome inference GEO:sample:GSM3370158:ebcb2dbf58e642a8a7396a88622e457a78effe84de7dbf0bd01c4cd1fdf47c87 low confidence tumor sample_accession: GSM3370158 sample_title: 88724T source_name: tumor tissue characteristics: gender: male; age: 26; tissue: Intrahepatic cholangiocarcinoma 88724T controlled vocabulary controlled vocabulary sample type match: tumor
sample_type normal tissue sample GSM3370159 Runtime Siftome inference GEO:sample:GSM3370159:b89f83684ceea8cf20bba75dfa0e489afe7753ad1bd6b0e57ae81d672d8c17bc medium confidence non-tumor sample_accession: GSM3370159 sample_title: 89290N source_name: adjacent non-tumor tissue characteristics: gender: female; age: 57; tissue: adjacent non-tumor liver tissue 89290N controlled vocabulary controlled vocabulary sample type match: non-tumor
sample_type tumor sample sample GSM3370160 Runtime Siftome inference GEO:sample:GSM3370160:9eff34d0bb54d219ed9be6b107e9b821777d658f254b97a66df5e8216090ad6d low confidence tumor sample_accession: GSM3370160 sample_title: 89290T source_name: tumor tissue characteristics: gender: female; age: 57; tissue: Intrahepatic cholangiocarcinoma 89290T controlled vocabulary controlled vocabulary sample type match: tumor
sample_type normal tissue sample GSM3370161 Runtime Siftome inference GEO:sample:GSM3370161:b742cc0ba19482526fb48cd5f73020fba0c2888238adaafc2e2b525997437dc4 medium confidence non-tumor sample_accession: GSM3370161 sample_title: 96484N source_name: adjacent non-tumor tissue characteristics: gender: male; age: 64; tissue: adjacent non-tumor liver tissue 96484N controlled vocabulary controlled vocabulary sample type match: non-tumor
sample_type tumor sample sample GSM3370162 Runtime Siftome inference GEO:sample:GSM3370162:bb0ab864ed228775bd751d18513c8df361cc82791bad374b9ebe869a6621d5d7 low confidence tumor sample_accession: GSM3370162 sample_title: 96484T source_name: tumor tissue characteristics: gender: male; age: 64; tissue: Intrahepatic cholangiocarcinoma 96484T controlled vocabulary controlled vocabulary sample type match: tumor
tissue liver dataset GSE119336 Runtime Siftome inference GEO:dataset:GSE119336:5088d66d28efb5cc601e18a21d4891e24b78abf3183cd03e6edd27b237c42b23 medium confidence hepatic dataset_accession: GSE119336 dataset_title: RNA over-editing leads to aggressiveness of intrahepatic cholangiocarcinoma [RNA-Seq] organism: Homo sapiens assay_type: bulk RNA-seq... controlled vocabulary controlled vocabulary tissue match: hepatic
tissue liver sample GSM3370133 Runtime Siftome inference GEO:sample:GSM3370133:715d8bc332df2d10c97cc5314cc83f5faa044bf8f47032dc67154b21c193e66b low confidence liver sample_accession: GSM3370133 sample_title: 090608N source_name: adjacent non-tumor tissue characteristics: gender: male; age: 72; tissue: adjacent non-tumor liver tissue 090608N controlled vocabulary controlled vocabulary tissue match: liver
tissue liver sample GSM3370134 Runtime Siftome inference GEO:sample:GSM3370134:9e311c666bf76129ba2e97a4706ee589dbea4dd53b82d6ef0b95675c73db0021 medium confidence hepatic sample_accession: GSM3370134 sample_title: 090608T source_name: tumor tissue characteristics: gender: male; age: 72; tissue: Intrahepatic cholangiocarcinoma 090608T controlled vocabulary controlled vocabulary tissue match: hepatic
tissue liver sample GSM3370135 Runtime Siftome inference GEO:sample:GSM3370135:e5e591a17a5ffa83eebcf1f10ed25d98ccec9247e0f3822f72525f582cfb6e48 low confidence liver sample_accession: GSM3370135 sample_title: 098699N source_name: adjacent non-tumor tissue characteristics: gender: male; age: 33; tissue: adjacent non-tumor liver tissue 098699N controlled vocabulary controlled vocabulary tissue match: liver
