Siftome Phase 3L

GSE56087

Next Generation Sequencing identifying the dosage compensation state in human endometrial carcinoma and adjacent tissues

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: 2014-03-21
Last update: 2019-05-15
Organization: Soochow University
Department: Not available
Public date: 2015-01-07
Experiment types: Expression profiling by high throughput sequencing
Platforms: GPL11154 Illumina HiSeq 2000 (Homo sapiens)
Series type: Series
SubSeries: Not available
BioProject: PRJNA242387
Supplementary files: TAR: GSE56087_RAW.tar
Organism: Homo sapiens
Assay: bulk RNA-seq
Samples: 18
Study design: Tumor vs matched 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 matched normal Tissue

Tumor samples and matched/adjacent normal controls detected.
Tissue-like source terms detected.
Case metadata contains tumor or disease terms.
Control metadata contains normal or healthy-control terms.

Analysis Readiness

Ready after review

94% DE readiness

Contrast completeness

25/25 pts

Both case and control groups are present in the proposed grouping.

Minimum group size

20/20 pts

Each contrast group has at least 2 samples.

Processed data availability

20/20 pts

Processed data is marked available in the GEO index.

Sample decision clarity

15/15 pts

All samples are assigned to a case or control group.

Blocking warnings

7/10 pts

Warnings are present, but none are critical blockers.

Metadata normalization

7/10 pts

Metadata quality is usable, but still deserves review.

Blockers

No readiness blockers detected.

Next Steps

Review the sample grouping CSV and contrast CSV before running differential expression.
Confirm processed count files and sample identifiers match the exported metadata.

Analysis Preparation Checklist

5/6 ready

Group labels reviewed

Needs review

Siftome proposed case and control labels, but no reviewer confirmation is stored yet.

Open the sample grouping CSV and confirm group labels before analysis.

Minimum sample count met

Ready

Both groups meet the minimum of 2 samples.

Confirm whether the cohort is large enough for the intended statistical analysis.

Processed counts available

Ready

Processed data availability is marked true in the GEO index.

Verify that downloaded processed files contain usable count or expression identifiers.

Ambiguous samples handled

Ready

No review-needed or unassigned samples are present in the proposed grouping.

Still scan the grouping table for biology-specific ambiguity.

Exclusion decisions recorded

Ready

No hard-excluded samples were detected by the current rules.

Record any manual exclusions in the downstream analysis notes.

Source links preserved

Ready

The dataset and sample accessions can be linked back to GEO.

Keep GEO dataset and sample links with exported metadata.

Bioinformatician Review

Standard analyst review

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

No expert-review triggers were detected by Siftome.

Why This Is Ranked Here

Patient tissue tumor-vs-normal

Exploratory only Dataset can inform exploration but is not strong enough for primary analysis.

Score Components

relevance 50% Organism normalized. Assay type normalized.
comparison suitability 10% Tumor and normal sample groups detected. No excluded sample type flags detected. Matched 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 matched normal Study design remains rule-derived: Tumor vs matched normal.
Specimen/source Tissue Specimen/source remains rule-derived: Tissue.
Likely case group tumor sample 9 samples
Likely control group normal tissue 9 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 matched 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 matched normal · Tissue · suitability 10%. Contributed to match or upgrade evidence.
Supporting fact Prioritized for patient tissue tumor-vs-normal triage. 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

No active manual corrections are applied to this dataset.

Organism · Normalization rules Organism remains rule-derived: Homo sapiens.
Assay · Normalization rules Assay remains rule-derived: bulk RNA-seq.
Study design · Classifier and grouping rules Study design remains rule-derived: Tumor vs matched normal.
Specimen/source · Normalization rules Specimen/source remains rule-derived: Tissue.

Dataset organism

Dataset field · Organism · Global correction

Wrong organism

Current derived value

Homo sapiens

Raw GEO organism

dataset_accession: GSE56087
organism: Homo sapiens
dataset_title: Next Generation Sequencing identifying the dosage compensation state in human endometrial carcinoma and adjacent tissues

Dataset assay

Dataset field · Assay · Global correction

Wrong assay

Current derived value

bulk RNA-seq

Raw GEO assay metadata

assay_type: bulk RNA-seq
experiment_types: Expression profiling by high throughput sequencing
platforms: GPL11154 Illumina HiSeq 2000 (Homo sapiens)
dataset_title: Next Generation Sequencing identifying the dosage compensation state in human endometrial carcinoma and adjacent tissues

Study design

Dataset field · Study design · Global correction

Wrong study design

Current derived value

Tumor vs matched normal

Raw GEO study and sample metadata

dataset_title: Next Generation Sequencing identifying the dosage compensation state in human endometrial carcinoma and adjacent tissues
experiment_types: Expression profiling by high throughput sequencing
sample_context: GSM1354841: source_name=adjacent normal tissue; characteristics=sample donor: donor No.1; gender: female; organ: endometrium; tissue: adjacent normal tissue
GSM1354842: source_name=endometrial tumor; characteristics=sample donor: donor No.1; gender: female; organ: endometrium; tissue: endometrial tumor
GSM1354843: source_name=adjacent normal tissue; characteristics=sample donor: donor No.2; gender: female; organ: endometrium; tissue: adjacent normal tissue
GSM1354844: source_name=endometrial tumor; characteristics=sample donor: donor No.2; gender: female; organ: endometrium; tissue: endometrial tumor
GSM1354845: source_name=adjacent normal tissue; characteristics=sample 
[Correction source preview truncated.]

Specimen/source type

Dataset field · Specimen/source · Global correction

Wrong specimen/source

Current derived value

Tissue

Raw GEO sample source metadata

dataset_title: Next Generation Sequencing identifying the dosage compensation state in human endometrial carcinoma and adjacent tissues
sample_context: GSM1354841: source_name=adjacent normal tissue; characteristics=sample donor: donor No.1; gender: female; organ: endometrium; tissue: adjacent normal tissue
GSM1354842: source_name=endometrial tumor; characteristics=sample donor: donor No.1; gender: female; organ: endometrium; tissue: endometrial tumor
GSM1354843: source_name=adjacent normal tissue; characteristics=sample donor: donor No.2; gender: female; organ: endometrium; tissue: adjacent normal tissue
GSM1354844: source_name=endometrial tumor; characteristics=sample donor: donor No.2; gender: female; organ: endometrium; tissue: endometrial tumor
GSM1354845: source_name=adjacent normal tissue; characteristics=sample donor: donor No.3; gender: female; organ: endometrium; tissue: adjace
[Correction source preview truncated.]

