Siftome Phase 3L

GSE148036

Lung transcriptional profiling of pulmonary tuberculosis, adenocarcinoma and sarcoidosis patients using RNA-Seq

Not suitable Dataset does not meet the current suitability threshold.
Sample grouping CSV Contrast CSV DESeq2 metadata CSV R handoff notes Handoff report Download instructions Open GEO dataset
Source
GEO
Search intent
Patient tissue tumor-vs-normal
Intent behavior
search-intent-behavior-v1
Submission date
2020-04-03
Last update
2020-11-02
Organization
institution of microbology
Department
liuch
Public date
2020-10-07
Experiment types
Expression profiling by high throughput sequencing
Platforms
GPL21290 Illumina HiSeq 3000 (Homo sapiens)
Series type
Series
SubSeries
Not available
BioProject
Not available
Supplementary files
TXT: GSE148036_PRJNA609278count_matrix.txt.gz
Organism
Homo sapiens
Assay
bulk RNA-seq
Samples
20
Study design
Tumor vs unmatched normal
Specimen/source
Tissue
Scoring version
intent-aware-scoring-v15
Ranking batch
b69568dd1e4fe1b9ee2d880bf5495d748a7e4c5c11e4107f02528c3be0e76012
Ranking created
2026-06-05T20:20:27.088676Z
Warning version
intent-aware-warnings-v2

Current Intent Interpretation

Patient tissue tumor-vs-normal

Expectations

Organism
Homo sapiens
Assay
bulk RNA-seq
Specimen/source
patient tissue or biopsy
Controls
matched normal, adjacent normal, paired normal, healthy tissue control, or otherwise normal tissue control

Rules

Default filters
Human only; Bulk RNA-seq only; Tumor-normal only; Tissue or biopsy only; Hide biofluid/model systems
Warning rules
missing or unclear control group, unclear disease context, unclear tissue source, mixed sample types, model-system markers, secondary assay context, missing processed data, or small cohort size
Score caps
non-human datasets stay below the primary recommendation band, missing colorectal/colon/rectal/CRC context stays below the primary recommendation band, biofluid and model-system datasets cannot reach Recommended by default, microarray and secondary assays are capped unless explicitly enabled, or small cohorts are capped below high-confidence recommendations
Downgraded contexts
microarray unless explicitly enabled, biofluid-only datasets, cell-line datasets, organoid datasets, xenograft or PDX datasets, non-colorectal disease contexts, or treatment-only experiments

Study Classification

Tumor vs unmatched normal Tissue

Analysis Readiness

Review before analysis
85% DE readiness

Contrast completeness

25/25 pts

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

Minimum group size

20/20 pts

Each contrast group has at least 2 samples.

Processed data availability

20/20 pts

Processed data is marked available in the GEO index.

Sample decision clarity

3/15 pts

Unassigned or review-needed samples remain before analysis.

Blocking warnings

7/10 pts

Warnings are present, but none are critical blockers.

Metadata normalization

10/10 pts

Metadata quality is high enough to support downstream handoff.

Blockers

  • 10 samples are still unassigned.

Next Steps

  • Resolve unassigned or review-needed samples in the grouping table.

Analysis Preparation Checklist

4/6 ready

Group labels reviewed

Needs review

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

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

Minimum sample count met

Ready

Both groups meet the minimum of 2 samples.

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

Processed counts available

Ready

Processed data availability is marked true in the GEO index.

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

Ambiguous samples handled

Needs review

0 review-needed samples and 10 unassigned samples remain.

Resolve ambiguous and unassigned samples before finalizing the contrast.

Exclusion decisions recorded

Ready

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

Record any manual exclusions in the downstream analysis notes.

Source links preserved

Ready

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

Keep GEO dataset and sample links with exported metadata.

Bioinformatician Review

Bioinformatician review required

Ask a bioinformatician to review grouping, count availability, exclusions, and design before DE.

  • Analysis readiness has blockers that must be resolved before DE.
  • One or more samples are unassigned and need manual grouping decisions.

Why This Is Ranked Here

Patient tissue tumor-vs-normal
Not suitable Dataset does not meet the current suitability threshold.

