Siftome Phase 3L

GSE126209

Gene expression profiling in Osteosarcomas

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
2019-02-07
Last update
2020-12-04
Organization
Sun Yat-Sen University
Department
Not available
Public date
2019-09-01
Experiment types
Expression profiling by high throughput sequencing
Platforms
GPL20301 Illumina HiSeq 4000 (Homo sapiens)
Series type
Series
SubSeries
Not available
BioProject
Not available
Supplementary files
TXT: GSE126209_Osteosarcoma.expression_matrix.txt.gz; TXT: GSE126209_Osteosarcoma.expression_matrix_part2.txt.gz
Organism
Homo sapiens
Assay
bulk RNA-seq
Samples
23
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
94% DE readiness

Contrast completeness

25/25 pts

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

Minimum group size

20/20 pts

Each contrast group has at least 2 samples.

Processed data availability

20/20 pts

Processed data is marked available in the GEO index.

Sample decision clarity

15/15 pts

All samples are assigned to a case or control group.

Blocking warnings

7/10 pts

Warnings are present, but none are critical blockers.

Metadata normalization

7/10 pts

Metadata quality is usable, but still deserves review.

Blockers

No readiness blockers detected.

Next Steps

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

Analysis Preparation Checklist

5/6 ready

Group labels reviewed

Needs review

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

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

Minimum sample count met

Ready

Both groups meet the minimum of 2 samples.

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

Processed counts available

Ready

Processed data availability is marked true in the GEO index.

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

Ambiguous samples handled

Ready

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

Still scan the grouping table for biology-specific ambiguity.

Exclusion decisions recorded

Ready

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

Record any manual exclusions in the downstream analysis notes.

Source links preserved

Ready

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

Keep GEO dataset and sample links with exported metadata.

Bioinformatician Review

Standard analyst review

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

No expert-review triggers were detected by Siftome.

Why This Is Ranked Here

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

Score Components

  • relevance 50% Organism normalized. Assay type normalized.
  • comparison suitability 0% 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. Non-colorectal cancer context downgraded for colorectal tumor-vs-normal tissue ranking.
  • metadata quality 70% Sample source clarity: All samples have source metadata and clear GSE/GSM accessions. Group clarity: Rule-based grouping found both case and control samples. Disease clarity: Disease or condition metadata was not normalized. Tissue clarity: Tissue metadata was not normalized. Treatment clarity: No unclear treatment split detected in the sample metadata. Replicate clarity: No pooled sample or technical replicate flags detected. Data availability clarity: Dataset-level processed or raw data availability is explicit.
  • data availability 100% Processed data available. Raw data available.
  • overall 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 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 12 samples
  • Likely control group normal tissue 11 samples

Warnings

  • DISEASE_LABEL_UNCLEAR warning Disease or condition label could not be normalized.
  • TISSUE_TYPE_MISSING warning Tissue or cell type could not be normalized.

Intent Interpretation

  • Active intent Patient tissue tumor-vs-normal Ranks human colorectal tissue or biopsy cohorts where tumor samples can be compared with normal controls.
  • Organism expectation Homo sapiens Dataset organism is interpreted as Homo sapiens.
  • Assay expectation bulk RNA-seq Dataset assay is interpreted as bulk RNA-seq.
  • Specimen assumption patient tissue or biopsy Derived specimen/source is Tissue.
  • Control-group assumption matched normal, adjacent normal, paired normal, healthy tissue control, or otherwise normal tissue control Derived study design is Tumor vs matched normal; likely groups are tumor sample vs normal tissue.
  • Score caps Applied when matching conditions are present non-human datasets stay below the primary recommendation band, missing colorectal/colon/rectal/CRC context stays below the primary recommendation band, biofluid and model-system datasets cannot reach Recommended by default, microarray and secondary assays are capped unless explicitly enabled, or small cohorts are capped below high-confidence recommendations
  • Warning rules 2 active warnings missing or unclear control group, unclear disease context, unclear tissue source, mixed sample types, model-system markers, secondary assay context, missing processed data, or small cohort size
  • Downgrade or exclusion reason Downgraded disease context: colorectal/GI relevance is unclear. Derived from current-intent ranking reasons and warnings.

