Siftome Phase 3L

GSE52248

Identification of mRNAs and lincRNAs associated with lung cancer progression using next-generation RNA sequencing from laser micro-dissected archival FFPE tissue specimens

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
2013-11-11
Last update
2019-05-15
Organization
Case Western Reserve University
Department
Center for RNA Molecular Biology
Public date
2014-12-01
Experiment types
Expression profiling by high throughput sequencing
Platforms
GPL10999 Illumina Genome Analyzer IIx (Homo sapiens)
Series type
Series
SubSeries
Not available
BioProject
PRJNA227275
Supplementary files
TXT: GSE52248_FPKM_genes.txt.gz; TXT: GSE52248_FPKM_lincRNAs.txt.gz; TXT: GSE52248_Normalized_read_counts_genes.txt.gz; TXT: GSE52248_Normalized_read_counts_lincRNAs.txt.gz
Organism
Homo sapiens
Assay
bulk RNA-seq
Samples
18
Study design
Tumor vs unmatched normal
Specimen/source
Tissue
Scoring version
intent-aware-scoring-v15
Ranking batch
b69568dd1e4fe1b9ee2d880bf5495d748a7e4c5c11e4107f02528c3be0e76012
Ranking created
2026-06-05T20:20:27.088676Z
Warning version
intent-aware-warnings-v2

Current Intent Interpretation

Patient tissue tumor-vs-normal

Expectations

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

Rules

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

Study Classification

Tumor vs unmatched normal Tissue

Analysis Readiness

Ready after review
100% 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

10/10 pts

No dataset warnings are present.

Metadata normalization

10/10 pts

Metadata quality is high enough to support downstream handoff.

Blockers

No readiness blockers detected.

Next Steps

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

Analysis Preparation Checklist

5/6 ready

Group labels reviewed

Needs review

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

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

Minimum sample count met

Ready

Both groups meet the minimum of 2 samples.

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

Processed counts available

Ready

Processed data availability is marked true in the GEO index.

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

Ambiguous samples handled

Ready

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

Still scan the grouping table for biology-specific ambiguity.

Exclusion decisions recorded

Ready

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

Record any manual exclusions in the downstream analysis notes.

Source links preserved

Ready

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

Keep GEO dataset and sample links with exported metadata.

Bioinformatician Review

Standard analyst review

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

No expert-review triggers were detected by Siftome.

Why This Is Ranked Here

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

Score Components

  • relevance 100% Disease or condition metadata normalized. 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 100% 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 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 12 samples
  • Likely control group normal tissue 6 samples

Warnings

No ranking warnings are active.

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 0 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: not a colorectal/GI cancer cohort. 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: not a colorectal/GI cancer cohort. Contributed to match or upgrade evidence.
  • Supporting fact Processed data is available for downstream review. Contributed to match or upgrade 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: 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: not a colorectal/GI cancer cohort. 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
GSE52248
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
GSE52248
  • 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
GSE52248
  • 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
GSE52248
  • 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: GSE52248
dataset_title: Identification of mRNAs and lincRNAs associated with lung cancer progression using next-generation RNA sequencing from laser micro-dissected archival FFPE tissue specimens
organism: Homo sapiens
assay_type: bulk RNA-seq
processed_data_available: true
raw_data_available: true
submission_date: 2013-11-11
last_update_date: 2019-05-15
organization_name: Case Western Reserve University
department: Center for RNA Molecular Biology
public_date: 2014-12-01
experiment_types: Expression profiling by high throughput sequencing
platforms: GPL10999 Illumina Genome Analyzer IIx (Homo sapiens)
sub_series: Not available
bioproject: PRJNA227275
supplementary_files: TXT: GSE52248_FPKM_genes.txt.gz; TXT: GSE52248_FPKM_lincRNAs.txt.gz; TXT: GSE52248_Normalized_read_counts_genes.txt.gz; TXT: GSE52248_Normalized_read_counts_lincRNAs.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: not a colorectal/GI cancer cohort.
  • Processed data is available for downstream review.

Why It May Not Be Suitable

  • Non-colorectal cancer context downgraded for colorectal tumor-vs-normal tissue ranking.
  • 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: not a colorectal/GI cancer cohort.
  • Comparison suitability score is below the Phase 1 recommended threshold.