Score Components

  • relevance 60% Organism normalized. Assay type normalized. Tissue metadata normalized.
  • comparison suitability 0% Tumor and normal sample groups detected. No excluded sample type flags detected. Tumor/normal design boosted for colorectal tumor-vs-normal tissue triage. Patient tissue or biopsy specimens boosted for tissue comparison triage. Non-colorectal cancer context downgraded for colorectal tumor-vs-normal tissue ranking.
  • metadata quality 85% Sample source clarity: All samples have source metadata and clear GSE/GSM accessions. Group clarity: Rule-based grouping found both case and control samples. Disease clarity: Disease or condition metadata was not normalized. Tissue clarity: Tissue metadata normalized. Treatment clarity: No unclear treatment split detected in the sample metadata. Replicate clarity: No pooled sample or technical replicate flags detected. Data availability clarity: Dataset-level processed or raw data availability is explicit.
  • data availability 100% Processed data available. Raw data available.
  • overall 34% Weighted score: 30% relevance, 30% comparison suitability, 25% metadata quality, 15% data availability. Overall score capped because comparison suitability is weak for the selected search intent. Overall score capped because tumor/normal grouping is from a non-colorectal cancer context.

Derived Classifications

  • Organism Homo sapiens Organism remains rule-derived: Homo sapiens.
  • Assay bulk RNA-seq Assay remains rule-derived: bulk RNA-seq.
  • Study design Tumor vs unmatched normal Study design remains rule-derived: Tumor vs unmatched normal.
  • Specimen/source Tissue Specimen/source remains rule-derived: Tissue.
  • Likely case group tumor sample 5 samples
  • Likely control group normal tissue 5 samples

Warnings

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

Intent Interpretation

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

Applied Review Decisions

No active review decisions affect this ranking.

Ranking Facts

  • Recommendation Not suitable Dataset does not meet the current suitability threshold.
  • Supporting fact Tumor vs unmatched normal · Tissue · suitability 0%. Contributed to match or upgrade evidence.
  • Supporting fact Prioritized assay: bulk RNA-seq is the active assay expectation. Contributed to match or upgrade evidence.
  • Supporting fact Downgraded disease context: colorectal/GI relevance is unclear. Contributed to match or upgrade evidence.
  • Supporting fact Processed data is available for downstream review. Contributed to match or upgrade evidence.
  • Supporting fact 1 warning require review. Contributed to match or upgrade evidence.
  • Caution fact Disease or condition label could not be normalized. Contributed to downgrade or manual-review evidence.
  • Caution fact Non-colorectal cancer context downgraded for colorectal tumor-vs-normal tissue ranking. Contributed to downgrade or manual-review evidence.
  • Caution fact Missing or unclear metadata: Disease clarity: Disease or condition metadata was not normalized. Contributed to downgrade or manual-review evidence.
  • Caution fact Missing or unclear metadata: Treatment clarity: No unclear treatment split detected in the sample metadata. Contributed to downgrade or manual-review evidence.
  • Caution fact Overall score capped because comparison suitability is weak for the selected search intent. Contributed to downgrade or manual-review evidence.
  • Caution fact Overall score capped because tumor/normal grouping is from a non-colorectal cancer context. Contributed to downgrade or manual-review evidence.
  • Caution fact Downgraded disease context: colorectal/GI relevance is unclear. Contributed to downgrade or manual-review evidence.
  • Caution fact Missing or unclear metadata: Downgraded disease context: colorectal/GI relevance is unclear. Contributed to downgrade or manual-review evidence.
  • Caution fact Comparison suitability score is below the Phase 1 recommended threshold. Contributed to downgrade or manual-review evidence.

Manual Corrections

0 active

Source Evidence

4 sources

GEO

Primary source

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

Dataset accession
GSE148036
Sample records
20 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
GSE148036
  • 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
GSE148036
  • 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
GSE148036
  • 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: GSE148036
dataset_title: Lung transcriptional profiling of pulmonary tuberculosis, adenocarcinoma and sarcoidosis patients using RNA-Seq
organism: Homo sapiens
assay_type: bulk RNA-seq
processed_data_available: true
raw_data_available: true
submission_date: 2020-04-03
last_update_date: 2020-11-02
organization_name: institution of microbology
department: liuch
public_date: 2020-10-07
experiment_types: Expression profiling by high throughput sequencing
platforms: GPL21290 Illumina HiSeq 3000 (Homo sapiens)
sub_series: Not available
bioproject: Not available
supplementary_files: TXT: GSE148036_PRJNA609278count_matrix.txt.gz
series_type: Series

