Siftome Phase 3L

GSE86958

Transcriptome of invasive mucinous adnocarcinoma of the lung and adjacent normal lung tissues from 6 patients based on RNA-seq method

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
2016-09-15
Last update
2019-05-15
Organization
Cincinnati Children's Hospital Medical Center
Department
Pulmonary Biology
Public date
2017-03-02
Experiment types
Expression profiling by high throughput sequencing
Platforms
GPL16791 Illumina HiSeq 2500 (Homo sapiens)
Series type
SubSeries
SubSeries
Not available
BioProject
PRJNA343087
Supplementary files
TAR: GSE86958_RAW.tar
Organism
Homo sapiens
Assay
bulk RNA-seq
Samples
12
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

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

Score Components

  • relevance 60% Organism normalized. Assay type normalized. Tissue metadata 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 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 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 6 samples
  • Likely control group normal tissue 6 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 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 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 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 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 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: Treatment clarity: No unclear treatment split detected in the sample metadata. Contributed to downgrade or manual-review evidence.
  • Caution fact Overall score capped because comparison suitability is weak for the selected search intent. Contributed to downgrade or manual-review evidence.
  • Caution fact Overall score capped because colorectal/CRC disease context is not explicit. Contributed to downgrade or manual-review evidence.
  • Caution fact Downgraded disease context: colorectal/GI relevance is unclear. Contributed to downgrade or manual-review evidence.
  • Caution fact Missing or unclear metadata: Downgraded disease context: colorectal/GI relevance is unclear. Contributed to downgrade or manual-review evidence.
  • Caution fact Comparison suitability score is below the Phase 1 recommended threshold. Contributed to downgrade or manual-review evidence.

Manual Corrections

0 active

Source Evidence

4 sources

GEO

Primary source

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

Dataset accession
GSE86958
Sample records
12 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
GSE86958
  • 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
GSE86958
  • 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
GSE86958
  • 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: GSE86958
dataset_title: Transcriptome of invasive mucinous adnocarcinoma of the lung and adjacent normal lung tissues from 6 patients based on RNA-seq method
organism: Homo sapiens
assay_type: bulk RNA-seq
processed_data_available: true
raw_data_available: true
submission_date: 2016-09-15
last_update_date: 2019-05-15
organization_name: Cincinnati Children's Hospital Medical Center
department: Pulmonary Biology
public_date: 2017-03-02
experiment_types: Expression profiling by high throughput sequencing
platforms: GPL16791 Illumina HiSeq 2500 (Homo sapiens)
sub_series: Not available
bioproject: PRJNA343087
supplementary_files: TAR: GSE86958_RAW.tar
series_type: SubSeries

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.
  • 1 warning require review.

Why It May Not Be Suitable

  • Disease or condition label 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: 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.