Warnings

No warnings

Normalized Fields

59 fields
Field Value Source Origin Confidence Evidence Reason
assay_type bulk RNA-seq dataset GSE52248 Runtime Siftome inference GEO:dataset:GSE52248:b419fba72ffc4f7ea78bab3416323284f080ff316a28c183b2eaeecd68fbbf31 high confidence bulk rna-seq dataset_accession: GSE52248 dataset_title: Identification of mRNAs and lincRNAs associated with lung cancer progression using next-generation RNA sequencing from laser micro-dis... keyword match keyword match: bulk rna-seq
disease colorectal cancer dataset GSE52248 Runtime Siftome inference GEO:dataset:GSE52248:b419fba72ffc4f7ea78bab3416323284f080ff316a28c183b2eaeecd68fbbf31 medium confidence read dataset_accession: GSE52248 dataset_title: Identification of mRNAs and lincRNAs associated with lung cancer progression using next-generation RNA sequencing from laser micro-dis... controlled vocabulary controlled vocabulary disease match: read
disease lung cancer dataset GSE52248 Runtime Siftome inference GEO:dataset:GSE52248:b419fba72ffc4f7ea78bab3416323284f080ff316a28c183b2eaeecd68fbbf31 high confidence lung cancer dataset_accession: GSE52248 dataset_title: Identification of mRNAs and lincRNAs associated with lung cancer progression using next-generation RNA sequencing from laser micro-dis... controlled vocabulary controlled vocabulary disease match: lung cancer
disease lung cancer sample GSM1261885 Runtime Siftome inference GEO:sample:GSM1261885:22a559efbbd1b713aa9e880873f99d2992bac647b0bf68b117d5efba902a6f3b high confidence lung carcinoma sample_accession: GSM1261885 sample_title: 1inv source_name: Tumor cells characteristics: patient id: 1; tissue source: laser micro-dissected archival FFPE tissue specimens; tis... controlled vocabulary controlled vocabulary disease match: lung carcinoma
disease lung cancer sample GSM1261888 Runtime Siftome inference GEO:sample:GSM1261888:b730475ecc6b79a069b3baf2ac88e2db0f3ddc56fd23a69f0770ac49c1aeae4e high confidence lung carcinoma sample_accession: GSM1261888 sample_title: 2inv source_name: Tumor cells characteristics: patient id: 2; tissue source: laser micro-dissected archival FFPE tissue specimens; tis... controlled vocabulary controlled vocabulary disease match: lung carcinoma
disease lung cancer sample GSM1261891 Runtime Siftome inference GEO:sample:GSM1261891:c60abf5663f71563efa7b72f0f7d699a68cc2ccc32d7f295b2e94b6bada76284 high confidence lung carcinoma sample_accession: GSM1261891 sample_title: 3inv source_name: Tumor cells characteristics: patient id: 3; tissue source: laser micro-dissected archival FFPE tissue specimens; tis... controlled vocabulary controlled vocabulary disease match: lung carcinoma
disease lung cancer sample GSM1261894 Runtime Siftome inference GEO:sample:GSM1261894:e9d2448df108ecba96b83389129fef3c913474608cb3c34319cb03ef17241edd high confidence lung carcinoma sample_accession: GSM1261894 sample_title: 4inv source_name: Tumor cells characteristics: patient id: 4; tissue source: laser micro-dissected archival FFPE tissue specimens; tis... controlled vocabulary controlled vocabulary disease match: lung carcinoma
disease lung cancer sample GSM1261897 Runtime Siftome inference GEO:sample:GSM1261897:34f4c03719ee981831d0394692d80093bc121e72d0c05aba2bf2048752a6dca9 high confidence lung carcinoma sample_accession: GSM1261897 sample_title: 5inv source_name: Tumor cells characteristics: patient id: 5; tissue source: laser micro-dissected archival FFPE tissue specimens; tis... controlled vocabulary controlled vocabulary disease match: lung carcinoma
disease lung cancer sample GSM1261900 Runtime Siftome inference GEO:sample:GSM1261900:2afe33a55b6cfd68a4c12b905459f3c96f59f5d69cc02363923798794f471a4a high confidence lung carcinoma sample_accession: GSM1261900 sample_title: 6inv source_name: Tumor cells characteristics: patient id: 6; tissue source: laser micro-dissected archival FFPE tissue specimens; tis... controlled vocabulary controlled vocabulary disease match: lung carcinoma
organism Homo sapiens dataset GSE52248 Runtime Siftome inference GEO:dataset:GSE52248:b419fba72ffc4f7ea78bab3416323284f080ff316a28c183b2eaeecd68fbbf31 high confidence homo sapiens dataset_accession: GSE52248 dataset_title: Identification of mRNAs and lincRNAs associated with lung cancer progression using next-generation RNA sequencing from laser micro-dis... keyword match keyword match: homo sapiens
primary_tissue primary tissue sample GSM1261884 Runtime Siftome inference GEO:sample:GSM1261884:c6c7237f6dff81f4d28201b5956751b7d852690f9c1956cde74f2fa47be89ba8 high confidence ffpe tissue sample_accession: GSM1261884 sample_title: 1ais source_name: Tumor cells characteristics: patient id: 1; tissue source: laser micro-dissected archival FFPE tissue specimens; tis... controlled vocabulary controlled vocabulary primary tissue match: ffpe tissue
primary_tissue primary tissue sample GSM1261885 Runtime Siftome inference GEO:sample:GSM1261885:22a559efbbd1b713aa9e880873f99d2992bac647b0bf68b117d5efba902a6f3b high confidence ffpe tissue sample_accession: GSM1261885 sample_title: 1inv source_name: Tumor cells characteristics: patient id: 1; tissue source: laser micro-dissected archival FFPE tissue specimens; tis... controlled vocabulary controlled vocabulary primary tissue match: ffpe tissue