Disease context

Dataset field · Disease context · Global correction

Wrong disease context

Current derived value

No disease context detected

Raw GEO disease context metadata

dataset_title: Next Generation Sequencing identifying the dosage compensation state in human endometrial carcinoma and adjacent tissues
sample_context: GSM1354841: source_name=adjacent normal tissue; characteristics=sample donor: donor No.1; gender: female; organ: endometrium; tissue: adjacent normal tissue
GSM1354842: source_name=endometrial tumor; characteristics=sample donor: donor No.1; gender: female; organ: endometrium; tissue: endometrial tumor
GSM1354843: source_name=adjacent normal tissue; characteristics=sample donor: donor No.2; gender: female; organ: endometrium; tissue: adjacent normal tissue
GSM1354844: source_name=endometrial tumor; characteristics=sample donor: donor No.2; gender: female; organ: endometrium; tissue: endometrial tumor
GSM1354845: source_name=adjacent normal tissue; characteristics=sample donor: donor No.3; gender: female; organ: endometrium; tissue: adjace
[Correction source preview truncated.]

Intent exclusion

Search intent · Intent eligibility · Patient tissue tumor-vs-normal

Exclude from intent

Current derived value

Eligible for Patient tissue tumor-vs-normal as Exploratory only

Raw GEO metadata for intent decision

dataset_accession: GSE56087
dataset_title: Next Generation Sequencing identifying the dosage compensation state in human endometrial carcinoma and adjacent tissues
organism: Homo sapiens
assay_type: bulk RNA-seq
sample_context: GSM1354841: source_name=adjacent normal tissue; characteristics=sample donor: donor No.1; gender: female; organ: endometrium; tissue: adjacent normal tissue
GSM1354842: source_name=endometrial tumor; characteristics=sample donor: donor No.1; gender: female; organ: endometrium; tissue: endometrial tumor
GSM1354843: source_name=adjacent normal tissue; characteristics=sample donor: donor No.2; gender: female; organ: endometrium; tissue: adjacent normal tissue
GSM1354844: source_name=endometrial tumor; characteristics=sample donor: donor No.2; gender: female; organ: endometrium; tissue: endometrial tumor
GSM1354845: source_name=adjacent normal tissue; characteristics=
[Correction source preview truncated.]

Intent-only inclusion

Search intent · Intent eligibility · Patient tissue tumor-vs-normal

Include only for intent

Current derived value

Eligible for Patient tissue tumor-vs-normal as Exploratory only

Raw GEO metadata for intent decision

dataset_accession: GSE56087
dataset_title: Next Generation Sequencing identifying the dosage compensation state in human endometrial carcinoma and adjacent tissues
organism: Homo sapiens
assay_type: bulk RNA-seq
sample_context: GSM1354841: source_name=adjacent normal tissue; characteristics=sample donor: donor No.1; gender: female; organ: endometrium; tissue: adjacent normal tissue
GSM1354842: source_name=endometrial tumor; characteristics=sample donor: donor No.1; gender: female; organ: endometrium; tissue: endometrial tumor
GSM1354843: source_name=adjacent normal tissue; characteristics=sample donor: donor No.2; gender: female; organ: endometrium; tissue: adjacent normal tissue
GSM1354844: source_name=endometrial tumor; characteristics=sample donor: donor No.2; gender: female; organ: endometrium; tissue: endometrial tumor
GSM1354845: source_name=adjacent normal tissue; characteristics=
[Correction source preview truncated.]

GSM1354841 grouping

Sample field · Grouping · Global correction · GSM1354841

Wrong grouping

Current derived value

normal tissue (control)

Raw GEO sample metadata

sample_accession: GSM1354841
sample_title: RNA-seq_Sample 1
source_name: adjacent normal tissue
characteristics: sample donor: donor No.1; gender: female; organ: endometrium; tissue: adjacent normal tissue

GSM1354841 exclusion decision

Sample field · Sample exclusion · Global correction · GSM1354841

Wrong sample exclusion

Current derived value

Included in derived sample grouping as normal tissue

Raw GEO sample metadata

sample_accession: GSM1354841
sample_title: RNA-seq_Sample 1
source_name: adjacent normal tissue
characteristics: sample donor: donor No.1; gender: female; organ: endometrium; tissue: adjacent normal tissue

GSM1354842 grouping

Sample field · Grouping · Global correction · GSM1354842

Wrong grouping

Current derived value

tumor sample (case)

Raw GEO sample metadata

sample_accession: GSM1354842
sample_title: RNA-seq_Sample 2
source_name: endometrial tumor
characteristics: sample donor: donor No.1; gender: female; organ: endometrium; tissue: endometrial tumor

GSM1354842 exclusion decision

Sample field · Sample exclusion · Global correction · GSM1354842

Wrong sample exclusion

Current derived value

Included in derived sample grouping as tumor sample

Raw GEO sample metadata

sample_accession: GSM1354842
sample_title: RNA-seq_Sample 2
source_name: endometrial tumor
characteristics: sample donor: donor No.1; gender: female; organ: endometrium; tissue: endometrial tumor

GSM1354843 grouping

Sample field · Grouping · Global correction · GSM1354843

Wrong grouping

Current derived value

normal tissue (control)

Raw GEO sample metadata

sample_accession: GSM1354843
sample_title: RNA-seq_Sample 3
source_name: adjacent normal tissue
characteristics: sample donor: donor No.2; gender: female; organ: endometrium; tissue: adjacent normal tissue