Why It Matched

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

Why It May Not Be Suitable

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

Warnings

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

Normalized Fields

33 fields
Field Value Source Origin Confidence Evidence Reason
assay_type bulk RNA-seq dataset GSE148036 Runtime Siftome inference GEO:dataset:GSE148036:1a989ade96b252b01aed99f45ecbdec0ff767afb83f9ceac496b30d4c003c471 high confidence bulk rna-seq dataset_accession: GSE148036 dataset_title: Lung transcriptional profiling of pulmonary tuberculosis, adenocarcinoma and sarcoidosis patients using RNA-Seq organism: Homo sapien... keyword match keyword match: bulk rna-seq
organism Homo sapiens dataset GSE148036 Runtime Siftome inference GEO:dataset:GSE148036:1a989ade96b252b01aed99f45ecbdec0ff767afb83f9ceac496b30d4c003c471 high confidence homo sapiens dataset_accession: GSE148036 dataset_title: Lung transcriptional profiling of pulmonary tuberculosis, adenocarcinoma and sarcoidosis patients using RNA-Seq organism: Homo sapien... keyword match keyword match: homo sapiens
sample_type normal tissue sample GSM4452862 Runtime Siftome inference GEO:sample:GSM4452862:d72bfb61aaa29932ba3316e2fe1be0a64a15df68094091fb39c229be5ae4e2f2 low confidence normal sample_accession: GSM4452862 sample_title: Normal Lung Tissue Rep1 source_name: NM001 characteristics: tissue: Lung; age: 52; Sex: Female; disease: Normal Normal Lung Tissue Rep1 controlled vocabulary controlled vocabulary sample type match: normal
sample_type normal tissue sample GSM4452863 Runtime Siftome inference GEO:sample:GSM4452863:bd0de54eded080cf427fe7e433480302386957e625c0e5227b5e1a8c032134be low confidence normal sample_accession: GSM4452863 sample_title: Normal Lung Tissue Rep2 source_name: NM002 characteristics: tissue: Lung; age: 26; Sex: Male; disease: Normal Normal Lung Tissue Rep2 controlled vocabulary controlled vocabulary sample type match: normal
sample_type normal tissue sample GSM4452864 Runtime Siftome inference GEO:sample:GSM4452864:77c59fdfb691e60df46614e4e5daeece476f02634f31723f26bd6e44dc7d6dbc low confidence normal sample_accession: GSM4452864 sample_title: Normal Lung Tissue Rep3 source_name: NM003 characteristics: tissue: Lung; age: 60; Sex: Male; disease: Normal Normal Lung Tissue Rep3 controlled vocabulary controlled vocabulary sample type match: normal
sample_type normal tissue sample GSM4452865 Runtime Siftome inference GEO:sample:GSM4452865:55e009499c1969fb29db092a55097ee4a877f3470d14d17929976eb738dd8125 low confidence normal sample_accession: GSM4452865 sample_title: Normal Lung Tissue Rep4 source_name: NM004 characteristics: tissue: Lung; age: 68; Sex: Female; disease: Normal Normal Lung Tissue Rep4 controlled vocabulary controlled vocabulary sample type match: normal
sample_type normal tissue sample GSM4452866 Runtime Siftome inference GEO:sample:GSM4452866:5ecef7915f7196554ba1f166848e4550d23a6f64b34d68dc6b820f1510e8c980 low confidence normal sample_accession: GSM4452866 sample_title: Normal Lung Tissue Rep5 source_name: NM005 characteristics: tissue: Lung; age: 36; Sex: Male; disease: Normal Normal Lung Tissue Rep5 controlled vocabulary controlled vocabulary sample type match: normal
sample_type tumor sample sample GSM4452872 Runtime Siftome inference GEO:sample:GSM4452872:4d4987b8b72e8bf02c79fe1d818ac9a1cdcab0338de50a2e688bf9ca2f037f4b medium confidence carcinoma sample_accession: GSM4452872 sample_title: Lung Adenocarcinoma Tissue Rep1 source_name: AD001 characteristics: tissue: Lung; age: 60; Sex: Male; disease: Adenocarcinoma Lung Ade... controlled vocabulary controlled vocabulary sample type match: carcinoma