Normalized Fields

39 fields
Field Value Source Origin Confidence Evidence Reason
assay_type bulk RNA-seq dataset GSE86958 Runtime Siftome inference GEO:dataset:GSE86958:9175b6d7936579d2f2426275a022d877ab0cdb555916d0e3631f9485d45a2109 high confidence bulk rna-seq dataset_accession: GSE86958 dataset_title: Transcriptome of invasive mucinous adnocarcinoma of the lung and adjacent normal lung tissues from 6 patients based on RNA-seq method ... keyword match keyword match: bulk rna-seq
normal_tissue_type adjacent normal sample GSM2311010 Runtime Siftome inference GEO:sample:GSM2311010:0f900c92a1cd4833a65067e1c8cc5409c1e3cc14f3f0032a14b4be5bae229eb1 high confidence adjacent normal sample_accession: GSM2311010 sample_title: Case1_Normal source_name: Adjacent normal lung tissues characteristics: subject status: invasive mucinous adenocarcinoma (IMA) patient... controlled vocabulary controlled vocabulary normal tissue type match: adjacent normal
normal_tissue_type adjacent normal sample GSM2311011 Runtime Siftome inference GEO:sample:GSM2311011:3f8496802f5c5d8d0415b7e754e6bba5e1f886a5d53b0785fd84694d8ef9fa63 high confidence adjacent normal sample_accession: GSM2311011 sample_title: Case2_Normal source_name: Adjacent normal lung tissues characteristics: subject status: invasive mucinous adenocarcinoma (IMA) patient... controlled vocabulary controlled vocabulary normal tissue type match: adjacent normal
normal_tissue_type adjacent normal sample GSM2311012 Runtime Siftome inference GEO:sample:GSM2311012:ffb35f3c54f3da37d3c123246fcfe9522661fdc1ad8b84ee6d3e999b9908e287 high confidence adjacent normal sample_accession: GSM2311012 sample_title: Case3_Normal source_name: Adjacent normal lung tissues characteristics: subject status: invasive mucinous adenocarcinoma (IMA) patient... controlled vocabulary controlled vocabulary normal tissue type match: adjacent normal
normal_tissue_type adjacent normal sample GSM2311013 Runtime Siftome inference GEO:sample:GSM2311013:190671107b513d597b4177366a0d39ddb8cdf3b208a844a119c0c85dc83e6b67 high confidence adjacent normal sample_accession: GSM2311013 sample_title: Case4_Normal source_name: Adjacent normal lung tissues characteristics: subject status: invasive mucinous adenocarcinoma (IMA) patient... controlled vocabulary controlled vocabulary normal tissue type match: adjacent normal
normal_tissue_type adjacent normal sample GSM2311014 Runtime Siftome inference GEO:sample:GSM2311014:a339c9343beaa247adb57333bfb0722b6ab71257cfd4f9116b59b30cfdddec40 high confidence adjacent normal sample_accession: GSM2311014 sample_title: Case5_Normal source_name: Adjacent normal lung tissues characteristics: subject status: invasive mucinous adenocarcinoma (IMA) patient... controlled vocabulary controlled vocabulary normal tissue type match: adjacent normal
normal_tissue_type adjacent normal sample GSM2311015 Runtime Siftome inference GEO:sample:GSM2311015:a574164e39eee6ec0195ec63cdae74f1f4a53b4367f293b33902d6300afc98db high confidence adjacent normal sample_accession: GSM2311015 sample_title: Case6_Normal source_name: Adjacent normal lung tissues characteristics: subject status: invasive mucinous adenocarcinoma (IMA) patient... controlled vocabulary controlled vocabulary normal tissue type match: adjacent normal
organism Homo sapiens dataset GSE86958 Runtime Siftome inference GEO:dataset:GSE86958:9175b6d7936579d2f2426275a022d877ab0cdb555916d0e3631f9485d45a2109 high confidence homo sapiens dataset_accession: GSE86958 dataset_title: Transcriptome of invasive mucinous adnocarcinoma of the lung and adjacent normal lung tissues from 6 patients based on RNA-seq method ... keyword match keyword match: homo sapiens
sample_type tumor sample sample GSM2311004 Runtime Siftome inference GEO:sample:GSM2311004:5007286b5e5a62cd3819f5e3e8d6f2cd6e4493a00adfca5c9fb506f405638afc low confidence tumor sample_accession: GSM2311004 sample_title: Case1_Tumor source_name: Invasive mucinous adenocarcinoma of the lung characteristics: subject status: invasive mucinous adenocarcinom... controlled vocabulary controlled vocabulary sample type match: tumor