Applied Review Decisions

No active review decisions affect this ranking.

Ranking Facts

  • Recommendation Not suitable Dataset does not meet the current suitability threshold.
  • Supporting fact Tumor vs matched normal · Tissue · suitability 0%. Contributed to match or upgrade evidence.
  • Supporting fact Prioritized for patient tissue tumor-vs-normal triage. Contributed to match or upgrade evidence.
  • Supporting fact Prioritized assay: bulk RNA-seq is the active assay expectation. Contributed to match or upgrade evidence.
  • Supporting fact Downgraded disease context: colorectal/GI relevance is unclear. Contributed to match or upgrade evidence.
  • Supporting fact Processed data is available for downstream review. Contributed to match or upgrade evidence.
  • Supporting fact 2 warnings require review. Contributed to match or upgrade evidence.
  • Caution fact Disease or condition label could not be normalized. Contributed to downgrade or manual-review evidence.
  • Caution fact Tissue or cell type could not be normalized. Contributed to downgrade or manual-review evidence.
  • Caution fact 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: Tissue clarity: Tissue metadata was not normalized. Contributed to downgrade or manual-review evidence.
  • Caution fact Missing or unclear metadata: Treatment clarity: No unclear treatment split detected in the sample metadata. Contributed to downgrade or manual-review evidence.
  • Caution fact Overall score capped because comparison suitability is weak for the selected search intent. Contributed to downgrade or manual-review evidence.
  • Caution fact Overall score capped because 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
GSE126209
Sample records
23 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
GSE126209
  • 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
GSE126209
  • 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
GSE126209
  • 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: GSE126209
dataset_title: Gene expression profiling in  Osteosarcomas
organism: Homo sapiens
assay_type: bulk RNA-seq
processed_data_available: true
raw_data_available: true
submission_date: 2019-02-07
last_update_date: 2020-12-04
organization_name: Sun Yat-Sen University
department: Not available
public_date: 2019-09-01
experiment_types: Expression profiling by high throughput sequencing
platforms: GPL20301 Illumina HiSeq 4000 (Homo sapiens)
sub_series: Not available
bioproject: Not available
supplementary_files: TXT: GSE126209_Osteosarcoma.expression_matrix.txt.gz; TXT: GSE126209_Osteosarcoma.expression_matrix_part2.txt.gz
series_type: Series

Why It Matched

  • Tumor vs matched normal · Tissue · suitability 0%.
  • Prioritized for patient tissue tumor-vs-normal triage.
  • Prioritized assay: bulk RNA-seq is the active assay expectation.
  • Downgraded disease context: colorectal/GI relevance is unclear.
  • Processed data is available for downstream review.
  • 2 warnings require review.

Why It May Not Be Suitable

  • Disease or condition label could not be normalized.
  • Tissue or cell type could not be normalized.
  • 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: Tissue clarity: Tissue metadata was not normalized.
  • Missing or unclear metadata: Treatment clarity: No unclear treatment split detected in the sample metadata.
  • Overall score capped because comparison suitability is weak for the selected search intent.
  • Overall score capped because 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.
  • warning TISSUE_TYPE_MISSING Tissue or cell type could not be normalized.