sample_type tumor sample sample GSM4452873 Runtime Siftome inference GEO:sample:GSM4452873:e6ba9bd156649539f87fba75d3895779405ce01ce9b426f6e7b25753495a1a93 medium confidence carcinoma sample_accession: GSM4452873 sample_title: Lung Adenocarcinoma Tissue Rep2 source_name: AD002 characteristics: tissue: Lung; age: 68; Sex: Female; disease: Adenocarcinoma Lung A... controlled vocabulary controlled vocabulary sample type match: carcinoma
sample_type tumor sample sample GSM4452874 Runtime Siftome inference GEO:sample:GSM4452874:aabff847e117621e49eb78d1e5538bc14c66ce7cb0647cbcf21ae56c7cad6f41 medium confidence carcinoma sample_accession: GSM4452874 sample_title: Lung Adenocarcinoma Tissue Rep3 source_name: AD003 characteristics: tissue: Lung; age: 75; Sex: Male; disease: Adenocarcinoma Lung Ade... controlled vocabulary controlled vocabulary sample type match: carcinoma
sample_type tumor sample sample GSM4452875 Runtime Siftome inference GEO:sample:GSM4452875:a8a22f9ccabc2405ff6830dd71243ff480aedec43734c456e28e384731ecfbdf medium confidence carcinoma sample_accession: GSM4452875 sample_title: Lung Adenocarcinoma Tissue Rep4 source_name: AD004 characteristics: tissue: Lung; age: 50; Sex: Female; disease: Adenocarcinoma Lung A... controlled vocabulary controlled vocabulary sample type match: carcinoma
sample_type tumor sample sample GSM4452876 Runtime Siftome inference GEO:sample:GSM4452876:331dd5b1822f76baacef2ecf4485d6461901092b2afa074448cf4ac65d46188e medium confidence carcinoma sample_accession: GSM4452876 sample_title: Lung Adenocarcinoma Tissue Rep5 source_name: AD005 characteristics: tissue: Lung; age: 70; Sex: Female; disease: Adenocarcinoma Lung A... controlled vocabulary controlled vocabulary sample type match: carcinoma
tissue lung dataset GSE148036 Runtime Siftome inference GEO:dataset:GSE148036:1a989ade96b252b01aed99f45ecbdec0ff767afb83f9ceac496b30d4c003c471 low confidence lung dataset_accession: GSE148036 dataset_title: Lung transcriptional profiling of pulmonary tuberculosis, adenocarcinoma and sarcoidosis patients using RNA-Seq organism: Homo sapien... controlled vocabulary controlled vocabulary tissue match: lung
tissue lung sample GSM4452862 Runtime Siftome inference GEO:sample:GSM4452862:d72bfb61aaa29932ba3316e2fe1be0a64a15df68094091fb39c229be5ae4e2f2 low confidence lung sample_accession: GSM4452862 sample_title: Normal Lung Tissue Rep1 source_name: NM001 characteristics: tissue: Lung; age: 52; Sex: Female; disease: Normal Normal Lung Tissue Rep1 controlled vocabulary controlled vocabulary tissue match: lung
tissue lung sample GSM4452863 Runtime Siftome inference GEO:sample:GSM4452863:bd0de54eded080cf427fe7e433480302386957e625c0e5227b5e1a8c032134be low confidence lung sample_accession: GSM4452863 sample_title: Normal Lung Tissue Rep2 source_name: NM002 characteristics: tissue: Lung; age: 26; Sex: Male; disease: Normal Normal Lung Tissue Rep2 controlled vocabulary controlled vocabulary tissue match: lung
tissue lung sample GSM4452864 Runtime Siftome inference GEO:sample:GSM4452864:77c59fdfb691e60df46614e4e5daeece476f02634f31723f26bd6e44dc7d6dbc low confidence lung sample_accession: GSM4452864 sample_title: Normal Lung Tissue Rep3 source_name: NM003 characteristics: tissue: Lung; age: 60; Sex: Male; disease: Normal Normal Lung Tissue Rep3 controlled vocabulary controlled vocabulary tissue match: lung