sample_type tumor sample sample GSM2311005 Runtime Siftome inference GEO:sample:GSM2311005:3bbde826db36da224c7204ee70c1b314e597bf5dc9c3ea2d845b28bc684f4f7e low confidence tumor sample_accession: GSM2311005 sample_title: Case2_Tumor source_name: Invasive mucinous adenocarcinoma of the lung characteristics: subject status: invasive mucinous adenocarcinom... controlled vocabulary controlled vocabulary sample type match: tumor
sample_type tumor sample sample GSM2311006 Runtime Siftome inference GEO:sample:GSM2311006:13498e5d9ee47db903b7acb1829d9d9e865448169ed26eb7aa7e82d42cc292a9 low confidence tumor sample_accession: GSM2311006 sample_title: Case3_Tumor source_name: Invasive mucinous adenocarcinoma of the lung characteristics: subject status: invasive mucinous adenocarcinom... controlled vocabulary controlled vocabulary sample type match: tumor
sample_type tumor sample sample GSM2311007 Runtime Siftome inference GEO:sample:GSM2311007:70e8c7bab8093d6f971394174848c807589837f1772962774609208e91a80444 low confidence tumor sample_accession: GSM2311007 sample_title: Case4_Tumor source_name: Invasive mucinous adenocarcinoma of the lung characteristics: subject status: invasive mucinous adenocarcinom... controlled vocabulary controlled vocabulary sample type match: tumor
sample_type tumor sample sample GSM2311008 Runtime Siftome inference GEO:sample:GSM2311008:40e7a2fbab1c2c9b558c9a14aa40e658a5e95843c6ed50ed72bb592eb6007373 low confidence tumor sample_accession: GSM2311008 sample_title: Case5_Tumor source_name: Invasive mucinous adenocarcinoma of the lung characteristics: subject status: invasive mucinous adenocarcinom... controlled vocabulary controlled vocabulary sample type match: tumor
sample_type tumor sample sample GSM2311009 Runtime Siftome inference GEO:sample:GSM2311009:bc2f579f17b00416ad3b1b2669d964f369fa3d7615fe965572d04268c5e2e79f low confidence tumor sample_accession: GSM2311009 sample_title: Case6_Tumor source_name: Invasive mucinous adenocarcinoma of the lung characteristics: subject status: invasive mucinous adenocarcinom... controlled vocabulary controlled vocabulary sample type match: tumor
sample_type normal tissue sample GSM2311010 Runtime Siftome inference GEO:sample:GSM2311010:0f900c92a1cd4833a65067e1c8cc5409c1e3cc14f3f0032a14b4be5bae229eb1 high confidence adjacent normal sample_accession: GSM2311010 sample_title: Case1_Normal source_name: Adjacent normal lung tissues characteristics: subject status: invasive mucinous adenocarcinoma (IMA) patient... controlled vocabulary controlled vocabulary sample type match: adjacent normal
sample_type tumor sample sample GSM2311010 Runtime Siftome inference GEO:sample:GSM2311010:0f900c92a1cd4833a65067e1c8cc5409c1e3cc14f3f0032a14b4be5bae229eb1 medium confidence carcinoma sample_accession: GSM2311010 sample_title: Case1_Normal source_name: Adjacent normal lung tissues characteristics: subject status: invasive mucinous adenocarcinoma (IMA) patient... controlled vocabulary controlled vocabulary sample type match: carcinoma
sample_type normal tissue sample GSM2311011 Runtime Siftome inference GEO:sample:GSM2311011:3f8496802f5c5d8d0415b7e754e6bba5e1f886a5d53b0785fd84694d8ef9fa63 high confidence adjacent normal sample_accession: GSM2311011 sample_title: Case2_Normal source_name: Adjacent normal lung tissues characteristics: subject status: invasive mucinous adenocarcinoma (IMA) patient... controlled vocabulary controlled vocabulary sample type match: adjacent normal
sample_type tumor sample sample GSM2311011 Runtime Siftome inference GEO:sample:GSM2311011:3f8496802f5c5d8d0415b7e754e6bba5e1f886a5d53b0785fd84694d8ef9fa63 medium confidence carcinoma sample_accession: GSM2311011 sample_title: Case2_Normal source_name: Adjacent normal lung tissues characteristics: subject status: invasive mucinous adenocarcinoma (IMA) patient... controlled vocabulary controlled vocabulary sample type match: carcinoma
sample_type normal tissue sample GSM2311012 Runtime Siftome inference GEO:sample:GSM2311012:ffb35f3c54f3da37d3c123246fcfe9522661fdc1ad8b84ee6d3e999b9908e287 high confidence adjacent normal sample_accession: GSM2311012 sample_title: Case3_Normal source_name: Adjacent normal lung tissues characteristics: subject status: invasive mucinous adenocarcinoma (IMA) patient... controlled vocabulary controlled vocabulary sample type match: adjacent normal