primary_tissue primary tissue sample GSM1261886 Runtime Siftome inference GEO:sample:GSM1261886:34034bab747b8456fe46910259ffdd880d55da928eb92cf6d21b35c051d1a9ff high confidence ffpe tissue sample_accession: GSM1261886 sample_title: 1nor source_name: Normal cells characteristics: patient id: 1; tissue source: laser micro-dissected archival FFPE tissue specimens; ti... controlled vocabulary controlled vocabulary primary tissue match: ffpe tissue
primary_tissue primary tissue sample GSM1261887 Runtime Siftome inference GEO:sample:GSM1261887:b13e6b32d9144c6786f5a011643fa85a5a77e86adf279370c758bddef733efad high confidence ffpe tissue sample_accession: GSM1261887 sample_title: 2ais source_name: Tumor cells characteristics: patient id: 2; tissue source: laser micro-dissected archival FFPE tissue specimens; tis... controlled vocabulary controlled vocabulary primary tissue match: ffpe tissue
primary_tissue primary tissue sample GSM1261888 Runtime Siftome inference GEO:sample:GSM1261888:b730475ecc6b79a069b3baf2ac88e2db0f3ddc56fd23a69f0770ac49c1aeae4e high confidence ffpe tissue sample_accession: GSM1261888 sample_title: 2inv source_name: Tumor cells characteristics: patient id: 2; tissue source: laser micro-dissected archival FFPE tissue specimens; tis... controlled vocabulary controlled vocabulary primary tissue match: ffpe tissue
primary_tissue primary tissue sample GSM1261889 Runtime Siftome inference GEO:sample:GSM1261889:93316ffea90618b410518eaad65cc7908a543530b47cac48b9f3ad838e806301 high confidence ffpe tissue sample_accession: GSM1261889 sample_title: 2nor source_name: Normal cells characteristics: patient id: 2; tissue source: laser micro-dissected archival FFPE tissue specimens; ti... controlled vocabulary controlled vocabulary primary tissue match: ffpe tissue
primary_tissue primary tissue sample GSM1261890 Runtime Siftome inference GEO:sample:GSM1261890:7264f790393720221734c192cd0b5332c676be2bc9236a0d66c306feecba7d33 high confidence ffpe tissue sample_accession: GSM1261890 sample_title: 3ais source_name: Tumor cells characteristics: patient id: 3; tissue source: laser micro-dissected archival FFPE tissue specimens; tis... controlled vocabulary controlled vocabulary primary tissue match: ffpe tissue
primary_tissue primary tissue sample GSM1261891 Runtime Siftome inference GEO:sample:GSM1261891:c60abf5663f71563efa7b72f0f7d699a68cc2ccc32d7f295b2e94b6bada76284 high confidence ffpe tissue sample_accession: GSM1261891 sample_title: 3inv source_name: Tumor cells characteristics: patient id: 3; tissue source: laser micro-dissected archival FFPE tissue specimens; tis... controlled vocabulary controlled vocabulary primary tissue match: ffpe tissue
primary_tissue primary tissue sample GSM1261892 Runtime Siftome inference GEO:sample:GSM1261892:5aeb91178cda3b5dd5fdb0d9b1fd989543c59a8560ba843a448cd1b1977e7c2b high confidence ffpe tissue sample_accession: GSM1261892 sample_title: 3nor source_name: Normal cells characteristics: patient id: 3; tissue source: laser micro-dissected archival FFPE tissue specimens; ti... controlled vocabulary controlled vocabulary primary tissue match: ffpe tissue
primary_tissue primary tissue sample GSM1261893 Runtime Siftome inference GEO:sample:GSM1261893:204d5fd071a702d299df2d19bd8088941c7b60a3e7aef7dc17c2548d8959e850 high confidence ffpe tissue sample_accession: GSM1261893 sample_title: 4ais source_name: Tumor cells characteristics: patient id: 4; tissue source: laser micro-dissected archival FFPE tissue specimens; tis... controlled vocabulary controlled vocabulary primary tissue match: ffpe tissue
primary_tissue primary tissue sample GSM1261894 Runtime Siftome inference GEO:sample:GSM1261894:e9d2448df108ecba96b83389129fef3c913474608cb3c34319cb03ef17241edd high confidence ffpe tissue sample_accession: GSM1261894 sample_title: 4inv source_name: Tumor cells characteristics: patient id: 4; tissue source: laser micro-dissected archival FFPE tissue specimens; tis... controlled vocabulary controlled vocabulary primary tissue match: ffpe tissue
primary_tissue primary tissue sample GSM1261895 Runtime Siftome inference GEO:sample:GSM1261895:3815a4f1d0be797a54af9a89dc56d47b94b47215982d6a81d81a8f1921d733da high confidence ffpe tissue sample_accession: GSM1261895 sample_title: 4nor source_name: Normal cells characteristics: patient id: 4; tissue source: laser micro-dissected archival FFPE tissue specimens; ti... controlled vocabulary controlled vocabulary primary tissue match: ffpe tissue
primary_tissue primary tissue sample GSM1261896 Runtime Siftome inference GEO:sample:GSM1261896:3cc6267e78cb7341cc573863d39d185379e3167aefeee7a8c086955afc2ebee8 high confidence ffpe tissue sample_accession: GSM1261896 sample_title: 5ais source_name: Tumor cells characteristics: patient id: 5; tissue source: laser micro-dissected archival FFPE tissue specimens; tis... controlled vocabulary controlled vocabulary primary tissue match: ffpe tissue