GSM1354843 exclusion decision

Sample field · Sample exclusion · Global correction · GSM1354843

Wrong sample exclusion

Current derived value

Included in derived sample grouping as normal tissue

Raw GEO sample metadata

sample_accession: GSM1354843
sample_title: RNA-seq_Sample 3
source_name: adjacent normal tissue
characteristics: sample donor: donor No.2; gender: female; organ: endometrium; tissue: adjacent normal tissue

GSM1354844 grouping

Sample field · Grouping · Global correction · GSM1354844

Wrong grouping

Current derived value

tumor sample (case)

Raw GEO sample metadata

sample_accession: GSM1354844
sample_title: RNA-seq_Sample 4
source_name: endometrial tumor
characteristics: sample donor: donor No.2; gender: female; organ: endometrium; tissue: endometrial tumor

GSM1354844 exclusion decision

Sample field · Sample exclusion · Global correction · GSM1354844

Wrong sample exclusion

Current derived value

Included in derived sample grouping as tumor sample

Raw GEO sample metadata

sample_accession: GSM1354844
sample_title: RNA-seq_Sample 4
source_name: endometrial tumor
characteristics: sample donor: donor No.2; gender: female; organ: endometrium; tissue: endometrial tumor

GSM1354845 grouping

Sample field · Grouping · Global correction · GSM1354845

Wrong grouping

Current derived value

normal tissue (control)

Raw GEO sample metadata

sample_accession: GSM1354845
sample_title: RNA-seq_Sample 5
source_name: adjacent normal tissue
characteristics: sample donor: donor No.3; gender: female; organ: endometrium; tissue: adjacent normal tissue

GSM1354845 exclusion decision

Sample field · Sample exclusion · Global correction · GSM1354845

Wrong sample exclusion

Current derived value

Included in derived sample grouping as normal tissue

Raw GEO sample metadata

sample_accession: GSM1354845
sample_title: RNA-seq_Sample 5
source_name: adjacent normal tissue
characteristics: sample donor: donor No.3; gender: female; organ: endometrium; tissue: adjacent normal tissue

GSM1354846 grouping

Sample field · Grouping · Global correction · GSM1354846

Wrong grouping

Current derived value

tumor sample (case)

Raw GEO sample metadata

sample_accession: GSM1354846
sample_title: RNA-seq_Sample 6
source_name: endometrial tumor
characteristics: sample donor: donor No.3; gender: female; organ: endometrium; tissue: endometrial tumor

GSM1354846 exclusion decision

Sample field · Sample exclusion · Global correction · GSM1354846

Wrong sample exclusion

Current derived value

Included in derived sample grouping as tumor sample

Raw GEO sample metadata

sample_accession: GSM1354846
sample_title: RNA-seq_Sample 6
source_name: endometrial tumor
characteristics: sample donor: donor No.3; gender: female; organ: endometrium; tissue: endometrial tumor

GSM1354847 grouping

Sample field · Grouping · Global correction · GSM1354847

Wrong grouping

Current derived value

normal tissue (control)

Raw GEO sample metadata

sample_accession: GSM1354847
sample_title: RNA-seq_Sample 7
source_name: adjacent normal tissue
characteristics: sample donor: donor No.4; gender: female; organ: endometrium; tissue: adjacent normal tissue

GSM1354847 exclusion decision

Sample field · Sample exclusion · Global correction · GSM1354847

Wrong sample exclusion

Current derived value

Included in derived sample grouping as normal tissue

Raw GEO sample metadata

sample_accession: GSM1354847
sample_title: RNA-seq_Sample 7
source_name: adjacent normal tissue
characteristics: sample donor: donor No.4; gender: female; organ: endometrium; tissue: adjacent normal tissue

GSM1354848 grouping

Sample field · Grouping · Global correction · GSM1354848

Wrong grouping

Current derived value

tumor sample (case)

Raw GEO sample metadata

sample_accession: GSM1354848
sample_title: RNA-seq_Sample 8
source_name: endometrial tumor
characteristics: sample donor: donor No.4; gender: female; organ: endometrium; tissue: endometrial tumor

GSM1354848 exclusion decision

Sample field · Sample exclusion · Global correction · GSM1354848

Wrong sample exclusion

Current derived value

Included in derived sample grouping as tumor sample

Raw GEO sample metadata

sample_accession: GSM1354848
sample_title: RNA-seq_Sample 8
source_name: endometrial tumor
characteristics: sample donor: donor No.4; gender: female; organ: endometrium; tissue: endometrial tumor

GSM1354849 grouping

Sample field · Grouping · Global correction · GSM1354849

Wrong grouping

Current derived value

normal tissue (control)

Raw GEO sample metadata

sample_accession: GSM1354849
sample_title: RNA-seq_Sample 9
source_name: adjacent normal tissue
characteristics: sample donor: donor No.5; gender: female; organ: endometrium; tissue: adjacent normal tissue

GSM1354849 exclusion decision

Sample field · Sample exclusion · Global correction · GSM1354849

Wrong sample exclusion

Current derived value

Included in derived sample grouping as normal tissue

Raw GEO sample metadata

sample_accession: GSM1354849
sample_title: RNA-seq_Sample 9
source_name: adjacent normal tissue
characteristics: sample donor: donor No.5; gender: female; organ: endometrium; tissue: adjacent normal tissue

GSM1354850 grouping

Sample field · Grouping · Global correction · GSM1354850

Wrong grouping

Current derived value

tumor sample (case)

Raw GEO sample metadata

sample_accession: GSM1354850
sample_title: RNA-seq_Sample 10
source_name: endometrial tumor
characteristics: sample donor: donor No.5; gender: female; organ: endometrium; tissue: endometrial tumor

GSM1354850 exclusion decision

Sample field · Sample exclusion · Global correction · GSM1354850

Wrong sample exclusion

Current derived value

Included in derived sample grouping as tumor sample

Raw GEO sample metadata

sample_accession: GSM1354850
sample_title: RNA-seq_Sample 10
source_name: endometrial tumor
characteristics: sample donor: donor No.5; gender: female; organ: endometrium; tissue: endometrial tumor