sample_type tumor sample sample GSM2311012 Runtime Siftome inference GEO:sample:GSM2311012:ffb35f3c54f3da37d3c123246fcfe9522661fdc1ad8b84ee6d3e999b9908e287 medium confidence carcinoma sample_accession: GSM2311012 sample_title: Case3_Normal source_name: Adjacent normal lung tissues characteristics: subject status: invasive mucinous adenocarcinoma (IMA) patient... controlled vocabulary controlled vocabulary sample type match: carcinoma
sample_type normal tissue sample GSM2311013 Runtime Siftome inference GEO:sample:GSM2311013:190671107b513d597b4177366a0d39ddb8cdf3b208a844a119c0c85dc83e6b67 high confidence adjacent normal sample_accession: GSM2311013 sample_title: Case4_Normal source_name: Adjacent normal lung tissues characteristics: subject status: invasive mucinous adenocarcinoma (IMA) patient... controlled vocabulary controlled vocabulary sample type match: adjacent normal
sample_type tumor sample sample GSM2311013 Runtime Siftome inference GEO:sample:GSM2311013:190671107b513d597b4177366a0d39ddb8cdf3b208a844a119c0c85dc83e6b67 medium confidence carcinoma sample_accession: GSM2311013 sample_title: Case4_Normal source_name: Adjacent normal lung tissues characteristics: subject status: invasive mucinous adenocarcinoma (IMA) patient... controlled vocabulary controlled vocabulary sample type match: carcinoma
sample_type normal tissue sample GSM2311014 Runtime Siftome inference GEO:sample:GSM2311014:a339c9343beaa247adb57333bfb0722b6ab71257cfd4f9116b59b30cfdddec40 high confidence adjacent normal sample_accession: GSM2311014 sample_title: Case5_Normal source_name: Adjacent normal lung tissues characteristics: subject status: invasive mucinous adenocarcinoma (IMA) patient... controlled vocabulary controlled vocabulary sample type match: adjacent normal
sample_type tumor sample sample GSM2311014 Runtime Siftome inference GEO:sample:GSM2311014:a339c9343beaa247adb57333bfb0722b6ab71257cfd4f9116b59b30cfdddec40 medium confidence carcinoma sample_accession: GSM2311014 sample_title: Case5_Normal source_name: Adjacent normal lung tissues characteristics: subject status: invasive mucinous adenocarcinoma (IMA) patient... controlled vocabulary controlled vocabulary sample type match: carcinoma
sample_type normal tissue sample GSM2311015 Runtime Siftome inference GEO:sample:GSM2311015:a574164e39eee6ec0195ec63cdae74f1f4a53b4367f293b33902d6300afc98db high confidence adjacent normal sample_accession: GSM2311015 sample_title: Case6_Normal source_name: Adjacent normal lung tissues characteristics: subject status: invasive mucinous adenocarcinoma (IMA) patient... controlled vocabulary controlled vocabulary sample type match: adjacent normal
sample_type tumor sample sample GSM2311015 Runtime Siftome inference GEO:sample:GSM2311015:a574164e39eee6ec0195ec63cdae74f1f4a53b4367f293b33902d6300afc98db medium confidence carcinoma sample_accession: GSM2311015 sample_title: Case6_Normal source_name: Adjacent normal lung tissues characteristics: subject status: invasive mucinous adenocarcinoma (IMA) patient... controlled vocabulary controlled vocabulary sample type match: carcinoma
tissue lung dataset GSE86958 Runtime Siftome inference GEO:dataset:GSE86958:9175b6d7936579d2f2426275a022d877ab0cdb555916d0e3631f9485d45a2109 low confidence lung dataset_accession: GSE86958 dataset_title: Transcriptome of invasive mucinous adnocarcinoma of the lung and adjacent normal lung tissues from 6 patients based on RNA-seq method ... controlled vocabulary controlled vocabulary tissue match: lung
tissue lung sample GSM2311004 Runtime Siftome inference GEO:sample:GSM2311004:5007286b5e5a62cd3819f5e3e8d6f2cd6e4493a00adfca5c9fb506f405638afc low confidence lung sample_accession: GSM2311004 sample_title: Case1_Tumor source_name: Invasive mucinous adenocarcinoma of the lung characteristics: subject status: invasive mucinous adenocarcinom... controlled vocabulary controlled vocabulary tissue match: lung
tissue lung sample GSM2311005 Runtime Siftome inference GEO:sample:GSM2311005:3bbde826db36da224c7204ee70c1b314e597bf5dc9c3ea2d845b28bc684f4f7e low confidence lung sample_accession: GSM2311005 sample_title: Case2_Tumor source_name: Invasive mucinous adenocarcinoma of the lung characteristics: subject status: invasive mucinous adenocarcinom... controlled vocabulary controlled vocabulary tissue match: lung