primary_tissue primary tissue sample GSM1261897 Runtime Siftome inference GEO:sample:GSM1261897:34f4c03719ee981831d0394692d80093bc121e72d0c05aba2bf2048752a6dca9 high confidence ffpe tissue sample_accession: GSM1261897 sample_title: 5inv source_name: Tumor cells characteristics: patient id: 5; tissue source: laser micro-dissected archival FFPE tissue specimens; tis... controlled vocabulary controlled vocabulary primary tissue match: ffpe tissue
primary_tissue primary tissue sample GSM1261898 Runtime Siftome inference GEO:sample:GSM1261898:549b1b0e12fc003aa800349c80d87d9f5481503381c092974c17e39e82ba8759 high confidence ffpe tissue sample_accession: GSM1261898 sample_title: 5nor source_name: Normal cells characteristics: patient id: 5; tissue source: laser micro-dissected archival FFPE tissue specimens; ti... controlled vocabulary controlled vocabulary primary tissue match: ffpe tissue
primary_tissue primary tissue sample GSM1261899 Runtime Siftome inference GEO:sample:GSM1261899:2be0f67bf7733c5f31a166f89197b068b5d727ca49746b4c17d952d5848b2847 high confidence ffpe tissue sample_accession: GSM1261899 sample_title: 6ais source_name: Tumor cells characteristics: patient id: 6; tissue source: laser micro-dissected archival FFPE tissue specimens; tis... controlled vocabulary controlled vocabulary primary tissue match: ffpe tissue
primary_tissue primary tissue sample GSM1261900 Runtime Siftome inference GEO:sample:GSM1261900:2afe33a55b6cfd68a4c12b905459f3c96f59f5d69cc02363923798794f471a4a high confidence ffpe tissue sample_accession: GSM1261900 sample_title: 6inv source_name: Tumor cells characteristics: patient id: 6; tissue source: laser micro-dissected archival FFPE tissue specimens; tis... controlled vocabulary controlled vocabulary primary tissue match: ffpe tissue
primary_tissue primary tissue sample GSM1261901 Runtime Siftome inference GEO:sample:GSM1261901:c2dda32b315cd555b34197f722b542b79509da87f5be76654242dfe12c29b35b high confidence ffpe tissue sample_accession: GSM1261901 sample_title: 6nor source_name: Normal cells characteristics: patient id: 6; tissue source: laser micro-dissected archival FFPE tissue specimens; ti... controlled vocabulary controlled vocabulary primary tissue match: ffpe tissue
sample_type tumor sample sample GSM1261884 Runtime Siftome inference GEO:sample:GSM1261884:c6c7237f6dff81f4d28201b5956751b7d852690f9c1956cde74f2fa47be89ba8 low confidence tumor sample_accession: GSM1261884 sample_title: 1ais source_name: Tumor cells characteristics: patient id: 1; tissue source: laser micro-dissected archival FFPE tissue specimens; tis... controlled vocabulary controlled vocabulary sample type match: tumor
sample_type tumor sample sample GSM1261885 Runtime Siftome inference GEO:sample:GSM1261885:22a559efbbd1b713aa9e880873f99d2992bac647b0bf68b117d5efba902a6f3b low confidence tumor sample_accession: GSM1261885 sample_title: 1inv source_name: Tumor cells characteristics: patient id: 1; tissue source: laser micro-dissected archival FFPE tissue specimens; tis... controlled vocabulary controlled vocabulary sample type match: tumor
sample_type normal tissue sample GSM1261886 Runtime Siftome inference GEO:sample:GSM1261886:34034bab747b8456fe46910259ffdd880d55da928eb92cf6d21b35c051d1a9ff low confidence normal sample_accession: GSM1261886 sample_title: 1nor source_name: Normal cells characteristics: patient id: 1; tissue source: laser micro-dissected archival FFPE tissue specimens; ti... controlled vocabulary controlled vocabulary sample type match: normal
sample_type tumor sample sample GSM1261887 Runtime Siftome inference GEO:sample:GSM1261887:b13e6b32d9144c6786f5a011643fa85a5a77e86adf279370c758bddef733efad low confidence tumor sample_accession: GSM1261887 sample_title: 2ais source_name: Tumor cells characteristics: patient id: 2; tissue source: laser micro-dissected archival FFPE tissue specimens; tis... controlled vocabulary controlled vocabulary sample type match: tumor
sample_type tumor sample sample GSM1261888 Runtime Siftome inference GEO:sample:GSM1261888:b730475ecc6b79a069b3baf2ac88e2db0f3ddc56fd23a69f0770ac49c1aeae4e low confidence tumor sample_accession: GSM1261888 sample_title: 2inv source_name: Tumor cells characteristics: patient id: 2; tissue source: laser micro-dissected archival FFPE tissue specimens; tis... controlled vocabulary controlled vocabulary sample type match: tumor
sample_type normal tissue sample GSM1261889 Runtime Siftome inference GEO:sample:GSM1261889:93316ffea90618b410518eaad65cc7908a543530b47cac48b9f3ad838e806301 low confidence normal sample_accession: GSM1261889 sample_title: 2nor source_name: Normal cells characteristics: patient id: 2; tissue source: laser micro-dissected archival FFPE tissue specimens; ti... controlled vocabulary controlled vocabulary sample type match: normal
sample_type tumor sample sample GSM1261890 Runtime Siftome inference GEO:sample:GSM1261890:7264f790393720221734c192cd0b5332c676be2bc9236a0d66c306feecba7d33 low confidence tumor sample_accession: GSM1261890 sample_title: 3ais source_name: Tumor cells characteristics: patient id: 3; tissue source: laser micro-dissected archival FFPE tissue specimens; tis... controlled vocabulary controlled vocabulary sample type match: tumor