tissue lung sample GSM4452865 Runtime Siftome inference GEO:sample:GSM4452865:55e009499c1969fb29db092a55097ee4a877f3470d14d17929976eb738dd8125 low confidence lung sample_accession: GSM4452865 sample_title: Normal Lung Tissue Rep4 source_name: NM004 characteristics: tissue: Lung; age: 68; Sex: Female; disease: Normal Normal Lung Tissue Rep4 controlled vocabulary controlled vocabulary tissue match: lung
tissue lung sample GSM4452866 Runtime Siftome inference GEO:sample:GSM4452866:5ecef7915f7196554ba1f166848e4550d23a6f64b34d68dc6b820f1510e8c980 low confidence lung sample_accession: GSM4452866 sample_title: Normal Lung Tissue Rep5 source_name: NM005 characteristics: tissue: Lung; age: 36; Sex: Male; disease: Normal Normal Lung Tissue Rep5 controlled vocabulary controlled vocabulary tissue match: lung
tissue lung sample GSM4452867 Runtime Siftome inference GEO:sample:GSM4452867:99528484a0e22f41577a4e6bf13b6abd5215ac6ef81fce95758f6515828faf31 low confidence lung sample_accession: GSM4452867 sample_title: Lung Tuberculosis Tissue Rep1 source_name: TB001 characteristics: tissue: Lung; age: 52; Sex: Female; disease: Tuberculosis Lung Tuber... controlled vocabulary controlled vocabulary tissue match: lung
tissue lung sample GSM4452868 Runtime Siftome inference GEO:sample:GSM4452868:bd6d328228d94d9d85c00df59254155ca57693c1a66dbe558dc3c44d51b73f09 low confidence lung sample_accession: GSM4452868 sample_title: Lung Tuberculosis Tissue Rep2 source_name: TB002 characteristics: tissue: Lung; age: 26; Sex: Male; disease: Tuberculosis Lung Tubercu... controlled vocabulary controlled vocabulary tissue match: lung
tissue lung sample GSM4452869 Runtime Siftome inference GEO:sample:GSM4452869:7161222202a7b2f1cf0637b8e9e46fd0f9e617b25bb38b8d25c83112ac438c96 low confidence lung sample_accession: GSM4452869 sample_title: Lung Tuberculosis Tissue Rep3 source_name: TB003 characteristics: tissue: Lung; age: 44; Sex: Male; disease: Tuberculosis Lung Tubercu... controlled vocabulary controlled vocabulary tissue match: lung
tissue lung sample GSM4452870 Runtime Siftome inference GEO:sample:GSM4452870:284af5a3b4c3898fc79af3e6f6105d1ba078b32faf001d272240ac9ac204f742 low confidence lung sample_accession: GSM4452870 sample_title: Lung Tuberculosis Tissue Rep4 source_name: TB004 characteristics: tissue: Lung; age: 52; Sex: Male; disease: Tuberculosis Lung Tubercu... controlled vocabulary controlled vocabulary tissue match: lung
tissue lung sample GSM4452871 Runtime Siftome inference GEO:sample:GSM4452871:1ff7a6aad3fcb261ac456737bf2c4f9dceb390341e14637ca3d90ba785199088 low confidence lung sample_accession: GSM4452871 sample_title: Lung Tuberculosis Tissue Rep5 source_name: TB005 characteristics: tissue: Lung; age: 55; Sex: Female; disease: Tuberculosis Lung Tuber... controlled vocabulary controlled vocabulary tissue match: lung
tissue lung sample GSM4452872 Runtime Siftome inference GEO:sample:GSM4452872:4d4987b8b72e8bf02c79fe1d818ac9a1cdcab0338de50a2e688bf9ca2f037f4b low confidence lung sample_accession: GSM4452872 sample_title: Lung Adenocarcinoma Tissue Rep1 source_name: AD001 characteristics: tissue: Lung; age: 60; Sex: Male; disease: Adenocarcinoma Lung Ade... controlled vocabulary controlled vocabulary tissue match: lung