Normalized Fields

30 fields
Field Value Source Origin Confidence Evidence Reason
assay_type bulk RNA-seq dataset GSE126209 Runtime Siftome inference GEO:dataset:GSE126209:6dff301faec4a877a0f843360b98d9a321ec7c23d130e45de8a11c85a70b0be0 high confidence bulk rna-seq dataset_accession: GSE126209 dataset_title: Gene expression profiling in Osteosarcomas organism: Homo sapiens assay_type: bulk RNA-seq processed_data_available: true raw_data_av... keyword match keyword match: bulk rna-seq
normal_tissue_type adjacent normal sample GSM3593745 Runtime Siftome inference GEO:sample:GSM3593745:e9069053bf05f53ffe63072166058029a697491749f80dbb6ab1dfa048ea2d15 high confidence adjacent normal sample_accession: GSM3593745 sample_title: RNA-seq of Homo sapiens: normal P1_N source_name: Osteosarcoma characteristics: tissue: adjacent normal; gender: male; age: 28; kshv i... controlled vocabulary controlled vocabulary normal tissue type match: adjacent normal
normal_tissue_type adjacent normal sample GSM3593748 Runtime Siftome inference GEO:sample:GSM3593748:587dafd02db48118eb8ae6ead7ce1145c235e263789ce794828867d1b2d169a1 high confidence adjacent normal sample_accession: GSM3593748 sample_title: RNA-seq of Homo sapiens: normal P3_N source_name: Osteosarcoma characteristics: tissue: adjacent normal; gender: male; age: 46; kshv i... controlled vocabulary controlled vocabulary normal tissue type match: adjacent normal
normal_tissue_type adjacent normal sample GSM3593750 Runtime Siftome inference GEO:sample:GSM3593750:ff52372f2d24010df2969e0737230186ff79781827950d7d5193ffa154da33cf high confidence adjacent normal sample_accession: GSM3593750 sample_title: RNA-seq of Homo sapiens: normal P5_N source_name: Osteosarcoma characteristics: tissue: adjacent normal; gender: male; age: 22; kshv i... controlled vocabulary controlled vocabulary normal tissue type match: adjacent normal
normal_tissue_type adjacent normal sample GSM3593752 Runtime Siftome inference GEO:sample:GSM3593752:c212afa85790edc0ea8bdfb2b4e15f5bc157cf956c1b0d19fe5d1e48a4ab4d40 high confidence adjacent normal sample_accession: GSM3593752 sample_title: RNA-seq of Homo sapiens: normal P9_N source_name: Osteosarcoma characteristics: tissue: adjacent normal; gender: male; age: 10; kshv i... controlled vocabulary controlled vocabulary normal tissue type match: adjacent normal
normal_tissue_type adjacent normal sample GSM3593754 Runtime Siftome inference GEO:sample:GSM3593754:36367410f609668ffdae639d77a2cd3b58f7411f87d533467dda58357a882695 high confidence adjacent normal sample_accession: GSM3593754 sample_title: RNA-seq of Homo sapiens: normal P11_N source_name: Osteosarcoma characteristics: tissue: adjacent normal; gender: female; age: 10; ksh... controlled vocabulary controlled vocabulary normal tissue type match: adjacent normal
organism Homo sapiens dataset GSE126209 Runtime Siftome inference GEO:dataset:GSE126209:6dff301faec4a877a0f843360b98d9a321ec7c23d130e45de8a11c85a70b0be0 high confidence homo sapiens dataset_accession: GSE126209 dataset_title: Gene expression profiling in Osteosarcomas organism: Homo sapiens assay_type: bulk RNA-seq processed_data_available: true raw_data_av... keyword match keyword match: homo sapiens
sample_type tumor sample sample GSM3593744 Runtime Siftome inference GEO:sample:GSM3593744:609ba5b7ead76fef473b4615d4577df39557f978a111ade9d08313bf332e6a38 low confidence tumor sample_accession: GSM3593744 sample_title: RNA-seq of Homo sapiens: tumor P1_T source_name: Osteosarcoma characteristics: tissue: tumor; gender: male; age: 28; kshv infection: p... controlled vocabulary controlled vocabulary sample type match: tumor
sample_type normal tissue sample GSM3593745 Runtime Siftome inference GEO:sample:GSM3593745:e9069053bf05f53ffe63072166058029a697491749f80dbb6ab1dfa048ea2d15 high confidence adjacent normal sample_accession: GSM3593745 sample_title: RNA-seq of Homo sapiens: normal P1_N source_name: Osteosarcoma characteristics: tissue: adjacent normal; gender: male; age: 28; kshv i... controlled vocabulary controlled vocabulary sample type match: adjacent normal
sample_type tumor sample sample GSM3593746 Runtime Siftome inference GEO:sample:GSM3593746:782e8c849cb3d4abed2dc7547dd14e77d6c8e32f6fd0f606e095bc7b5431cd93 low confidence tumor sample_accession: GSM3593746 sample_title: RNA-seq of Homo sapiens: tumor P2_T source_name: Osteosarcoma characteristics: tissue: tumor; gender: female; age: 15; kshv infection:... controlled vocabulary controlled vocabulary sample type match: tumor