GSM1354851 grouping

Sample field · Grouping · Global correction · GSM1354851

Wrong grouping

Current derived value

tumor sample (case)

Raw GEO sample metadata

sample_accession: GSM1354851
sample_title: RNA-seq_Sample 11
source_name: endometrial tumor
characteristics: sample donor: donor No.6; gender: female; organ: endometrium; tissue: endometrial tumor

GSM1354851 exclusion decision

Sample field · Sample exclusion · Global correction · GSM1354851

Wrong sample exclusion

Current derived value

Included in derived sample grouping as tumor sample

Raw GEO sample metadata

sample_accession: GSM1354851
sample_title: RNA-seq_Sample 11
source_name: endometrial tumor
characteristics: sample donor: donor No.6; gender: female; organ: endometrium; tissue: endometrial tumor

GSM1354852 grouping

Sample field · Grouping · Global correction · GSM1354852

Wrong grouping

Current derived value

normal tissue (control)

Raw GEO sample metadata

sample_accession: GSM1354852
sample_title: RNA-seq_Sample 12
source_name: adjacent normal tissue
characteristics: sample donor: donor No.6; gender: female; organ: endometrium; tissue: adjacent normal tissue

GSM1354852 exclusion decision

Sample field · Sample exclusion · Global correction · GSM1354852

Wrong sample exclusion

Current derived value

Included in derived sample grouping as normal tissue

Raw GEO sample metadata

sample_accession: GSM1354852
sample_title: RNA-seq_Sample 12
source_name: adjacent normal tissue
characteristics: sample donor: donor No.6; gender: female; organ: endometrium; tissue: adjacent normal tissue

GSM1354853 grouping

Sample field · Grouping · Global correction · GSM1354853

Wrong grouping

Current derived value

normal tissue (control)

Raw GEO sample metadata

sample_accession: GSM1354853
sample_title: RNA-seq_Sample 13
source_name: adjacent normal tissue
characteristics: sample donor: donor No.7; gender: female; organ: endometrium; tissue: adjacent normal tissue

GSM1354853 exclusion decision

Sample field · Sample exclusion · Global correction · GSM1354853

Wrong sample exclusion

Current derived value

Included in derived sample grouping as normal tissue

Raw GEO sample metadata

sample_accession: GSM1354853
sample_title: RNA-seq_Sample 13
source_name: adjacent normal tissue
characteristics: sample donor: donor No.7; gender: female; organ: endometrium; tissue: adjacent normal tissue

GSM1354854 grouping

Sample field · Grouping · Global correction · GSM1354854

Wrong grouping

Current derived value

tumor sample (case)

Raw GEO sample metadata

sample_accession: GSM1354854
sample_title: RNA-seq_Sample 14
source_name: endometrial tumor
characteristics: sample donor: donor No.7; gender: female; organ: endometrium; tissue: endometrial tumor

GSM1354854 exclusion decision

Sample field · Sample exclusion · Global correction · GSM1354854

Wrong sample exclusion

Current derived value

Included in derived sample grouping as tumor sample

Raw GEO sample metadata

sample_accession: GSM1354854
sample_title: RNA-seq_Sample 14
source_name: endometrial tumor
characteristics: sample donor: donor No.7; gender: female; organ: endometrium; tissue: endometrial tumor

GSM1354855 grouping

Sample field · Grouping · Global correction · GSM1354855

Wrong grouping

Current derived value

normal tissue (control)

Raw GEO sample metadata

sample_accession: GSM1354855
sample_title: RNA-seq_Sample 15
source_name: adjacent normal tissue
characteristics: sample donor: donor No.8; gender: female; organ: endometrium; tissue: adjacent normal tissue

GSM1354855 exclusion decision

Sample field · Sample exclusion · Global correction · GSM1354855

Wrong sample exclusion

Current derived value

Included in derived sample grouping as normal tissue

Raw GEO sample metadata

sample_accession: GSM1354855
sample_title: RNA-seq_Sample 15
source_name: adjacent normal tissue
characteristics: sample donor: donor No.8; gender: female; organ: endometrium; tissue: adjacent normal tissue

GSM1354856 grouping

Sample field · Grouping · Global correction · GSM1354856

Wrong grouping

Current derived value

tumor sample (case)

Raw GEO sample metadata

sample_accession: GSM1354856
sample_title: RNA-seq_Sample 16
source_name: endometrial tumor
characteristics: sample donor: donor No.8; gender: female; organ: endometrium; tissue: endometrial tumor

GSM1354856 exclusion decision

Sample field · Sample exclusion · Global correction · GSM1354856

Wrong sample exclusion

Current derived value

Included in derived sample grouping as tumor sample

Raw GEO sample metadata

sample_accession: GSM1354856
sample_title: RNA-seq_Sample 16
source_name: endometrial tumor
characteristics: sample donor: donor No.8; gender: female; organ: endometrium; tissue: endometrial tumor

GSM1354857 grouping

Sample field · Grouping · Global correction · GSM1354857

Wrong grouping

Current derived value

normal tissue (control)

Raw GEO sample metadata

sample_accession: GSM1354857
sample_title: RNA-seq_Sample 17
source_name: adjacent normal tissue
characteristics: sample donor: donor No.9; gender: female; organ: endometrium; tissue: adjacent normal tissue

GSM1354857 exclusion decision

Sample field · Sample exclusion · Global correction · GSM1354857

Wrong sample exclusion

Current derived value

Included in derived sample grouping as normal tissue

Raw GEO sample metadata

sample_accession: GSM1354857
sample_title: RNA-seq_Sample 17
source_name: adjacent normal tissue
characteristics: sample donor: donor No.9; gender: female; organ: endometrium; tissue: adjacent normal tissue

GSM1354858 grouping

Sample field · Grouping · Global correction · GSM1354858

Wrong grouping

Current derived value

tumor sample (case)

Raw GEO sample metadata

sample_accession: GSM1354858
sample_title: RNA-seq_Sample 18
source_name: endometrial tumor
characteristics: sample donor: donor No.9; gender: female; organ: endometrium; tissue: endometrial tumor

GSM1354858 exclusion decision

Sample field · Sample exclusion · Global correction · GSM1354858

Wrong sample exclusion

Current derived value

Included in derived sample grouping as tumor sample

Raw GEO sample metadata

sample_accession: GSM1354858
sample_title: RNA-seq_Sample 18
source_name: endometrial tumor
characteristics: sample donor: donor No.9; gender: female; organ: endometrium; tissue: endometrial tumor

Source Evidence

4 sources

GEO

Primary source

Original dataset metadata, sample metadata, source links, and GEO data availability flags.