tissue lung sample GSM2311006 Runtime Siftome inference GEO:sample:GSM2311006:13498e5d9ee47db903b7acb1829d9d9e865448169ed26eb7aa7e82d42cc292a9 low confidence lung sample_accession: GSM2311006 sample_title: Case3_Tumor source_name: Invasive mucinous adenocarcinoma of the lung characteristics: subject status: invasive mucinous adenocarcinom... controlled vocabulary controlled vocabulary tissue match: lung
tissue lung sample GSM2311007 Runtime Siftome inference GEO:sample:GSM2311007:70e8c7bab8093d6f971394174848c807589837f1772962774609208e91a80444 low confidence lung sample_accession: GSM2311007 sample_title: Case4_Tumor source_name: Invasive mucinous adenocarcinoma of the lung characteristics: subject status: invasive mucinous adenocarcinom... controlled vocabulary controlled vocabulary tissue match: lung
tissue lung sample GSM2311008 Runtime Siftome inference GEO:sample:GSM2311008:40e7a2fbab1c2c9b558c9a14aa40e658a5e95843c6ed50ed72bb592eb6007373 low confidence lung sample_accession: GSM2311008 sample_title: Case5_Tumor source_name: Invasive mucinous adenocarcinoma of the lung characteristics: subject status: invasive mucinous adenocarcinom... controlled vocabulary controlled vocabulary tissue match: lung
tissue lung sample GSM2311009 Runtime Siftome inference GEO:sample:GSM2311009:bc2f579f17b00416ad3b1b2669d964f369fa3d7615fe965572d04268c5e2e79f low confidence lung sample_accession: GSM2311009 sample_title: Case6_Tumor source_name: Invasive mucinous adenocarcinoma of the lung characteristics: subject status: invasive mucinous adenocarcinom... controlled vocabulary controlled vocabulary tissue match: lung
tissue lung sample GSM2311010 Runtime Siftome inference GEO:sample:GSM2311010:0f900c92a1cd4833a65067e1c8cc5409c1e3cc14f3f0032a14b4be5bae229eb1 low confidence lung sample_accession: GSM2311010 sample_title: Case1_Normal source_name: Adjacent normal lung tissues characteristics: subject status: invasive mucinous adenocarcinoma (IMA) patient... controlled vocabulary controlled vocabulary tissue match: lung
tissue lung sample GSM2311011 Runtime Siftome inference GEO:sample:GSM2311011:3f8496802f5c5d8d0415b7e754e6bba5e1f886a5d53b0785fd84694d8ef9fa63 low confidence lung sample_accession: GSM2311011 sample_title: Case2_Normal source_name: Adjacent normal lung tissues characteristics: subject status: invasive mucinous adenocarcinoma (IMA) patient... controlled vocabulary controlled vocabulary tissue match: lung
tissue lung sample GSM2311012 Runtime Siftome inference GEO:sample:GSM2311012:ffb35f3c54f3da37d3c123246fcfe9522661fdc1ad8b84ee6d3e999b9908e287 low confidence lung sample_accession: GSM2311012 sample_title: Case3_Normal source_name: Adjacent normal lung tissues characteristics: subject status: invasive mucinous adenocarcinoma (IMA) patient... controlled vocabulary controlled vocabulary tissue match: lung
tissue lung sample GSM2311013 Runtime Siftome inference GEO:sample:GSM2311013:190671107b513d597b4177366a0d39ddb8cdf3b208a844a119c0c85dc83e6b67 low confidence lung sample_accession: GSM2311013 sample_title: Case4_Normal source_name: Adjacent normal lung tissues characteristics: subject status: invasive mucinous adenocarcinoma (IMA) patient... controlled vocabulary controlled vocabulary tissue match: lung
tissue lung sample GSM2311014 Runtime Siftome inference GEO:sample:GSM2311014:a339c9343beaa247adb57333bfb0722b6ab71257cfd4f9116b59b30cfdddec40 low confidence lung sample_accession: GSM2311014 sample_title: Case5_Normal source_name: Adjacent normal lung tissues characteristics: subject status: invasive mucinous adenocarcinoma (IMA) patient... controlled vocabulary controlled vocabulary tissue match: lung
tissue lung sample GSM2311015 Runtime Siftome inference GEO:sample:GSM2311015:a574164e39eee6ec0195ec63cdae74f1f4a53b4367f293b33902d6300afc98db low confidence lung sample_accession: GSM2311015 sample_title: Case6_Normal source_name: Adjacent normal lung tissues characteristics: subject status: invasive mucinous adenocarcinoma (IMA) patient... controlled vocabulary controlled vocabulary tissue match: lung