sample_type tumor sample sample GSM3593747 Runtime Siftome inference GEO:sample:GSM3593747:a2bd5e871631b1f661f9ac59c1f5ba2208144de31392ef9cfb88a00618910e4a low confidence tumor sample_accession: GSM3593747 sample_title: RNA-seq of Homo sapiens: tumor P3_T source_name: Osteosarcoma characteristics: tissue: tumor; gender: male; age: 46; kshv infection: n... controlled vocabulary controlled vocabulary sample type match: tumor
sample_type normal tissue sample GSM3593748 Runtime Siftome inference GEO:sample:GSM3593748:587dafd02db48118eb8ae6ead7ce1145c235e263789ce794828867d1b2d169a1 high confidence adjacent normal sample_accession: GSM3593748 sample_title: RNA-seq of Homo sapiens: normal P3_N source_name: Osteosarcoma characteristics: tissue: adjacent normal; gender: male; age: 46; kshv i... controlled vocabulary controlled vocabulary sample type match: adjacent normal
sample_type tumor sample sample GSM3593749 Runtime Siftome inference GEO:sample:GSM3593749:7402e3a5af310b0e73f2a223ce6b52da9d668814cff22ff6db3e8af966ffc4f2 low confidence tumor sample_accession: GSM3593749 sample_title: RNA-seq of Homo sapiens: tumor P5_T source_name: Osteosarcoma characteristics: tissue: tumor; gender: male; age: 22; kshv infection: p... controlled vocabulary controlled vocabulary sample type match: tumor
sample_type normal tissue sample GSM3593750 Runtime Siftome inference GEO:sample:GSM3593750:ff52372f2d24010df2969e0737230186ff79781827950d7d5193ffa154da33cf high confidence adjacent normal sample_accession: GSM3593750 sample_title: RNA-seq of Homo sapiens: normal P5_N source_name: Osteosarcoma characteristics: tissue: adjacent normal; gender: male; age: 22; kshv i... controlled vocabulary controlled vocabulary sample type match: adjacent normal
sample_type tumor sample sample GSM3593751 Runtime Siftome inference GEO:sample:GSM3593751:29b9df6a4c2db70a9ff7c0a9e503bc434b4432ecf240e691476ea9fe920219b9 low confidence tumor sample_accession: GSM3593751 sample_title: RNA-seq of Homo sapiens: tumor P9_T source_name: Osteosarcoma characteristics: tissue: tumor; gender: male; age: 10; kshv infection: p... controlled vocabulary controlled vocabulary sample type match: tumor
sample_type normal tissue sample GSM3593752 Runtime Siftome inference GEO:sample:GSM3593752:c212afa85790edc0ea8bdfb2b4e15f5bc157cf956c1b0d19fe5d1e48a4ab4d40 high confidence adjacent normal sample_accession: GSM3593752 sample_title: RNA-seq of Homo sapiens: normal P9_N source_name: Osteosarcoma characteristics: tissue: adjacent normal; gender: male; age: 10; kshv i... controlled vocabulary controlled vocabulary sample type match: adjacent normal
sample_type tumor sample sample GSM3593753 Runtime Siftome inference GEO:sample:GSM3593753:f3791026f4d5ec505cc7575528ef961cb6dd30fb0cd30f30faadfc90efb8769e low confidence tumor sample_accession: GSM3593753 sample_title: RNA-seq of Homo sapiens: tumor P11_T source_name: Osteosarcoma characteristics: tissue: tumor; gender: female; age: 10; kshv infection... controlled vocabulary controlled vocabulary sample type match: tumor
sample_type normal tissue sample GSM3593754 Runtime Siftome inference GEO:sample:GSM3593754:36367410f609668ffdae639d77a2cd3b58f7411f87d533467dda58357a882695 high confidence adjacent normal sample_accession: GSM3593754 sample_title: RNA-seq of Homo sapiens: normal P11_N source_name: Osteosarcoma characteristics: tissue: adjacent normal; gender: female; age: 10; ksh... controlled vocabulary controlled vocabulary sample type match: adjacent normal
sample_type normal tissue sample GSM4272756 Runtime Siftome inference GEO:sample:GSM4272756:6c7692bb9ec7da1ef45d50b3c8b9f7d908b74f246d8fa14388a43475f2c68bd1 low confidence normal sample_accession: GSM4272756 sample_title: RNA-seq of Homo sapiens: normal P14_N source_name: Osteosarcoma characteristics: tissue: normal; gender: male; age: 53; kshv infection... controlled vocabulary controlled vocabulary sample type match: normal
sample_type tumor sample sample GSM4272757 Runtime Siftome inference GEO:sample:GSM4272757:7462d9a627beeb7c56841f30b7f288b49547e910d3a0894bf9c1744297ffdb17 low confidence tumor sample_accession: GSM4272757 sample_title: RNA-seq of Homo sapiens: tumor P14_T source_name: Osteosarcoma characteristics: tissue: tumor; gender: male; age: 53; kshv infection: ... controlled vocabulary controlled vocabulary sample type match: tumor