Dataset accession: GSE56087
Sample records: 18 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: GSE56087

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.

Expression Atlas

Not imported

Planned source for curated expression experiment links.

GEO accession: GSE56087

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.

PubMed

Unavailable

Publication context when PubMed identifiers are already known.

GEO accession: GSE56087

No PubMed identifier is present in the current runtime metadata.
No live PubMed search is performed from the dataset detail page.

Dataset Feedback

0 stored

No project feedback stored for this dataset.

Original GEO Metadata

dataset_accession: GSE56087
dataset_title: Next Generation Sequencing identifying the dosage compensation state in human endometrial carcinoma and adjacent tissues
organism: Homo sapiens
assay_type: bulk RNA-seq
processed_data_available: true
raw_data_available: true
submission_date: 2014-03-21
last_update_date: 2019-05-15
organization_name: Soochow University
department: Not available
public_date: 2015-01-07
experiment_types: Expression profiling by high throughput sequencing
platforms: GPL11154 Illumina HiSeq 2000 (Homo sapiens)
sub_series: Not available
bioproject: PRJNA242387
supplementary_files: TAR: GSE56087_RAW.tar
series_type: Series

Why It Matched

Tumor vs matched normal · Tissue · suitability 10%.
Prioritized for patient tissue tumor-vs-normal triage.
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

29 fields

Field Value Source Origin Confidence Evidence Reason

assay_type bulk RNA-seq dataset GSE56087 Runtime Siftome inference GEO:dataset:GSE56087:3d84fab678f30e2d6fa58c2365f14f1dcc458c9537e003952a1c18ad6fcb5715 high confidence bulk rna-seq dataset_accession: GSE56087 dataset_title: Next Generation Sequencing identifying the dosage compensation state in human endometrial carcinoma and adjacent tissues organism: Hom... keyword match keyword match: bulk rna-seq

normal_tissue_type adjacent normal sample GSM1354841 Runtime Siftome inference GEO:sample:GSM1354841:c6cad524d0d427be9154d89d1491f3fd675c533a1885432659b75337f42f1b85 high confidence adjacent normal sample_accession: GSM1354841 sample_title: RNA-seq_Sample 1 source_name: adjacent normal tissue characteristics: sample donor: donor No.1; gender: female; organ: endometrium; ti... controlled vocabulary controlled vocabulary normal tissue type match: adjacent normal

normal_tissue_type adjacent normal sample GSM1354843 Runtime Siftome inference GEO:sample:GSM1354843:571eb5f1b0cfc3909242283e26bad250cfe329fbcca0c4aa971662793de64a2b high confidence adjacent normal sample_accession: GSM1354843 sample_title: RNA-seq_Sample 3 source_name: adjacent normal tissue characteristics: sample donor: donor No.2; gender: female; organ: endometrium; ti... controlled vocabulary controlled vocabulary normal tissue type match: adjacent normal

normal_tissue_type adjacent normal sample GSM1354845 Runtime Siftome inference GEO:sample:GSM1354845:a0da452ebaf257400dae32d679fc2856ece3cb57ec6a1768d28b98fbf13bb287 high confidence adjacent normal sample_accession: GSM1354845 sample_title: RNA-seq_Sample 5 source_name: adjacent normal tissue characteristics: sample donor: donor No.3; gender: female; organ: endometrium; ti... controlled vocabulary controlled vocabulary normal tissue type match: adjacent normal

normal_tissue_type adjacent normal sample GSM1354847 Runtime Siftome inference GEO:sample:GSM1354847:4a67b88a1284c1c0ac066f5f6f884b7d2c454aa51de07b1fb3d9494ccc8d035a high confidence adjacent normal sample_accession: GSM1354847 sample_title: RNA-seq_Sample 7 source_name: adjacent normal tissue characteristics: sample donor: donor No.4; gender: female; organ: endometrium; ti... controlled vocabulary controlled vocabulary normal tissue type match: adjacent normal

normal_tissue_type adjacent normal sample GSM1354849 Runtime Siftome inference GEO:sample:GSM1354849:27660bae27ae6bc7aa258c2367c0d8237666f05365490904bf1a26ab69d9894a high confidence adjacent normal sample_accession: GSM1354849 sample_title: RNA-seq_Sample 9 source_name: adjacent normal tissue characteristics: sample donor: donor No.5; gender: female; organ: endometrium; ti... controlled vocabulary controlled vocabulary normal tissue type match: adjacent normal

normal_tissue_type adjacent normal sample GSM1354852 Runtime Siftome inference GEO:sample:GSM1354852:f5eb8829dfe9486fef3bf6810af68d237f039d70bb570667ee9fe326ad530f53 high confidence adjacent normal sample_accession: GSM1354852 sample_title: RNA-seq_Sample 12 source_name: adjacent normal tissue characteristics: sample donor: donor No.6; gender: female; organ: endometrium; t... controlled vocabulary controlled vocabulary normal tissue type match: adjacent normal

normal_tissue_type adjacent normal sample GSM1354853 Runtime Siftome inference GEO:sample:GSM1354853:c82d0d1fc85f1a991a0e6e3057683d5b2d6527e228678743920ef6a904cef784 high confidence adjacent normal sample_accession: GSM1354853 sample_title: RNA-seq_Sample 13 source_name: adjacent normal tissue characteristics: sample donor: donor No.7; gender: female; organ: endometrium; t... controlled vocabulary controlled vocabulary normal tissue type match: adjacent normal