Sample Group Preview

Possible case samples

Samples currently treated as the comparison case group.

6
  • GSM2311004 Case1_Tumor tumor sample Case marker detected. Invasive mucinous adenocarcinoma of the lung subject status: invasive mucinous adenocarcinoma (IMA) patient; subject/case id: Case1; tissue: lung; tissue subtype: Invasive mucinous adenocarcinoma of the lung
  • GSM2311005 Case2_Tumor tumor sample Case marker detected. Invasive mucinous adenocarcinoma of the lung subject status: invasive mucinous adenocarcinoma (IMA) patient; subject/case id: Case2; tissue: lung; tissue subtype: Invasive mucinous adenocarcinoma of the lung
  • GSM2311006 Case3_Tumor tumor sample Case marker detected. Invasive mucinous adenocarcinoma of the lung subject status: invasive mucinous adenocarcinoma (IMA) patient; subject/case id: Case3; tissue: lung; tissue subtype: Invasive mucinous adenocarcinoma of the lung
  • GSM2311007 Case4_Tumor tumor sample Case marker detected. Invasive mucinous adenocarcinoma of the lung subject status: invasive mucinous adenocarcinoma (IMA) patient; subject/case id: Case4; tissue: lung; tissue subtype: Invasive mucinous adenocarcinoma of the lung
  • GSM2311008 Case5_Tumor tumor sample Case marker detected. Invasive mucinous adenocarcinoma of the lung subject status: invasive mucinous adenocarcinoma (IMA) patient; subject/case id: Case5; tissue: lung; tissue subtype: Invasive mucinous adenocarcinoma of the lung
  • GSM2311009 Case6_Tumor tumor sample Case marker detected. Invasive mucinous adenocarcinoma of the lung subject status: invasive mucinous adenocarcinoma (IMA) patient; subject/case id: Case6; tissue: lung; tissue subtype: Invasive mucinous adenocarcinoma of the lung

Possible control samples

Samples currently treated as controls or baseline.

6
  • GSM2311010 Case1_Normal normal tissue Control marker detected. Adjacent normal lung tissues subject status: invasive mucinous adenocarcinoma (IMA) patient; subject/case id: Case1; tissue: lung; tissue subtype: Adjacent normal lung tissues
  • GSM2311011 Case2_Normal normal tissue Control marker detected. Adjacent normal lung tissues subject status: invasive mucinous adenocarcinoma (IMA) patient; subject/case id: Case2; tissue: lung; tissue subtype: Adjacent normal lung tissues
  • GSM2311012 Case3_Normal normal tissue Control marker detected. Adjacent normal lung tissues subject status: invasive mucinous adenocarcinoma (IMA) patient; subject/case id: Case3; tissue: lung; tissue subtype: Adjacent normal lung tissues
  • GSM2311013 Case4_Normal normal tissue Control marker detected. Adjacent normal lung tissues subject status: invasive mucinous adenocarcinoma (IMA) patient; subject/case id: Case4; tissue: lung; tissue subtype: Adjacent normal lung tissues
  • GSM2311014 Case5_Normal normal tissue Control marker detected. Adjacent normal lung tissues subject status: invasive mucinous adenocarcinoma (IMA) patient; subject/case id: Case5; tissue: lung; tissue subtype: Adjacent normal lung tissues
  • GSM2311015 Case6_Normal normal tissue Control marker detected. Adjacent normal lung tissues subject status: invasive mucinous adenocarcinoma (IMA) patient; subject/case id: Case6; tissue: lung; tissue subtype: Adjacent normal lung tissues