tissue lung sample GSM4452873 Runtime Siftome inference GEO:sample:GSM4452873:e6ba9bd156649539f87fba75d3895779405ce01ce9b426f6e7b25753495a1a93 low confidence lung sample_accession: GSM4452873 sample_title: Lung Adenocarcinoma Tissue Rep2 source_name: AD002 characteristics: tissue: Lung; age: 68; Sex: Female; disease: Adenocarcinoma Lung A... controlled vocabulary controlled vocabulary tissue match: lung
tissue lung sample GSM4452874 Runtime Siftome inference GEO:sample:GSM4452874:aabff847e117621e49eb78d1e5538bc14c66ce7cb0647cbcf21ae56c7cad6f41 low confidence lung sample_accession: GSM4452874 sample_title: Lung Adenocarcinoma Tissue Rep3 source_name: AD003 characteristics: tissue: Lung; age: 75; Sex: Male; disease: Adenocarcinoma Lung Ade... controlled vocabulary controlled vocabulary tissue match: lung
tissue lung sample GSM4452875 Runtime Siftome inference GEO:sample:GSM4452875:a8a22f9ccabc2405ff6830dd71243ff480aedec43734c456e28e384731ecfbdf low confidence lung sample_accession: GSM4452875 sample_title: Lung Adenocarcinoma Tissue Rep4 source_name: AD004 characteristics: tissue: Lung; age: 50; Sex: Female; disease: Adenocarcinoma Lung A... controlled vocabulary controlled vocabulary tissue match: lung
tissue lung sample GSM4452876 Runtime Siftome inference GEO:sample:GSM4452876:331dd5b1822f76baacef2ecf4485d6461901092b2afa074448cf4ac65d46188e low confidence lung sample_accession: GSM4452876 sample_title: Lung Adenocarcinoma Tissue Rep5 source_name: AD005 characteristics: tissue: Lung; age: 70; Sex: Female; disease: Adenocarcinoma Lung A... controlled vocabulary controlled vocabulary tissue match: lung
tissue lung sample GSM4452877 Runtime Siftome inference GEO:sample:GSM4452877:6400c8aeba5d5b2a540ad01ab036882abd31dec1effefd76fef33229b9660a9f low confidence lung sample_accession: GSM4452877 sample_title: Lung Sacrodosis Tissue Rep1 source_name: SA001 characteristics: tissue: Lung; age: 36; Sex: Male; disease: Sacrodosis Lung Sacrodosis ... controlled vocabulary controlled vocabulary tissue match: lung
tissue lung sample GSM4452878 Runtime Siftome inference GEO:sample:GSM4452878:95dcb6a4a5c6ad451db8f9b638a2e2f0bbb87f3150da7012652b84f9b08d218d low confidence lung sample_accession: GSM4452878 sample_title: Lung Sacrodosis Tissue Rep2 source_name: SA002 characteristics: tissue: Lung; age: 34; Sex: Female; disease: Sacrodosis Lung Sacrodosi... controlled vocabulary controlled vocabulary tissue match: lung
tissue lung sample GSM4452879 Runtime Siftome inference GEO:sample:GSM4452879:24e72d7a12ed380828a258a77f2871d1f85d4fb7806e15d6f07789509d617c45 low confidence lung sample_accession: GSM4452879 sample_title: Lung Sacrodosis Tissue Rep3 source_name: SA003 characteristics: tissue: Lung; age: 46; Sex: Male; disease: Sacrodosis Lung Sacrodosis ... controlled vocabulary controlled vocabulary tissue match: lung
tissue lung sample GSM4452880 Runtime Siftome inference GEO:sample:GSM4452880:a27c2d8ca0ba35bb0da1abb608e88f5ff4138f3f0dca7f43d3111c89b54de9c0 low confidence lung sample_accession: GSM4452880 sample_title: Lung Sacrodosis Tissue Rep4 source_name: SA004 characteristics: tissue: Lung; age: 27; Sex: Female; disease: Sacrodosis Lung Sacrodosi... controlled vocabulary controlled vocabulary tissue match: lung
tissue lung sample GSM4452881 Runtime Siftome inference GEO:sample:GSM4452881:7516c7f9ce1ca8181a89c9194b0de2c20b8a080214dc706f1f1e56cb82f1e0eb low confidence lung sample_accession: GSM4452881 sample_title: Lung Sacrodosis Tissue Rep5 source_name: SA005 characteristics: tissue: Lung; age: 30; Sex: Female; disease: Sacrodosis Lung Sacrodosi... controlled vocabulary controlled vocabulary tissue match: lung