normal_tissue_type adjacent normal sample GSM1354855 Runtime Siftome inference GEO:sample:GSM1354855:bd0e5aece2ed4c4a25753d9eaa6aa186a6515bc873da5bf4fb4c4ca0ead94b34 high confidence adjacent normal sample_accession: GSM1354855 sample_title: RNA-seq_Sample 15 source_name: adjacent normal tissue characteristics: sample donor: donor No.8; gender: female; organ: endometrium; t... controlled vocabulary controlled vocabulary normal tissue type match: adjacent normal

normal_tissue_type adjacent normal sample GSM1354857 Runtime Siftome inference GEO:sample:GSM1354857:cc027c8d37606e169d71728fe88093a9ca6f11238bf7dcc2078c6b2c837db417 high confidence adjacent normal sample_accession: GSM1354857 sample_title: RNA-seq_Sample 17 source_name: adjacent normal tissue characteristics: sample donor: donor No.9; gender: female; organ: endometrium; t... controlled vocabulary controlled vocabulary normal tissue type match: adjacent normal

organism Homo sapiens dataset GSE56087 Runtime Siftome inference GEO:dataset:GSE56087:3d84fab678f30e2d6fa58c2365f14f1dcc458c9537e003952a1c18ad6fcb5715 high confidence homo sapiens dataset_accession: GSE56087 dataset_title: Next Generation Sequencing identifying the dosage compensation state in human endometrial carcinoma and adjacent tissues organism: Hom... keyword match keyword match: homo sapiens

sample_type normal tissue sample GSM1354841 Runtime Siftome inference GEO:sample:GSM1354841:c6cad524d0d427be9154d89d1491f3fd675c533a1885432659b75337f42f1b85 high confidence adjacent normal sample_accession: GSM1354841 sample_title: RNA-seq_Sample 1 source_name: adjacent normal tissue characteristics: sample donor: donor No.1; gender: female; organ: endometrium; ti... controlled vocabulary controlled vocabulary sample type match: adjacent normal

sample_type tumor sample sample GSM1354842 Runtime Siftome inference GEO:sample:GSM1354842:ae4517e10db095a7c8fc35fc33a1d43d37add25c8f7e6487af1960479e1ec146 low confidence tumor sample_accession: GSM1354842 sample_title: RNA-seq_Sample 2 source_name: endometrial tumor characteristics: sample donor: donor No.1; gender: female; organ: endometrium; tissue:... controlled vocabulary controlled vocabulary sample type match: tumor

sample_type normal tissue sample GSM1354843 Runtime Siftome inference GEO:sample:GSM1354843:571eb5f1b0cfc3909242283e26bad250cfe329fbcca0c4aa971662793de64a2b high confidence adjacent normal sample_accession: GSM1354843 sample_title: RNA-seq_Sample 3 source_name: adjacent normal tissue characteristics: sample donor: donor No.2; gender: female; organ: endometrium; ti... controlled vocabulary controlled vocabulary sample type match: adjacent normal

sample_type tumor sample sample GSM1354844 Runtime Siftome inference GEO:sample:GSM1354844:3f9ab3ad17e9282cd4ec727582da03fcbcea2358dcec21dfad1d09c388f46b93 low confidence tumor sample_accession: GSM1354844 sample_title: RNA-seq_Sample 4 source_name: endometrial tumor characteristics: sample donor: donor No.2; gender: female; organ: endometrium; tissue:... controlled vocabulary controlled vocabulary sample type match: tumor

sample_type normal tissue sample GSM1354845 Runtime Siftome inference GEO:sample:GSM1354845:a0da452ebaf257400dae32d679fc2856ece3cb57ec6a1768d28b98fbf13bb287 high confidence adjacent normal sample_accession: GSM1354845 sample_title: RNA-seq_Sample 5 source_name: adjacent normal tissue characteristics: sample donor: donor No.3; gender: female; organ: endometrium; ti... controlled vocabulary controlled vocabulary sample type match: adjacent normal

sample_type tumor sample sample GSM1354846 Runtime Siftome inference GEO:sample:GSM1354846:b49e9938f53e35ee03ba7958ddc96f4ab2184eaf9436c5aea450fb71bb158d4d low confidence tumor sample_accession: GSM1354846 sample_title: RNA-seq_Sample 6 source_name: endometrial tumor characteristics: sample donor: donor No.3; gender: female; organ: endometrium; tissue:... controlled vocabulary controlled vocabulary sample type match: tumor

sample_type normal tissue sample GSM1354847 Runtime Siftome inference GEO:sample:GSM1354847:4a67b88a1284c1c0ac066f5f6f884b7d2c454aa51de07b1fb3d9494ccc8d035a high confidence adjacent normal sample_accession: GSM1354847 sample_title: RNA-seq_Sample 7 source_name: adjacent normal tissue characteristics: sample donor: donor No.4; gender: female; organ: endometrium; ti... controlled vocabulary controlled vocabulary sample type match: adjacent normal

sample_type tumor sample sample GSM1354848 Runtime Siftome inference GEO:sample:GSM1354848:6b67d3b517dfaac74b6858bf4d7515b5bb88208f5d71a0936b41f77f9a943e29 low confidence tumor sample_accession: GSM1354848 sample_title: RNA-seq_Sample 8 source_name: endometrial tumor characteristics: sample donor: donor No.4; gender: female; organ: endometrium; tissue:... controlled vocabulary controlled vocabulary sample type match: tumor

sample_type normal tissue sample GSM1354849 Runtime Siftome inference GEO:sample:GSM1354849:27660bae27ae6bc7aa258c2367c0d8237666f05365490904bf1a26ab69d9894a high confidence adjacent normal sample_accession: GSM1354849 sample_title: RNA-seq_Sample 9 source_name: adjacent normal tissue characteristics: sample donor: donor No.5; gender: female; organ: endometrium; ti... controlled vocabulary controlled vocabulary sample type match: adjacent normal