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

tumor sample

6 samples
  • GSM2311004 Case1_Tumor Invasive mucinous adenocarcinoma of the lung subject status: invasive mucinous adenocarcinoma (IMA) patient; subject/case id: Case1; tissue: lung; tissue subtype: Invasive mucinous adenocarcinoma of the lung
  • GSM2311005 Case2_Tumor Invasive mucinous adenocarcinoma of the lung subject status: invasive mucinous adenocarcinoma (IMA) patient; subject/case id: Case2; tissue: lung; tissue subtype: Invasive mucinous adenocarcinoma of the lung
  • GSM2311006 Case3_Tumor Invasive mucinous adenocarcinoma of the lung subject status: invasive mucinous adenocarcinoma (IMA) patient; subject/case id: Case3; tissue: lung; tissue subtype: Invasive mucinous adenocarcinoma of the lung
  • GSM2311007 Case4_Tumor Invasive mucinous adenocarcinoma of the lung subject status: invasive mucinous adenocarcinoma (IMA) patient; subject/case id: Case4; tissue: lung; tissue subtype: Invasive mucinous adenocarcinoma of the lung
  • GSM2311008 Case5_Tumor Invasive mucinous adenocarcinoma of the lung subject status: invasive mucinous adenocarcinoma (IMA) patient; subject/case id: Case5; tissue: lung; tissue subtype: Invasive mucinous adenocarcinoma of the lung
  • GSM2311009 Case6_Tumor Invasive mucinous adenocarcinoma of the lung subject status: invasive mucinous adenocarcinoma (IMA) patient; subject/case id: Case6; tissue: lung; tissue subtype: Invasive mucinous adenocarcinoma of the lung

normal tissue

6 samples
  • GSM2311010 Case1_Normal Adjacent normal lung tissues subject status: invasive mucinous adenocarcinoma (IMA) patient; subject/case id: Case1; tissue: lung; tissue subtype: Adjacent normal lung tissues
  • GSM2311011 Case2_Normal Adjacent normal lung tissues subject status: invasive mucinous adenocarcinoma (IMA) patient; subject/case id: Case2; tissue: lung; tissue subtype: Adjacent normal lung tissues
  • GSM2311012 Case3_Normal Adjacent normal lung tissues subject status: invasive mucinous adenocarcinoma (IMA) patient; subject/case id: Case3; tissue: lung; tissue subtype: Adjacent normal lung tissues
  • GSM2311013 Case4_Normal Adjacent normal lung tissues subject status: invasive mucinous adenocarcinoma (IMA) patient; subject/case id: Case4; tissue: lung; tissue subtype: Adjacent normal lung tissues
  • GSM2311014 Case5_Normal Adjacent normal lung tissues subject status: invasive mucinous adenocarcinoma (IMA) patient; subject/case id: Case5; tissue: lung; tissue subtype: Adjacent normal lung tissues
  • GSM2311015 Case6_Normal Adjacent normal lung tissues subject status: invasive mucinous adenocarcinoma (IMA) patient; subject/case id: Case6; tissue: lung; tissue subtype: Adjacent normal lung tissues

Score Breakdown

60%

relevance

  • Organism normalized.
  • Assay type normalized.
  • Tissue metadata 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.
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.
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

12 samples

Review Audit Trail

0 decisions

No review decisions have been stored for this dataset.