Sample Group Preview

Possible case samples

Samples currently treated as the comparison case group.

5
  • GSM4452872 Lung Adenocarcinoma Tissue Rep1 tumor sample Case marker detected. AD001 tissue: Lung; age: 60; Sex: Male; disease: Adenocarcinoma
  • GSM4452873 Lung Adenocarcinoma Tissue Rep2 tumor sample Case marker detected. AD002 tissue: Lung; age: 68; Sex: Female; disease: Adenocarcinoma
  • GSM4452874 Lung Adenocarcinoma Tissue Rep3 tumor sample Case marker detected. AD003 tissue: Lung; age: 75; Sex: Male; disease: Adenocarcinoma
  • GSM4452875 Lung Adenocarcinoma Tissue Rep4 tumor sample Case marker detected. AD004 tissue: Lung; age: 50; Sex: Female; disease: Adenocarcinoma
  • GSM4452876 Lung Adenocarcinoma Tissue Rep5 tumor sample Case marker detected. AD005 tissue: Lung; age: 70; Sex: Female; disease: Adenocarcinoma

Possible control samples

Samples currently treated as controls or baseline.

5
  • GSM4452862 Normal Lung Tissue Rep1 normal tissue Control marker detected. NM001 tissue: Lung; age: 52; Sex: Female; disease: Normal
  • GSM4452863 Normal Lung Tissue Rep2 normal tissue Control marker detected. NM002 tissue: Lung; age: 26; Sex: Male; disease: Normal
  • GSM4452864 Normal Lung Tissue Rep3 normal tissue Control marker detected. NM003 tissue: Lung; age: 60; Sex: Male; disease: Normal
  • GSM4452865 Normal Lung Tissue Rep4 normal tissue Control marker detected. NM004 tissue: Lung; age: 68; Sex: Female; disease: Normal
  • GSM4452866 Normal Lung Tissue Rep5 normal tissue Control marker detected. NM005 tissue: Lung; age: 36; Sex: Male; disease: Normal

Unassigned samples

Samples with no explicit case or control marker.

10
  • GSM4452867 Lung Tuberculosis Tissue Rep1 unassigned No explicit case or control marker detected. TB001 tissue: Lung; age: 52; Sex: Female; disease: Tuberculosis
  • GSM4452868 Lung Tuberculosis Tissue Rep2 unassigned No explicit case or control marker detected. TB002 tissue: Lung; age: 26; Sex: Male; disease: Tuberculosis
  • GSM4452869 Lung Tuberculosis Tissue Rep3 unassigned No explicit case or control marker detected. TB003 tissue: Lung; age: 44; Sex: Male; disease: Tuberculosis
  • GSM4452870 Lung Tuberculosis Tissue Rep4 unassigned No explicit case or control marker detected. TB004 tissue: Lung; age: 52; Sex: Male; disease: Tuberculosis
  • GSM4452871 Lung Tuberculosis Tissue Rep5 unassigned No explicit case or control marker detected. TB005 tissue: Lung; age: 55; Sex: Female; disease: Tuberculosis
  • GSM4452877 Lung Sacrodosis Tissue Rep1 unassigned No explicit case or control marker detected. SA001 tissue: Lung; age: 36; Sex: Male; disease: Sacrodosis
  • GSM4452878 Lung Sacrodosis Tissue Rep2 unassigned No explicit case or control marker detected. SA002 tissue: Lung; age: 34; Sex: Female; disease: Sacrodosis
  • GSM4452879 Lung Sacrodosis Tissue Rep3 unassigned No explicit case or control marker detected. SA003 tissue: Lung; age: 46; Sex: Male; disease: Sacrodosis
  • GSM4452880 Lung Sacrodosis Tissue Rep4 unassigned No explicit case or control marker detected. SA004 tissue: Lung; age: 27; Sex: Female; disease: Sacrodosis
  • GSM4452881 Lung Sacrodosis Tissue Rep5 unassigned No explicit case or control marker detected. SA005 tissue: Lung; age: 30; Sex: Female; disease: Sacrodosis

Excluded samples

Samples excluded from grouping by hard exclusion rules.

0

No samples

Ambiguous samples

Samples that need manual review before trusting grouping.

0

No samples

Metadata Quality Components

Persisted metadata quality

85 pts
Clarity
85%
Weight
100 pts

Sample source clarity: All samples have source metadata and clear GSE/GSM accessions. Group clarity: Rule-based grouping found both case and control samples. Disease clarity: Disease or condition metadata was not normalized. Tissue clarity: Tissue metadata normalized. Treatment clarity: No unclear treatment split detected in the sample metadata. Replicate clarity: No pooled sample or technical replicate flags detected. Data availability clarity: Dataset-level processed or raw data availability is explicit.