tissue liver sample GSM3370136 Runtime Siftome inference GEO:sample:GSM3370136:a0c0df59778b9a2ba1e013bf322d63760277b66f3330f79161f07077af69ebe0 medium confidence hepatic sample_accession: GSM3370136 sample_title: 098699T source_name: tumor tissue characteristics: gender: male; age: 33; tissue: Intrahepatic cholangiocarcinoma 098699T controlled vocabulary controlled vocabulary tissue match: hepatic
tissue liver sample GSM3370137 Runtime Siftome inference GEO:sample:GSM3370137:3d5ea51545aba9c061429dd9345a9cdfb64c66cbe664fa05a99e1fce2ac4bb74 low confidence liver sample_accession: GSM3370137 sample_title: 099535N source_name: adjacent non-tumor tissue characteristics: gender: female; age: 61; tissue: adjacent non-tumor liver tissue 099535N controlled vocabulary controlled vocabulary tissue match: liver
tissue liver sample GSM3370138 Runtime Siftome inference GEO:sample:GSM3370138:f8e09fedb8f87380f9ca0cdc79ae3f272f5e00eeb7a3d5cafc720ad96c296719 medium confidence hepatic sample_accession: GSM3370138 sample_title: 099535T source_name: tumor tissue characteristics: gender: female; age: 61; tissue: Intrahepatic cholangiocarcinoma 099535T controlled vocabulary controlled vocabulary tissue match: hepatic
tissue liver sample GSM3370139 Runtime Siftome inference GEO:sample:GSM3370139:7fbf6599373966be0ee591a9cfea1339ff490dfd4ab6c1c9cdc5507c99aec098 low confidence liver sample_accession: GSM3370139 sample_title: 11770N source_name: adjacent non-tumor tissue characteristics: gender: male; age: 55; tissue: adjacent non-tumor liver tissue 11770N controlled vocabulary controlled vocabulary tissue match: liver
tissue liver sample GSM3370140 Runtime Siftome inference GEO:sample:GSM3370140:60f66690ef72d2e88b806bd60359bc32d6d9e8b094c8a02afda98d1a37b22b04 medium confidence hepatic sample_accession: GSM3370140 sample_title: 11770T source_name: tumor tissue characteristics: gender: male; age: 55; tissue: Intrahepatic cholangiocarcinoma 11770T controlled vocabulary controlled vocabulary tissue match: hepatic
tissue liver sample GSM3370141 Runtime Siftome inference GEO:sample:GSM3370141:6e47b8e7f1761f5f8157434d938adb26f449dcfcecaab1114609e8478a88b327 low confidence liver sample_accession: GSM3370141 sample_title: 81023N source_name: adjacent non-tumor tissue characteristics: gender: female; age: 49; tissue: adjacent non-tumor liver tissue 81023N controlled vocabulary controlled vocabulary tissue match: liver
tissue liver sample GSM3370142 Runtime Siftome inference GEO:sample:GSM3370142:c2aa896c4b9af7de2cd20858a5bfe05a0aa62072e49b92e32f58a3af0fc79070 medium confidence hepatic sample_accession: GSM3370142 sample_title: 81023T source_name: tumor tissue characteristics: gender: female; age: 49; tissue: Intrahepatic cholangiocarcinoma 81023T controlled vocabulary controlled vocabulary tissue match: hepatic
tissue liver sample GSM3370143 Runtime Siftome inference GEO:sample:GSM3370143:cff65e2665f36472dc9f616dac4f660246a928c44b852bbb484d0c1c234a7d93 low confidence liver sample_accession: GSM3370143 sample_title: 81032N source_name: adjacent non-tumor tissue characteristics: gender: male; age: 50; tissue: adjacent non-tumor liver tissue 81032N controlled vocabulary controlled vocabulary tissue match: liver
tissue liver sample GSM3370144 Runtime Siftome inference GEO:sample:GSM3370144:c88c5297b79d75037476d4a84fcf5d44a9f03911855cda5c2376a60600f477ac medium confidence hepatic sample_accession: GSM3370144 sample_title: 81032T source_name: tumor tissue characteristics: gender: male; age: 50; tissue: Intrahepatic cholangiocarcinoma 81032T controlled vocabulary controlled vocabulary tissue match: hepatic