sample_type normal tissue sample GSM4272758 Runtime Siftome inference GEO:sample:GSM4272758:a34e417ea32ec6a652ef1bb97d235b989e5cf32c7018e25ab30194562b2e56b0 low confidence normal sample_accession: GSM4272758 sample_title: RNA-seq of Homo sapiens: normal P16_N source_name: Osteosarcoma characteristics: tissue: normal; gender: male; age: 39; kshv infection... controlled vocabulary controlled vocabulary sample type match: normal
sample_type tumor sample sample GSM4272759 Runtime Siftome inference GEO:sample:GSM4272759:6b2fbddd6f7ef22956aadbb540b3d63b88803beafac2133eadecf257eca8604f low confidence tumor sample_accession: GSM4272759 sample_title: RNA-seq of Homo sapiens: tumor P16_T source_name: Osteosarcoma characteristics: tissue: tumor; gender: male; age: 39; kshv infection: ... controlled vocabulary controlled vocabulary sample type match: tumor
sample_type normal tissue sample GSM4272760 Runtime Siftome inference GEO:sample:GSM4272760:fc4e200683d9b591468d9e7cf1a248d2bba9064bad8ea89620cc5e8684180d04 low confidence normal sample_accession: GSM4272760 sample_title: RNA-seq of Homo sapiens: normal P120_N source_name: Osteosarcoma characteristics: tissue: normal; gender: male; age: 15; kshv infectio... controlled vocabulary controlled vocabulary sample type match: normal
sample_type tumor sample sample GSM4272761 Runtime Siftome inference GEO:sample:GSM4272761:415cb88dcf87dbb588162e77558273dbeb04764f0817d8b7cfcfc5bccc945c14 low confidence tumor sample_accession: GSM4272761 sample_title: RNA-seq of Homo sapiens: tumor P20_T source_name: Osteosarcoma characteristics: tissue: tumor; gender: male; age: 15; kshv infection: ... controlled vocabulary controlled vocabulary sample type match: tumor
sample_type normal tissue sample GSM4272762 Runtime Siftome inference GEO:sample:GSM4272762:f24f1fc9ae94ab9ff99a2aee2c6b8e470ee023838b0af1f38be80f8e6d09e309 low confidence normal sample_accession: GSM4272762 sample_title: RNA-seq of Homo sapiens: normal P21_N source_name: Osteosarcoma characteristics: tissue: normal; gender: male; age: 15; kshv infection... controlled vocabulary controlled vocabulary sample type match: normal
sample_type tumor sample sample GSM4272763 Runtime Siftome inference GEO:sample:GSM4272763:125a4bf56c56c5dbb6f47430eac0ac0322884f77951d091ea8fda72fc56354e5 low confidence tumor sample_accession: GSM4272763 sample_title: RNA-seq of Homo sapiens: tumor P21_T source_name: Osteosarcoma characteristics: tissue: tumor; gender: male; age: 15; kshv infection: ... controlled vocabulary controlled vocabulary sample type match: tumor
sample_type normal tissue sample GSM4955769 Runtime Siftome inference GEO:sample:GSM4955769:8e7662d434f489136770d4bb70c6681c7ede03cfa9dd7ff37dc47f4b60e7b163 low confidence normal sample_accession: GSM4955769 sample_title: RNA-seq of Homo sapiens: normal H2_Normal source_name: Osteosarcoma characteristics: tissue: normal; gender: female; age: 5; kshv infe... controlled vocabulary controlled vocabulary sample type match: normal
sample_type tumor sample sample GSM4955770 Runtime Siftome inference GEO:sample:GSM4955770:5ff438cd1783c29a91de82c91cc5118f8e22ad1fb0d7fb744d51f14033c49075 low confidence tumor sample_accession: GSM4955770 sample_title: RNA-seq of Homo sapiens: tumor H2_Tumor source_name: Osteosarcoma characteristics: tissue: tumor; gender: female; age: 5; kshv infecti... controlled vocabulary controlled vocabulary sample type match: tumor
sample_type normal tissue sample GSM4955771 Runtime Siftome inference GEO:sample:GSM4955771:98846a5b92bd37a24e105a29bcdeb6e5b04ed213548d280c8fed264d95c2d47f low confidence normal sample_accession: GSM4955771 sample_title: RNA-seq of Homo sapiens: normal H9_Normal source_name: Osteosarcoma characteristics: tissue: normal; gender: male; age: 45; kshv infec... controlled vocabulary controlled vocabulary sample type match: normal
sample_type tumor sample sample GSM4955772 Runtime Siftome inference GEO:sample:GSM4955772:f5b8f13ec31c62e75f825e76664b1bfc169d682dcde742ce7e258c8a0d6af48b low confidence tumor sample_accession: GSM4955772 sample_title: RNA-seq of Homo sapiens: tumor H9_Tumor source_name: Osteosarcoma characteristics: tissue: tumor; gender: male; age: 45; kshv infectio... controlled vocabulary controlled vocabulary sample type match: tumor