Detected Sample Groups

normal tissue

5 samples
  • GSM4452862 Normal Lung Tissue Rep1 NM001 tissue: Lung; age: 52; Sex: Female; disease: Normal
  • GSM4452863 Normal Lung Tissue Rep2 NM002 tissue: Lung; age: 26; Sex: Male; disease: Normal
  • GSM4452864 Normal Lung Tissue Rep3 NM003 tissue: Lung; age: 60; Sex: Male; disease: Normal
  • GSM4452865 Normal Lung Tissue Rep4 NM004 tissue: Lung; age: 68; Sex: Female; disease: Normal
  • GSM4452866 Normal Lung Tissue Rep5 NM005 tissue: Lung; age: 36; Sex: Male; disease: Normal

unassigned

10 samples
  • GSM4452867 Lung Tuberculosis Tissue Rep1 TB001 tissue: Lung; age: 52; Sex: Female; disease: Tuberculosis
  • GSM4452868 Lung Tuberculosis Tissue Rep2 TB002 tissue: Lung; age: 26; Sex: Male; disease: Tuberculosis
  • GSM4452869 Lung Tuberculosis Tissue Rep3 TB003 tissue: Lung; age: 44; Sex: Male; disease: Tuberculosis
  • GSM4452870 Lung Tuberculosis Tissue Rep4 TB004 tissue: Lung; age: 52; Sex: Male; disease: Tuberculosis
  • GSM4452871 Lung Tuberculosis Tissue Rep5 TB005 tissue: Lung; age: 55; Sex: Female; disease: Tuberculosis
  • GSM4452877 Lung Sacrodosis Tissue Rep1 SA001 tissue: Lung; age: 36; Sex: Male; disease: Sacrodosis
  • GSM4452878 Lung Sacrodosis Tissue Rep2 SA002 tissue: Lung; age: 34; Sex: Female; disease: Sacrodosis
  • GSM4452879 Lung Sacrodosis Tissue Rep3 SA003 tissue: Lung; age: 46; Sex: Male; disease: Sacrodosis
  • GSM4452880 Lung Sacrodosis Tissue Rep4 SA004 tissue: Lung; age: 27; Sex: Female; disease: Sacrodosis
  • GSM4452881 Lung Sacrodosis Tissue Rep5 SA005 tissue: Lung; age: 30; Sex: Female; disease: Sacrodosis

tumor sample

5 samples
  • GSM4452872 Lung Adenocarcinoma Tissue Rep1 AD001 tissue: Lung; age: 60; Sex: Male; disease: Adenocarcinoma
  • GSM4452873 Lung Adenocarcinoma Tissue Rep2 AD002 tissue: Lung; age: 68; Sex: Female; disease: Adenocarcinoma
  • GSM4452874 Lung Adenocarcinoma Tissue Rep3 AD003 tissue: Lung; age: 75; Sex: Male; disease: Adenocarcinoma
  • GSM4452875 Lung Adenocarcinoma Tissue Rep4 AD004 tissue: Lung; age: 50; Sex: Female; disease: Adenocarcinoma
  • GSM4452876 Lung Adenocarcinoma Tissue Rep5 AD005 tissue: Lung; age: 70; Sex: Female; disease: Adenocarcinoma

Score Breakdown

60%

relevance

  • Organism normalized.
  • Assay type normalized.
  • Tissue metadata normalized.
0%

comparison suitability

  • Tumor and normal sample groups detected.
  • No excluded sample type flags detected.
  • Tumor/normal design boosted for colorectal tumor-vs-normal tissue triage.
  • Patient tissue or biopsy specimens boosted for tissue comparison triage.
  • Non-colorectal cancer context downgraded for colorectal tumor-vs-normal tissue ranking.
85%

metadata quality

  • Sample source clarity: All samples have source metadata and clear GSE/GSM accessions.
  • Group clarity: Rule-based grouping found both case and control samples.
  • Disease clarity: Disease or condition metadata was not normalized.
  • Tissue clarity: Tissue metadata normalized.
  • Treatment clarity: No unclear treatment split detected in the sample metadata.
  • Replicate clarity: No pooled sample or technical replicate flags detected.
  • Data availability clarity: Dataset-level processed or raw data availability is explicit.
100%

data availability

  • Processed data available.
  • Raw data available.
34%

overall

  • Weighted score: 30% relevance, 30% comparison suitability, 25% metadata quality, 15% data availability.
  • Overall score capped because comparison suitability is weak for the selected search intent.
  • Overall score capped because tumor/normal grouping is from a non-colorectal cancer context.

Sample Links

20 samples

Review Audit Trail

0 decisions

No review decisions have been stored for this dataset.