tissue liver sample GSM3370145 Runtime Siftome inference GEO:sample:GSM3370145:93428a4dd3b96e400ec9ffb0cb59cf3c3cff84f53600794c0fac1da98a9b69b2 low confidence liver sample_accession: GSM3370145 sample_title: 85421N source_name: adjacent non-tumor tissue characteristics: gender: male; age: 53; tissue: adjacent non-tumor liver tissue 85421N controlled vocabulary controlled vocabulary tissue match: liver
tissue liver sample GSM3370146 Runtime Siftome inference GEO:sample:GSM3370146:7210dbe72f1871da3f21301089e5e1550085482d33fc1b62dde3ecb7321acb56 medium confidence hepatic sample_accession: GSM3370146 sample_title: 85421T source_name: tumor tissue characteristics: gender: male; age: 53; tissue: Intrahepatic cholangiocarcinoma 85421T controlled vocabulary controlled vocabulary tissue match: hepatic
tissue liver sample GSM3370147 Runtime Siftome inference GEO:sample:GSM3370147:23312ab27642bdcab67bd71cfaf13720745b4efab58f86e6031e57165a0f53a2 low confidence liver sample_accession: GSM3370147 sample_title: 86279N source_name: adjacent non-tumor tissue characteristics: gender: female; age: 65; tissue: adjacent non-tumor liver tissue 86279N controlled vocabulary controlled vocabulary tissue match: liver
tissue liver sample GSM3370148 Runtime Siftome inference GEO:sample:GSM3370148:36c531cb5b3a947eb9272c39b273fe0f3a486428bf527d60baca633149d9b78d medium confidence hepatic sample_accession: GSM3370148 sample_title: 86279T source_name: tumor tissue characteristics: gender: female; age: 65; tissue: Intrahepatic cholangiocarcinoma 86279T controlled vocabulary controlled vocabulary tissue match: hepatic
tissue liver sample GSM3370149 Runtime Siftome inference GEO:sample:GSM3370149:d5d8fed84dd505c70ee812e84f4a32ff93efe92c5ac5c3bce18765b3dd0f9419 low confidence liver sample_accession: GSM3370149 sample_title: 86960N source_name: adjacent non-tumor tissue characteristics: gender: male; age: 60; tissue: adjacent non-tumor liver tissue 86960N controlled vocabulary controlled vocabulary tissue match: liver
tissue liver sample GSM3370150 Runtime Siftome inference GEO:sample:GSM3370150:72e5ebdf717aa477958d48e170a8052be9ed926c5720ca5619888bc03f4da90b medium confidence hepatic sample_accession: GSM3370150 sample_title: 86960T source_name: tumor tissue characteristics: gender: male; age: 60; tissue: Intrahepatic cholangiocarcinoma 86960T controlled vocabulary controlled vocabulary tissue match: hepatic
tissue liver sample GSM3370151 Runtime Siftome inference GEO:sample:GSM3370151:6768302b1acf5a345d550536142537d3959b0cc18653c9a1ec5303cc74d3c71f low confidence liver sample_accession: GSM3370151 sample_title: 87823N source_name: adjacent non-tumor tissue characteristics: gender: male; age: 48; tissue: adjacent non-tumor liver tissue 87823N controlled vocabulary controlled vocabulary tissue match: liver
tissue liver sample GSM3370152 Runtime Siftome inference GEO:sample:GSM3370152:c2504e1618613f6a69b6f8cca3affccc10745cef7ac9f22aec5bd02002816995 medium confidence hepatic sample_accession: GSM3370152 sample_title: 87823T source_name: tumor tissue characteristics: gender: male; age: 48; tissue: Intrahepatic cholangiocarcinoma 87823T controlled vocabulary controlled vocabulary tissue match: hepatic
tissue liver sample GSM3370153 Runtime Siftome inference GEO:sample:GSM3370153:00e0b2afb6791527cb816bea459f7d6e3eaac691529bdabfde664cb41528b811 low confidence liver sample_accession: GSM3370153 sample_title: 88659N source_name: adjacent non-tumor tissue characteristics: gender: male; age: 47; tissue: adjacent non-tumor liver tissue 88659N controlled vocabulary controlled vocabulary tissue match: liver