sample_type tumor sample sample GSM1261891 Runtime Siftome inference GEO:sample:GSM1261891:c60abf5663f71563efa7b72f0f7d699a68cc2ccc32d7f295b2e94b6bada76284 low confidence tumor sample_accession: GSM1261891 sample_title: 3inv source_name: Tumor cells characteristics: patient id: 3; tissue source: laser micro-dissected archival FFPE tissue specimens; tis... controlled vocabulary controlled vocabulary sample type match: tumor
sample_type normal tissue sample GSM1261892 Runtime Siftome inference GEO:sample:GSM1261892:5aeb91178cda3b5dd5fdb0d9b1fd989543c59a8560ba843a448cd1b1977e7c2b low confidence normal sample_accession: GSM1261892 sample_title: 3nor source_name: Normal cells characteristics: patient id: 3; tissue source: laser micro-dissected archival FFPE tissue specimens; ti... controlled vocabulary controlled vocabulary sample type match: normal
sample_type tumor sample sample GSM1261893 Runtime Siftome inference GEO:sample:GSM1261893:204d5fd071a702d299df2d19bd8088941c7b60a3e7aef7dc17c2548d8959e850 low confidence tumor sample_accession: GSM1261893 sample_title: 4ais source_name: Tumor cells characteristics: patient id: 4; tissue source: laser micro-dissected archival FFPE tissue specimens; tis... controlled vocabulary controlled vocabulary sample type match: tumor
sample_type tumor sample sample GSM1261894 Runtime Siftome inference GEO:sample:GSM1261894:e9d2448df108ecba96b83389129fef3c913474608cb3c34319cb03ef17241edd low confidence tumor sample_accession: GSM1261894 sample_title: 4inv source_name: Tumor cells characteristics: patient id: 4; tissue source: laser micro-dissected archival FFPE tissue specimens; tis... controlled vocabulary controlled vocabulary sample type match: tumor
sample_type normal tissue sample GSM1261895 Runtime Siftome inference GEO:sample:GSM1261895:3815a4f1d0be797a54af9a89dc56d47b94b47215982d6a81d81a8f1921d733da low confidence normal sample_accession: GSM1261895 sample_title: 4nor source_name: Normal cells characteristics: patient id: 4; tissue source: laser micro-dissected archival FFPE tissue specimens; ti... controlled vocabulary controlled vocabulary sample type match: normal
sample_type tumor sample sample GSM1261896 Runtime Siftome inference GEO:sample:GSM1261896:3cc6267e78cb7341cc573863d39d185379e3167aefeee7a8c086955afc2ebee8 low confidence tumor sample_accession: GSM1261896 sample_title: 5ais source_name: Tumor cells characteristics: patient id: 5; tissue source: laser micro-dissected archival FFPE tissue specimens; tis... controlled vocabulary controlled vocabulary sample type match: tumor
sample_type tumor sample sample GSM1261897 Runtime Siftome inference GEO:sample:GSM1261897:34f4c03719ee981831d0394692d80093bc121e72d0c05aba2bf2048752a6dca9 low confidence tumor sample_accession: GSM1261897 sample_title: 5inv source_name: Tumor cells characteristics: patient id: 5; tissue source: laser micro-dissected archival FFPE tissue specimens; tis... controlled vocabulary controlled vocabulary sample type match: tumor
sample_type normal tissue sample GSM1261898 Runtime Siftome inference GEO:sample:GSM1261898:549b1b0e12fc003aa800349c80d87d9f5481503381c092974c17e39e82ba8759 low confidence normal sample_accession: GSM1261898 sample_title: 5nor source_name: Normal cells characteristics: patient id: 5; tissue source: laser micro-dissected archival FFPE tissue specimens; ti... controlled vocabulary controlled vocabulary sample type match: normal
sample_type tumor sample sample GSM1261899 Runtime Siftome inference GEO:sample:GSM1261899:2be0f67bf7733c5f31a166f89197b068b5d727ca49746b4c17d952d5848b2847 low confidence tumor sample_accession: GSM1261899 sample_title: 6ais source_name: Tumor cells characteristics: patient id: 6; tissue source: laser micro-dissected archival FFPE tissue specimens; tis... controlled vocabulary controlled vocabulary sample type match: tumor
sample_type tumor sample sample GSM1261900 Runtime Siftome inference GEO:sample:GSM1261900:2afe33a55b6cfd68a4c12b905459f3c96f59f5d69cc02363923798794f471a4a low confidence tumor sample_accession: GSM1261900 sample_title: 6inv source_name: Tumor cells characteristics: patient id: 6; tissue source: laser micro-dissected archival FFPE tissue specimens; tis... controlled vocabulary controlled vocabulary sample type match: tumor
sample_type normal tissue sample GSM1261901 Runtime Siftome inference GEO:sample:GSM1261901:c2dda32b315cd555b34197f722b542b79509da87f5be76654242dfe12c29b35b low confidence normal sample_accession: GSM1261901 sample_title: 6nor source_name: Normal cells characteristics: patient id: 6; tissue source: laser micro-dissected archival FFPE tissue specimens; ti... controlled vocabulary controlled vocabulary sample type match: normal