Sample Group Preview

Possible case samples

Samples currently treated as the comparison case group.

12
  • GSM3593744 RNA-seq of Homo sapiens: tumor P1_T tumor sample Case marker detected. Osteosarcoma tissue: tumor; gender: male; age: 28; kshv infection: positive
  • GSM3593746 RNA-seq of Homo sapiens: tumor P2_T tumor sample Case marker detected. Osteosarcoma tissue: tumor; gender: female; age: 15; kshv infection: negative
  • GSM3593747 RNA-seq of Homo sapiens: tumor P3_T tumor sample Case marker detected. Osteosarcoma tissue: tumor; gender: male; age: 46; kshv infection: negative
  • GSM3593749 RNA-seq of Homo sapiens: tumor P5_T tumor sample Case marker detected. Osteosarcoma tissue: tumor; gender: male; age: 22; kshv infection: positive
  • GSM3593751 RNA-seq of Homo sapiens: tumor P9_T tumor sample Case marker detected. Osteosarcoma tissue: tumor; gender: male; age: 10; kshv infection: positive
  • GSM3593753 RNA-seq of Homo sapiens: tumor P11_T tumor sample Case marker detected. Osteosarcoma tissue: tumor; gender: female; age: 10; kshv infection: positive
  • GSM4272757 RNA-seq of Homo sapiens: tumor P14_T tumor sample Case marker detected. Osteosarcoma tissue: tumor; gender: male; age: 53; kshv infection: negative
  • GSM4272759 RNA-seq of Homo sapiens: tumor P16_T tumor sample Case marker detected. Osteosarcoma tissue: tumor; gender: male; age: 39; kshv infection: negative
  • GSM4272761 RNA-seq of Homo sapiens: tumor P20_T tumor sample Case marker detected. Osteosarcoma tissue: tumor; gender: male; age: 15; kshv infection: positive
  • GSM4272763 RNA-seq of Homo sapiens: tumor P21_T tumor sample Case marker detected. Osteosarcoma tissue: tumor; gender: male; age: 15; kshv infection: positive
  • GSM4955770 RNA-seq of Homo sapiens: tumor H2_Tumor tumor sample Case marker detected. Osteosarcoma tissue: tumor; gender: female; age: 5; kshv infection: positive
  • GSM4955772 RNA-seq of Homo sapiens: tumor H9_Tumor tumor sample Case marker detected. Osteosarcoma tissue: tumor; gender: male; age: 45; kshv infection: positive