tissue liver sample GSM3370154 Runtime Siftome inference GEO:sample:GSM3370154:65026e89243759dc1f50b230cc0507c2da43b7ea5d12ac4ad40522fbce95ccaa medium confidence hepatic sample_accession: GSM3370154 sample_title: 88659T source_name: tumor tissue characteristics: gender: male; age: 47; tissue: Intrahepatic cholangiocarcinoma 88659T controlled vocabulary controlled vocabulary tissue match: hepatic
tissue liver sample GSM3370155 Runtime Siftome inference GEO:sample:GSM3370155:d40d81d03c5ff917795537285f12faa4c97a54730ecd7e674587240ce8609187 low confidence liver sample_accession: GSM3370155 sample_title: 88674N source_name: adjacent non-tumor tissue characteristics: gender: male; age: 44; tissue: adjacent non-tumor liver tissue 88674N controlled vocabulary controlled vocabulary tissue match: liver
tissue liver sample GSM3370156 Runtime Siftome inference GEO:sample:GSM3370156:8e66072aee12f60fe5c20a99a2f48db5bdf3ea5c834d54ffdcf556ba6d10844a medium confidence hepatic sample_accession: GSM3370156 sample_title: 88674T source_name: tumor tissue characteristics: gender: male; age: 44; tissue: Intrahepatic cholangiocarcinoma 88674T controlled vocabulary controlled vocabulary tissue match: hepatic
tissue liver sample GSM3370157 Runtime Siftome inference GEO:sample:GSM3370157:e5968800dda7267401445dcbf8f855cde428a00308543fec9b73bec8c19c9773 low confidence liver sample_accession: GSM3370157 sample_title: 88724N source_name: adjacent non-tumor tissue characteristics: gender: male; age: 26; tissue: adjacent non-tumor liver tissue 88724N controlled vocabulary controlled vocabulary tissue match: liver
tissue liver sample GSM3370158 Runtime Siftome inference GEO:sample:GSM3370158:ebcb2dbf58e642a8a7396a88622e457a78effe84de7dbf0bd01c4cd1fdf47c87 medium confidence hepatic sample_accession: GSM3370158 sample_title: 88724T source_name: tumor tissue characteristics: gender: male; age: 26; tissue: Intrahepatic cholangiocarcinoma 88724T controlled vocabulary controlled vocabulary tissue match: hepatic
tissue liver sample GSM3370159 Runtime Siftome inference GEO:sample:GSM3370159:b89f83684ceea8cf20bba75dfa0e489afe7753ad1bd6b0e57ae81d672d8c17bc low confidence liver sample_accession: GSM3370159 sample_title: 89290N source_name: adjacent non-tumor tissue characteristics: gender: female; age: 57; tissue: adjacent non-tumor liver tissue 89290N controlled vocabulary controlled vocabulary tissue match: liver
tissue liver sample GSM3370160 Runtime Siftome inference GEO:sample:GSM3370160:9eff34d0bb54d219ed9be6b107e9b821777d658f254b97a66df5e8216090ad6d medium confidence hepatic sample_accession: GSM3370160 sample_title: 89290T source_name: tumor tissue characteristics: gender: female; age: 57; tissue: Intrahepatic cholangiocarcinoma 89290T controlled vocabulary controlled vocabulary tissue match: hepatic
tissue liver sample GSM3370161 Runtime Siftome inference GEO:sample:GSM3370161:b742cc0ba19482526fb48cd5f73020fba0c2888238adaafc2e2b525997437dc4 low confidence liver sample_accession: GSM3370161 sample_title: 96484N source_name: adjacent non-tumor tissue characteristics: gender: male; age: 64; tissue: adjacent non-tumor liver tissue 96484N controlled vocabulary controlled vocabulary tissue match: liver
tissue liver sample GSM3370162 Runtime Siftome inference GEO:sample:GSM3370162:bb0ab864ed228775bd751d18513c8df361cc82791bad374b9ebe869a6621d5d7 medium confidence hepatic sample_accession: GSM3370162 sample_title: 96484T source_name: tumor tissue characteristics: gender: male; age: 64; tissue: Intrahepatic cholangiocarcinoma 96484T controlled vocabulary controlled vocabulary tissue match: hepatic