sample_type tumor sample sample GSM1354850 Runtime Siftome inference GEO:sample:GSM1354850:13a3226712a34491adc4345c054944379ba2535632cec02acfcada9159323272 low confidence tumor sample_accession: GSM1354850 sample_title: RNA-seq_Sample 10 source_name: endometrial tumor characteristics: sample donor: donor No.5; gender: female; organ: endometrium; tissue... controlled vocabulary controlled vocabulary sample type match: tumor

sample_type tumor sample sample GSM1354851 Runtime Siftome inference GEO:sample:GSM1354851:d185e80eeae2d51c939ae8f8d5d5b2046bdb86d996b9f5b65d960b0c557504b0 low confidence tumor sample_accession: GSM1354851 sample_title: RNA-seq_Sample 11 source_name: endometrial tumor characteristics: sample donor: donor No.6; gender: female; organ: endometrium; tissue... controlled vocabulary controlled vocabulary sample type match: tumor

sample_type normal tissue sample GSM1354852 Runtime Siftome inference GEO:sample:GSM1354852:f5eb8829dfe9486fef3bf6810af68d237f039d70bb570667ee9fe326ad530f53 high confidence adjacent normal sample_accession: GSM1354852 sample_title: RNA-seq_Sample 12 source_name: adjacent normal tissue characteristics: sample donor: donor No.6; gender: female; organ: endometrium; t... controlled vocabulary controlled vocabulary sample type match: adjacent normal

sample_type normal tissue sample GSM1354853 Runtime Siftome inference GEO:sample:GSM1354853:c82d0d1fc85f1a991a0e6e3057683d5b2d6527e228678743920ef6a904cef784 high confidence adjacent normal sample_accession: GSM1354853 sample_title: RNA-seq_Sample 13 source_name: adjacent normal tissue characteristics: sample donor: donor No.7; gender: female; organ: endometrium; t... controlled vocabulary controlled vocabulary sample type match: adjacent normal

sample_type tumor sample sample GSM1354854 Runtime Siftome inference GEO:sample:GSM1354854:76c6f635702f58de24f4b42a11d4f9c92d5d70d5708eada17ff813b17afe07e2 low confidence tumor sample_accession: GSM1354854 sample_title: RNA-seq_Sample 14 source_name: endometrial tumor characteristics: sample donor: donor No.7; gender: female; organ: endometrium; tissue... controlled vocabulary controlled vocabulary sample type match: tumor

sample_type normal tissue sample GSM1354855 Runtime Siftome inference GEO:sample:GSM1354855:bd0e5aece2ed4c4a25753d9eaa6aa186a6515bc873da5bf4fb4c4ca0ead94b34 high confidence adjacent normal sample_accession: GSM1354855 sample_title: RNA-seq_Sample 15 source_name: adjacent normal tissue characteristics: sample donor: donor No.8; gender: female; organ: endometrium; t... controlled vocabulary controlled vocabulary sample type match: adjacent normal

sample_type tumor sample sample GSM1354856 Runtime Siftome inference GEO:sample:GSM1354856:b9e48aa66623f978f6871d6d3632cb34212aeadbfcb7f96f9c3b0805dce6717c low confidence tumor sample_accession: GSM1354856 sample_title: RNA-seq_Sample 16 source_name: endometrial tumor characteristics: sample donor: donor No.8; gender: female; organ: endometrium; tissue... controlled vocabulary controlled vocabulary sample type match: tumor

sample_type normal tissue sample GSM1354857 Runtime Siftome inference GEO:sample:GSM1354857:cc027c8d37606e169d71728fe88093a9ca6f11238bf7dcc2078c6b2c837db417 high confidence adjacent normal sample_accession: GSM1354857 sample_title: RNA-seq_Sample 17 source_name: adjacent normal tissue characteristics: sample donor: donor No.9; gender: female; organ: endometrium; t... controlled vocabulary controlled vocabulary sample type match: adjacent normal

sample_type tumor sample sample GSM1354858 Runtime Siftome inference GEO:sample:GSM1354858:7ce7bb3dfc3b6a3cf3ecdc017746589b7b289943966d2ac201e18eaa7d52abec low confidence tumor sample_accession: GSM1354858 sample_title: RNA-seq_Sample 18 source_name: endometrial tumor characteristics: sample donor: donor No.9; gender: female; organ: endometrium; tissue... controlled vocabulary controlled vocabulary sample type match: tumor

Sample Group Preview

Possible case samples

Samples currently treated as the comparison case group.

9

GSM1354842 RNA-seq_Sample 2 tumor sample Case marker detected. endometrial tumor sample donor: donor No.1; gender: female; organ: endometrium; tissue: endometrial tumor
GSM1354844 RNA-seq_Sample 4 tumor sample Case marker detected. endometrial tumor sample donor: donor No.2; gender: female; organ: endometrium; tissue: endometrial tumor
GSM1354846 RNA-seq_Sample 6 tumor sample Case marker detected. endometrial tumor sample donor: donor No.3; gender: female; organ: endometrium; tissue: endometrial tumor
GSM1354848 RNA-seq_Sample 8 tumor sample Case marker detected. endometrial tumor sample donor: donor No.4; gender: female; organ: endometrium; tissue: endometrial tumor
GSM1354850 RNA-seq_Sample 10 tumor sample Case marker detected. endometrial tumor sample donor: donor No.5; gender: female; organ: endometrium; tissue: endometrial tumor
GSM1354851 RNA-seq_Sample 11 tumor sample Case marker detected. endometrial tumor sample donor: donor No.6; gender: female; organ: endometrium; tissue: endometrial tumor
GSM1354854 RNA-seq_Sample 14 tumor sample Case marker detected. endometrial tumor sample donor: donor No.7; gender: female; organ: endometrium; tissue: endometrial tumor
GSM1354856 RNA-seq_Sample 16 tumor sample Case marker detected. endometrial tumor sample donor: donor No.8; gender: female; organ: endometrium; tissue: endometrial tumor
GSM1354858 RNA-seq_Sample 18 tumor sample Case marker detected. endometrial tumor sample donor: donor No.9; gender: female; organ: endometrium; tissue: endometrial tumor

Possible control samples

Samples currently treated as controls or baseline.