Possible control samples

Samples currently treated as controls or baseline.

11
  • GSM3593745 RNA-seq of Homo sapiens: normal P1_N normal tissue Control marker detected. Osteosarcoma tissue: adjacent normal; gender: male; age: 28; kshv infection: positive
  • GSM3593748 RNA-seq of Homo sapiens: normal P3_N normal tissue Control marker detected. Osteosarcoma tissue: adjacent normal; gender: male; age: 46; kshv infection: negative
  • GSM3593750 RNA-seq of Homo sapiens: normal P5_N normal tissue Control marker detected. Osteosarcoma tissue: adjacent normal; gender: male; age: 22; kshv infection: negative
  • GSM3593752 RNA-seq of Homo sapiens: normal P9_N normal tissue Control marker detected. Osteosarcoma tissue: adjacent normal; gender: male; age: 10; kshv infection: negative
  • GSM3593754 RNA-seq of Homo sapiens: normal P11_N normal tissue Control marker detected. Osteosarcoma tissue: adjacent normal; gender: female; age: 10; kshv infection: negative
  • GSM4272756 RNA-seq of Homo sapiens: normal P14_N normal tissue Control marker detected. Osteosarcoma tissue: normal; gender: male; age: 53; kshv infection: negative
  • GSM4272758 RNA-seq of Homo sapiens: normal P16_N normal tissue Control marker detected. Osteosarcoma tissue: normal; gender: male; age: 39; kshv infection: negative
  • GSM4272760 RNA-seq of Homo sapiens: normal P120_N normal tissue Control marker detected. Osteosarcoma tissue: normal; gender: male; age: 15; kshv infection: negative
  • GSM4272762 RNA-seq of Homo sapiens: normal P21_N normal tissue Control marker detected. Osteosarcoma tissue: normal; gender: male; age: 15; kshv infection: negative
  • GSM4955769 RNA-seq of Homo sapiens: normal H2_Normal normal tissue Control marker detected. Osteosarcoma tissue: normal; gender: female; age: 5; kshv infection: negative
  • GSM4955771 RNA-seq of Homo sapiens: normal H9_Normal normal tissue Control marker detected. Osteosarcoma tissue: normal; gender: male; age: 45; kshv infection: negative

Unassigned samples

Samples with no explicit case or control marker.

0

No samples

Excluded samples

Samples excluded from grouping by hard exclusion rules.

0

No samples

Ambiguous samples

Samples that need manual review before trusting grouping.