Sample Group Preview

Possible case samples

Samples currently treated as the comparison case group.

15
  • GSM3370134 090608T tumor sample Case marker detected. tumor tissue gender: male; age: 72; tissue: Intrahepatic cholangiocarcinoma
  • GSM3370136 098699T tumor sample Case marker detected. tumor tissue gender: male; age: 33; tissue: Intrahepatic cholangiocarcinoma
  • GSM3370138 099535T tumor sample Case marker detected. tumor tissue gender: female; age: 61; tissue: Intrahepatic cholangiocarcinoma
  • GSM3370140 11770T tumor sample Case marker detected. tumor tissue gender: male; age: 55; tissue: Intrahepatic cholangiocarcinoma
  • GSM3370142 81023T tumor sample Case marker detected. tumor tissue gender: female; age: 49; tissue: Intrahepatic cholangiocarcinoma
  • GSM3370144 81032T tumor sample Case marker detected. tumor tissue gender: male; age: 50; tissue: Intrahepatic cholangiocarcinoma
  • GSM3370146 85421T tumor sample Case marker detected. tumor tissue gender: male; age: 53; tissue: Intrahepatic cholangiocarcinoma
  • GSM3370148 86279T tumor sample Case marker detected. tumor tissue gender: female; age: 65; tissue: Intrahepatic cholangiocarcinoma
  • GSM3370150 86960T tumor sample Case marker detected. tumor tissue gender: male; age: 60; tissue: Intrahepatic cholangiocarcinoma
  • GSM3370152 87823T tumor sample Case marker detected. tumor tissue gender: male; age: 48; tissue: Intrahepatic cholangiocarcinoma
  • GSM3370154 88659T tumor sample Case marker detected. tumor tissue gender: male; age: 47; tissue: Intrahepatic cholangiocarcinoma
  • GSM3370156 88674T tumor sample Case marker detected. tumor tissue gender: male; age: 44; tissue: Intrahepatic cholangiocarcinoma
  • GSM3370158 88724T tumor sample Case marker detected. tumor tissue gender: male; age: 26; tissue: Intrahepatic cholangiocarcinoma
  • GSM3370160 89290T tumor sample Case marker detected. tumor tissue gender: female; age: 57; tissue: Intrahepatic cholangiocarcinoma
  • GSM3370162 96484T tumor sample Case marker detected. tumor tissue gender: male; age: 64; tissue: Intrahepatic cholangiocarcinoma

Possible control samples

Samples currently treated as controls or baseline.

15
  • GSM3370133 090608N normal tissue Control marker detected. adjacent non-tumor tissue gender: male; age: 72; tissue: adjacent non-tumor liver tissue
  • GSM3370135 098699N normal tissue Control marker detected. adjacent non-tumor tissue gender: male; age: 33; tissue: adjacent non-tumor liver tissue
  • GSM3370137 099535N normal tissue Control marker detected. adjacent non-tumor tissue gender: female; age: 61; tissue: adjacent non-tumor liver tissue
  • GSM3370139 11770N normal tissue Control marker detected. adjacent non-tumor tissue gender: male; age: 55; tissue: adjacent non-tumor liver tissue
  • GSM3370141 81023N normal tissue Control marker detected. adjacent non-tumor tissue gender: female; age: 49; tissue: adjacent non-tumor liver tissue
  • GSM3370143 81032N normal tissue Control marker detected. adjacent non-tumor tissue gender: male; age: 50; tissue: adjacent non-tumor liver tissue
  • GSM3370145 85421N normal tissue Control marker detected. adjacent non-tumor tissue gender: male; age: 53; tissue: adjacent non-tumor liver tissue
  • GSM3370147 86279N normal tissue Control marker detected. adjacent non-tumor tissue gender: female; age: 65; tissue: adjacent non-tumor liver tissue
  • GSM3370149 86960N normal tissue Control marker detected. adjacent non-tumor tissue gender: male; age: 60; tissue: adjacent non-tumor liver tissue
  • GSM3370151 87823N normal tissue Control marker detected. adjacent non-tumor tissue gender: male; age: 48; tissue: adjacent non-tumor liver tissue
  • GSM3370153 88659N normal tissue Control marker detected. adjacent non-tumor tissue gender: male; age: 47; tissue: adjacent non-tumor liver tissue
  • GSM3370155 88674N normal tissue Control marker detected. adjacent non-tumor tissue gender: male; age: 44; tissue: adjacent non-tumor liver tissue
  • GSM3370157 88724N normal tissue Control marker detected. adjacent non-tumor tissue gender: male; age: 26; tissue: adjacent non-tumor liver tissue
  • GSM3370159 89290N normal tissue Control marker detected. adjacent non-tumor tissue gender: female; age: 57; tissue: adjacent non-tumor liver tissue
  • GSM3370161 96484N normal tissue Control marker detected. adjacent non-tumor tissue gender: male; age: 64; tissue: adjacent non-tumor liver tissue