tissue lung dataset GSE52248 Runtime Siftome inference GEO:dataset:GSE52248:b419fba72ffc4f7ea78bab3416323284f080ff316a28c183b2eaeecd68fbbf31 low confidence lung dataset_accession: GSE52248 dataset_title: Identification of mRNAs and lincRNAs associated with lung cancer progression using next-generation RNA sequencing from laser micro-dis... controlled vocabulary controlled vocabulary tissue match: lung
tissue lung sample GSM1261885 Runtime Siftome inference GEO:sample:GSM1261885:22a559efbbd1b713aa9e880873f99d2992bac647b0bf68b117d5efba902a6f3b low confidence lung sample_accession: GSM1261885 sample_title: 1inv source_name: Tumor cells characteristics: patient id: 1; tissue source: laser micro-dissected archival FFPE tissue specimens; tis... controlled vocabulary controlled vocabulary tissue match: lung
tissue lung sample GSM1261886 Runtime Siftome inference GEO:sample:GSM1261886:34034bab747b8456fe46910259ffdd880d55da928eb92cf6d21b35c051d1a9ff low confidence lung sample_accession: GSM1261886 sample_title: 1nor source_name: Normal cells characteristics: patient id: 1; tissue source: laser micro-dissected archival FFPE tissue specimens; ti... controlled vocabulary controlled vocabulary tissue match: lung
tissue lung sample GSM1261888 Runtime Siftome inference GEO:sample:GSM1261888:b730475ecc6b79a069b3baf2ac88e2db0f3ddc56fd23a69f0770ac49c1aeae4e low confidence lung sample_accession: GSM1261888 sample_title: 2inv source_name: Tumor cells characteristics: patient id: 2; tissue source: laser micro-dissected archival FFPE tissue specimens; tis... controlled vocabulary controlled vocabulary tissue match: lung
tissue lung sample GSM1261889 Runtime Siftome inference GEO:sample:GSM1261889:93316ffea90618b410518eaad65cc7908a543530b47cac48b9f3ad838e806301 low confidence lung sample_accession: GSM1261889 sample_title: 2nor source_name: Normal cells characteristics: patient id: 2; tissue source: laser micro-dissected archival FFPE tissue specimens; ti... controlled vocabulary controlled vocabulary tissue match: lung
tissue lung sample GSM1261891 Runtime Siftome inference GEO:sample:GSM1261891:c60abf5663f71563efa7b72f0f7d699a68cc2ccc32d7f295b2e94b6bada76284 low confidence lung sample_accession: GSM1261891 sample_title: 3inv source_name: Tumor cells characteristics: patient id: 3; tissue source: laser micro-dissected archival FFPE tissue specimens; tis... controlled vocabulary controlled vocabulary tissue match: lung
tissue lung sample GSM1261892 Runtime Siftome inference GEO:sample:GSM1261892:5aeb91178cda3b5dd5fdb0d9b1fd989543c59a8560ba843a448cd1b1977e7c2b low confidence lung sample_accession: GSM1261892 sample_title: 3nor source_name: Normal cells characteristics: patient id: 3; tissue source: laser micro-dissected archival FFPE tissue specimens; ti... controlled vocabulary controlled vocabulary tissue match: lung
tissue lung sample GSM1261894 Runtime Siftome inference GEO:sample:GSM1261894:e9d2448df108ecba96b83389129fef3c913474608cb3c34319cb03ef17241edd low confidence lung sample_accession: GSM1261894 sample_title: 4inv source_name: Tumor cells characteristics: patient id: 4; tissue source: laser micro-dissected archival FFPE tissue specimens; tis... controlled vocabulary controlled vocabulary tissue match: lung
tissue lung sample GSM1261895 Runtime Siftome inference GEO:sample:GSM1261895:3815a4f1d0be797a54af9a89dc56d47b94b47215982d6a81d81a8f1921d733da low confidence lung sample_accession: GSM1261895 sample_title: 4nor source_name: Normal cells characteristics: patient id: 4; tissue source: laser micro-dissected archival FFPE tissue specimens; ti... controlled vocabulary controlled vocabulary tissue match: lung
tissue lung sample GSM1261897 Runtime Siftome inference GEO:sample:GSM1261897:34f4c03719ee981831d0394692d80093bc121e72d0c05aba2bf2048752a6dca9 low confidence lung sample_accession: GSM1261897 sample_title: 5inv source_name: Tumor cells characteristics: patient id: 5; tissue source: laser micro-dissected archival FFPE tissue specimens; tis... controlled vocabulary controlled vocabulary tissue match: lung
tissue lung sample GSM1261898 Runtime Siftome inference GEO:sample:GSM1261898:549b1b0e12fc003aa800349c80d87d9f5481503381c092974c17e39e82ba8759 low confidence lung sample_accession: GSM1261898 sample_title: 5nor source_name: Normal cells characteristics: patient id: 5; tissue source: laser micro-dissected archival FFPE tissue specimens; ti... controlled vocabulary controlled vocabulary tissue match: lung
tissue lung sample GSM1261900 Runtime Siftome inference GEO:sample:GSM1261900:2afe33a55b6cfd68a4c12b905459f3c96f59f5d69cc02363923798794f471a4a low confidence lung sample_accession: GSM1261900 sample_title: 6inv source_name: Tumor cells characteristics: patient id: 6; tissue source: laser micro-dissected archival FFPE tissue specimens; tis... controlled vocabulary controlled vocabulary tissue match: lung
tissue lung sample GSM1261901 Runtime Siftome inference GEO:sample:GSM1261901:c2dda32b315cd555b34197f722b542b79509da87f5be76654242dfe12c29b35b low confidence lung sample_accession: GSM1261901 sample_title: 6nor source_name: Normal cells characteristics: patient id: 6; tissue source: laser micro-dissected archival FFPE tissue specimens; ti... controlled vocabulary controlled vocabulary tissue match: lung