0

No samples

Metadata Quality Components

Persisted metadata quality

70 pts
Clarity
70%
Weight
100 pts

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

Detected Sample Groups

tumor sample

12 samples
  • GSM3593744 RNA-seq of Homo sapiens: tumor P1_T Osteosarcoma tissue: tumor; gender: male; age: 28; kshv infection: positive
  • GSM3593746 RNA-seq of Homo sapiens: tumor P2_T Osteosarcoma tissue: tumor; gender: female; age: 15; kshv infection: negative
  • GSM3593747 RNA-seq of Homo sapiens: tumor P3_T Osteosarcoma tissue: tumor; gender: male; age: 46; kshv infection: negative
  • GSM3593749 RNA-seq of Homo sapiens: tumor P5_T Osteosarcoma tissue: tumor; gender: male; age: 22; kshv infection: positive
  • GSM3593751 RNA-seq of Homo sapiens: tumor P9_T Osteosarcoma tissue: tumor; gender: male; age: 10; kshv infection: positive
  • GSM3593753 RNA-seq of Homo sapiens: tumor P11_T Osteosarcoma tissue: tumor; gender: female; age: 10; kshv infection: positive
  • GSM4272757 RNA-seq of Homo sapiens: tumor P14_T Osteosarcoma tissue: tumor; gender: male; age: 53; kshv infection: negative
  • GSM4272759 RNA-seq of Homo sapiens: tumor P16_T Osteosarcoma tissue: tumor; gender: male; age: 39; kshv infection: negative
  • GSM4272761 RNA-seq of Homo sapiens: tumor P20_T Osteosarcoma tissue: tumor; gender: male; age: 15; kshv infection: positive
  • GSM4272763 RNA-seq of Homo sapiens: tumor P21_T Osteosarcoma tissue: tumor; gender: male; age: 15; kshv infection: positive
  • GSM4955770 RNA-seq of Homo sapiens: tumor H2_Tumor Osteosarcoma tissue: tumor; gender: female; age: 5; kshv infection: positive
  • GSM4955772 RNA-seq of Homo sapiens: tumor H9_Tumor Osteosarcoma tissue: tumor; gender: male; age: 45; kshv infection: positive

normal tissue

11 samples
  • GSM3593745 RNA-seq of Homo sapiens: normal P1_N Osteosarcoma tissue: adjacent normal; gender: male; age: 28; kshv infection: positive
  • GSM3593748 RNA-seq of Homo sapiens: normal P3_N Osteosarcoma tissue: adjacent normal; gender: male; age: 46; kshv infection: negative
  • GSM3593750 RNA-seq of Homo sapiens: normal P5_N Osteosarcoma tissue: adjacent normal; gender: male; age: 22; kshv infection: negative
  • GSM3593752 RNA-seq of Homo sapiens: normal P9_N Osteosarcoma tissue: adjacent normal; gender: male; age: 10; kshv infection: negative
  • GSM3593754 RNA-seq of Homo sapiens: normal P11_N Osteosarcoma tissue: adjacent normal; gender: female; age: 10; kshv infection: negative
  • GSM4272756 RNA-seq of Homo sapiens: normal P14_N Osteosarcoma tissue: normal; gender: male; age: 53; kshv infection: negative
  • GSM4272758 RNA-seq of Homo sapiens: normal P16_N Osteosarcoma tissue: normal; gender: male; age: 39; kshv infection: negative
  • GSM4272760 RNA-seq of Homo sapiens: normal P120_N Osteosarcoma tissue: normal; gender: male; age: 15; kshv infection: negative
  • GSM4272762 RNA-seq of Homo sapiens: normal P21_N Osteosarcoma tissue: normal; gender: male; age: 15; kshv infection: negative
  • GSM4955769 RNA-seq of Homo sapiens: normal H2_Normal Osteosarcoma tissue: normal; gender: female; age: 5; kshv infection: negative
  • GSM4955771 RNA-seq of Homo sapiens: normal H9_Normal Osteosarcoma tissue: normal; gender: male; age: 45; kshv infection: negative

Score Breakdown

50%

relevance

  • Organism normalized.
  • Assay type normalized.
0%

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.
  • Non-colorectal cancer context downgraded for colorectal tumor-vs-normal tissue ranking.
70%

metadata quality

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

data availability

  • Processed data available.
  • Raw data available.
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

23 samples

Review Audit Trail

0 decisions

No review decisions have been stored for this dataset.