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

85 pts
Clarity
85%
Weight
100 pts

Sample source clarity: All samples have source metadata and clear GSE/GSM accessions. Group clarity: Rule-based grouping found both case and control samples. Disease clarity: Disease or condition metadata was not 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

normal tissue

15 samples
  • GSM3370133 090608N adjacent non-tumor tissue gender: male; age: 72; tissue: adjacent non-tumor liver tissue
  • GSM3370135 098699N adjacent non-tumor tissue gender: male; age: 33; tissue: adjacent non-tumor liver tissue
  • GSM3370137 099535N adjacent non-tumor tissue gender: female; age: 61; tissue: adjacent non-tumor liver tissue
  • GSM3370139 11770N adjacent non-tumor tissue gender: male; age: 55; tissue: adjacent non-tumor liver tissue
  • GSM3370141 81023N adjacent non-tumor tissue gender: female; age: 49; tissue: adjacent non-tumor liver tissue
  • GSM3370143 81032N adjacent non-tumor tissue gender: male; age: 50; tissue: adjacent non-tumor liver tissue
  • GSM3370145 85421N adjacent non-tumor tissue gender: male; age: 53; tissue: adjacent non-tumor liver tissue
  • GSM3370147 86279N adjacent non-tumor tissue gender: female; age: 65; tissue: adjacent non-tumor liver tissue
  • GSM3370149 86960N adjacent non-tumor tissue gender: male; age: 60; tissue: adjacent non-tumor liver tissue
  • GSM3370151 87823N adjacent non-tumor tissue gender: male; age: 48; tissue: adjacent non-tumor liver tissue
  • GSM3370153 88659N adjacent non-tumor tissue gender: male; age: 47; tissue: adjacent non-tumor liver tissue
  • GSM3370155 88674N adjacent non-tumor tissue gender: male; age: 44; tissue: adjacent non-tumor liver tissue
  • GSM3370157 88724N adjacent non-tumor tissue gender: male; age: 26; tissue: adjacent non-tumor liver tissue
  • GSM3370159 89290N adjacent non-tumor tissue gender: female; age: 57; tissue: adjacent non-tumor liver tissue
  • GSM3370161 96484N adjacent non-tumor tissue gender: male; age: 64; tissue: adjacent non-tumor liver tissue

tumor sample

15 samples
  • GSM3370134 090608T tumor tissue gender: male; age: 72; tissue: Intrahepatic cholangiocarcinoma
  • GSM3370136 098699T tumor tissue gender: male; age: 33; tissue: Intrahepatic cholangiocarcinoma
  • GSM3370138 099535T tumor tissue gender: female; age: 61; tissue: Intrahepatic cholangiocarcinoma
  • GSM3370140 11770T tumor tissue gender: male; age: 55; tissue: Intrahepatic cholangiocarcinoma
  • GSM3370142 81023T tumor tissue gender: female; age: 49; tissue: Intrahepatic cholangiocarcinoma
  • GSM3370144 81032T tumor tissue gender: male; age: 50; tissue: Intrahepatic cholangiocarcinoma
  • GSM3370146 85421T tumor tissue gender: male; age: 53; tissue: Intrahepatic cholangiocarcinoma
  • GSM3370148 86279T tumor tissue gender: female; age: 65; tissue: Intrahepatic cholangiocarcinoma
  • GSM3370150 86960T tumor tissue gender: male; age: 60; tissue: Intrahepatic cholangiocarcinoma
  • GSM3370152 87823T tumor tissue gender: male; age: 48; tissue: Intrahepatic cholangiocarcinoma
  • GSM3370154 88659T tumor tissue gender: male; age: 47; tissue: Intrahepatic cholangiocarcinoma
  • GSM3370156 88674T tumor tissue gender: male; age: 44; tissue: Intrahepatic cholangiocarcinoma
  • GSM3370158 88724T tumor tissue gender: male; age: 26; tissue: Intrahepatic cholangiocarcinoma
  • GSM3370160 89290T tumor tissue gender: female; age: 57; tissue: Intrahepatic cholangiocarcinoma
  • GSM3370162 96484T tumor tissue gender: male; age: 64; tissue: Intrahepatic cholangiocarcinoma

Score Breakdown

60%

relevance

  • 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.
85%

metadata quality

  • Sample source clarity: All samples have source metadata and clear GSE/GSM accessions.
  • Group clarity: Rule-based grouping found both case and control samples.
  • Disease clarity: Disease or condition metadata was not 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

30 samples

Review Audit Trail

0 decisions

No review decisions have been stored for this dataset.