9

GSM1354841 RNA-seq_Sample 1 normal tissue Control marker detected. adjacent normal tissue sample donor: donor No.1; gender: female; organ: endometrium; tissue: adjacent normal tissue
GSM1354843 RNA-seq_Sample 3 normal tissue Control marker detected. adjacent normal tissue sample donor: donor No.2; gender: female; organ: endometrium; tissue: adjacent normal tissue
GSM1354845 RNA-seq_Sample 5 normal tissue Control marker detected. adjacent normal tissue sample donor: donor No.3; gender: female; organ: endometrium; tissue: adjacent normal tissue
GSM1354847 RNA-seq_Sample 7 normal tissue Control marker detected. adjacent normal tissue sample donor: donor No.4; gender: female; organ: endometrium; tissue: adjacent normal tissue
GSM1354849 RNA-seq_Sample 9 normal tissue Control marker detected. adjacent normal tissue sample donor: donor No.5; gender: female; organ: endometrium; tissue: adjacent normal tissue
GSM1354852 RNA-seq_Sample 12 normal tissue Control marker detected. adjacent normal tissue sample donor: donor No.6; gender: female; organ: endometrium; tissue: adjacent normal tissue
GSM1354853 RNA-seq_Sample 13 normal tissue Control marker detected. adjacent normal tissue sample donor: donor No.7; gender: female; organ: endometrium; tissue: adjacent normal tissue
GSM1354855 RNA-seq_Sample 15 normal tissue Control marker detected. adjacent normal tissue sample donor: donor No.8; gender: female; organ: endometrium; tissue: adjacent normal tissue
GSM1354857 RNA-seq_Sample 17 normal tissue Control marker detected. adjacent normal tissue sample donor: donor No.9; gender: female; organ: endometrium; tissue: adjacent normal 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

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

9 samples

GSM1354841 RNA-seq_Sample 1 adjacent normal tissue sample donor: donor No.1; gender: female; organ: endometrium; tissue: adjacent normal tissue
GSM1354843 RNA-seq_Sample 3 adjacent normal tissue sample donor: donor No.2; gender: female; organ: endometrium; tissue: adjacent normal tissue
GSM1354845 RNA-seq_Sample 5 adjacent normal tissue sample donor: donor No.3; gender: female; organ: endometrium; tissue: adjacent normal tissue
GSM1354847 RNA-seq_Sample 7 adjacent normal tissue sample donor: donor No.4; gender: female; organ: endometrium; tissue: adjacent normal tissue
GSM1354849 RNA-seq_Sample 9 adjacent normal tissue sample donor: donor No.5; gender: female; organ: endometrium; tissue: adjacent normal tissue
GSM1354852 RNA-seq_Sample 12 adjacent normal tissue sample donor: donor No.6; gender: female; organ: endometrium; tissue: adjacent normal tissue
GSM1354853 RNA-seq_Sample 13 adjacent normal tissue sample donor: donor No.7; gender: female; organ: endometrium; tissue: adjacent normal tissue
GSM1354855 RNA-seq_Sample 15 adjacent normal tissue sample donor: donor No.8; gender: female; organ: endometrium; tissue: adjacent normal tissue
GSM1354857 RNA-seq_Sample 17 adjacent normal tissue sample donor: donor No.9; gender: female; organ: endometrium; tissue: adjacent normal tissue

tumor sample

9 samples

GSM1354842 RNA-seq_Sample 2 endometrial tumor sample donor: donor No.1; gender: female; organ: endometrium; tissue: endometrial tumor
GSM1354844 RNA-seq_Sample 4 endometrial tumor sample donor: donor No.2; gender: female; organ: endometrium; tissue: endometrial tumor
GSM1354846 RNA-seq_Sample 6 endometrial tumor sample donor: donor No.3; gender: female; organ: endometrium; tissue: endometrial tumor
GSM1354848 RNA-seq_Sample 8 endometrial tumor sample donor: donor No.4; gender: female; organ: endometrium; tissue: endometrial tumor
GSM1354850 RNA-seq_Sample 10 endometrial tumor sample donor: donor No.5; gender: female; organ: endometrium; tissue: endometrial tumor
GSM1354851 RNA-seq_Sample 11 endometrial tumor sample donor: donor No.6; gender: female; organ: endometrium; tissue: endometrial tumor
GSM1354854 RNA-seq_Sample 14 endometrial tumor sample donor: donor No.7; gender: female; organ: endometrium; tissue: endometrial tumor
GSM1354856 RNA-seq_Sample 16 endometrial tumor sample donor: donor No.8; gender: female; organ: endometrium; tissue: endometrial tumor
GSM1354858 RNA-seq_Sample 18 endometrial tumor sample donor: donor No.9; gender: female; organ: endometrium; tissue: endometrial tumor

Score Breakdown

50%

relevance

Organism normalized.
Assay type normalized.

10%

comparison suitability

Tumor and normal sample groups detected.
No excluded sample type flags detected.
Matched 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

18 samples

GSM1354841 RNA-seq_Sample 1
GSM1354842 RNA-seq_Sample 2
GSM1354843 RNA-seq_Sample 3
GSM1354844 RNA-seq_Sample 4
GSM1354845 RNA-seq_Sample 5
GSM1354846 RNA-seq_Sample 6
GSM1354847 RNA-seq_Sample 7
GSM1354848 RNA-seq_Sample 8
GSM1354849 RNA-seq_Sample 9
GSM1354850 RNA-seq_Sample 10
GSM1354851 RNA-seq_Sample 11
GSM1354852 RNA-seq_Sample 12
GSM1354853 RNA-seq_Sample 13
GSM1354854 RNA-seq_Sample 14
GSM1354855 RNA-seq_Sample 15
GSM1354856 RNA-seq_Sample 16
GSM1354857 RNA-seq_Sample 17
GSM1354858 RNA-seq_Sample 18

Review Audit Trail

0 decisions

No review decisions have been stored for this dataset.