Sample Group Preview

Possible case samples

Samples currently treated as the comparison case group.

12
  • GSM1261884 1ais tumor sample Case marker detected. Tumor cells patient id: 1; tissue source: laser micro-dissected archival FFPE tissue specimens; tissue type: non-invasive adenocarcinoma in situ (ais)
  • GSM1261885 1inv tumor sample Case marker detected. Tumor cells patient id: 1; tissue source: laser micro-dissected archival FFPE tissue specimens; tissue type: invasive lung carcinoma (inv)
  • GSM1261887 2ais tumor sample Case marker detected. Tumor cells patient id: 2; tissue source: laser micro-dissected archival FFPE tissue specimens; tissue type: non-invasive adenocarcinoma in situ (ais)
  • GSM1261888 2inv tumor sample Case marker detected. Tumor cells patient id: 2; tissue source: laser micro-dissected archival FFPE tissue specimens; tissue type: invasive lung carcinoma (inv)
  • GSM1261890 3ais tumor sample Case marker detected. Tumor cells patient id: 3; tissue source: laser micro-dissected archival FFPE tissue specimens; tissue type: non-invasive adenocarcinoma in situ (ais)
  • GSM1261891 3inv tumor sample Case marker detected. Tumor cells patient id: 3; tissue source: laser micro-dissected archival FFPE tissue specimens; tissue type: invasive lung carcinoma (inv)
  • GSM1261893 4ais tumor sample Case marker detected. Tumor cells patient id: 4; tissue source: laser micro-dissected archival FFPE tissue specimens; tissue type: non-invasive adenocarcinoma in situ (ais)
  • GSM1261894 4inv tumor sample Case marker detected. Tumor cells patient id: 4; tissue source: laser micro-dissected archival FFPE tissue specimens; tissue type: invasive lung carcinoma (inv)
  • GSM1261896 5ais tumor sample Case marker detected. Tumor cells patient id: 5; tissue source: laser micro-dissected archival FFPE tissue specimens; tissue type: non-invasive adenocarcinoma in situ (ais)
  • GSM1261897 5inv tumor sample Case marker detected. Tumor cells patient id: 5; tissue source: laser micro-dissected archival FFPE tissue specimens; tissue type: invasive lung carcinoma (inv)
  • GSM1261899 6ais tumor sample Case marker detected. Tumor cells patient id: 6; tissue source: laser micro-dissected archival FFPE tissue specimens; tissue type: non-invasive adenocarcinoma in situ (ais)
  • GSM1261900 6inv tumor sample Case marker detected. Tumor cells patient id: 6; tissue source: laser micro-dissected archival FFPE tissue specimens; tissue type: invasive lung carcinoma (inv)

Possible control samples

Samples currently treated as controls or baseline.

6
  • GSM1261886 1nor normal tissue Control marker detected. Normal cells patient id: 1; tissue source: laser micro-dissected archival FFPE tissue specimens; tissue type: surrounding normal lung (nor)
  • GSM1261889 2nor normal tissue Control marker detected. Normal cells patient id: 2; tissue source: laser micro-dissected archival FFPE tissue specimens; tissue type: surrounding normal lung (nor)
  • GSM1261892 3nor normal tissue Control marker detected. Normal cells patient id: 3; tissue source: laser micro-dissected archival FFPE tissue specimens; tissue type: surrounding normal lung (nor)
  • GSM1261895 4nor normal tissue Control marker detected. Normal cells patient id: 4; tissue source: laser micro-dissected archival FFPE tissue specimens; tissue type: surrounding normal lung (nor)
  • GSM1261898 5nor normal tissue Control marker detected. Normal cells patient id: 5; tissue source: laser micro-dissected archival FFPE tissue specimens; tissue type: surrounding normal lung (nor)
  • GSM1261901 6nor normal tissue Control marker detected. Normal cells patient id: 6; tissue source: laser micro-dissected archival FFPE tissue specimens; tissue type: surrounding normal lung (nor)

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

100 pts
Clarity
100%
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 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

12 samples
  • GSM1261884 1ais Tumor cells patient id: 1; tissue source: laser micro-dissected archival FFPE tissue specimens; tissue type: non-invasive adenocarcinoma in situ (ais)
  • GSM1261885 1inv Tumor cells patient id: 1; tissue source: laser micro-dissected archival FFPE tissue specimens; tissue type: invasive lung carcinoma (inv)
  • GSM1261887 2ais Tumor cells patient id: 2; tissue source: laser micro-dissected archival FFPE tissue specimens; tissue type: non-invasive adenocarcinoma in situ (ais)
  • GSM1261888 2inv Tumor cells patient id: 2; tissue source: laser micro-dissected archival FFPE tissue specimens; tissue type: invasive lung carcinoma (inv)
  • GSM1261890 3ais Tumor cells patient id: 3; tissue source: laser micro-dissected archival FFPE tissue specimens; tissue type: non-invasive adenocarcinoma in situ (ais)
  • GSM1261891 3inv Tumor cells patient id: 3; tissue source: laser micro-dissected archival FFPE tissue specimens; tissue type: invasive lung carcinoma (inv)
  • GSM1261893 4ais Tumor cells patient id: 4; tissue source: laser micro-dissected archival FFPE tissue specimens; tissue type: non-invasive adenocarcinoma in situ (ais)
  • GSM1261894 4inv Tumor cells patient id: 4; tissue source: laser micro-dissected archival FFPE tissue specimens; tissue type: invasive lung carcinoma (inv)
  • GSM1261896 5ais Tumor cells patient id: 5; tissue source: laser micro-dissected archival FFPE tissue specimens; tissue type: non-invasive adenocarcinoma in situ (ais)
  • GSM1261897 5inv Tumor cells patient id: 5; tissue source: laser micro-dissected archival FFPE tissue specimens; tissue type: invasive lung carcinoma (inv)
  • GSM1261899 6ais Tumor cells patient id: 6; tissue source: laser micro-dissected archival FFPE tissue specimens; tissue type: non-invasive adenocarcinoma in situ (ais)
  • GSM1261900 6inv Tumor cells patient id: 6; tissue source: laser micro-dissected archival FFPE tissue specimens; tissue type: invasive lung carcinoma (inv)

normal tissue

6 samples
  • GSM1261886 1nor Normal cells patient id: 1; tissue source: laser micro-dissected archival FFPE tissue specimens; tissue type: surrounding normal lung (nor)
  • GSM1261889 2nor Normal cells patient id: 2; tissue source: laser micro-dissected archival FFPE tissue specimens; tissue type: surrounding normal lung (nor)
  • GSM1261892 3nor Normal cells patient id: 3; tissue source: laser micro-dissected archival FFPE tissue specimens; tissue type: surrounding normal lung (nor)
  • GSM1261895 4nor Normal cells patient id: 4; tissue source: laser micro-dissected archival FFPE tissue specimens; tissue type: surrounding normal lung (nor)
  • GSM1261898 5nor Normal cells patient id: 5; tissue source: laser micro-dissected archival FFPE tissue specimens; tissue type: surrounding normal lung (nor)
  • GSM1261901 6nor Normal cells patient id: 6; tissue source: laser micro-dissected archival FFPE tissue specimens; tissue type: surrounding normal lung (nor)

Score Breakdown

100%

relevance

  • Disease or condition metadata normalized.
  • 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.
100%

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 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

18 samples

Review Audit Trail

0 decisions

No review decisions have been stored for this dataset.