Siftome Phase 3L

GSE228376

Gene expression profiling study to identify molecular markers exhibiting distinct characteristics of Pseudomyxoma Peritonei [Fresh Frozen]

Exploratory only Dataset can inform exploration but is not strong enough for primary analysis.
Sample grouping CSV Contrast CSV DESeq2 metadata CSV R handoff notes Handoff report Download instructions Open GEO dataset
Source
GEO
Search intent
Patient tissue tumor-vs-normal
Intent behavior
search-intent-behavior-v1
Submission date
2023-03-28
Last update
2025-02-24
Organization
Korea Research Institute of Bioscience and Biotechnology
Department
Not available
Public date
2024-10-09
Experiment types
Expression profiling by high throughput sequencing
Platforms
GPL24676 Illumina NovaSeq 6000 (Homo sapiens)
Series type
Series
SubSeries
Not available
BioProject
PRJNA949593
Supplementary files
XLSX: GSE228376_PMP_fresh_sample_log2CPM.xlsx; XLSX: GSE228376_Pseudomyxoma_Peritonei_Fresh_Frozen_clinical_information.xlsx; TAR: GSE228376_RAW.tar
Organism
Homo sapiens
Assay
bulk RNA-seq
Samples
19
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
94% DE readiness

Contrast completeness

25/25 pts

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

Minimum group size

20/20 pts

Each contrast group has at least 2 samples.

Processed data availability

20/20 pts

Processed data is marked available in the GEO index.

Sample decision clarity

15/15 pts

All samples are assigned to a case or control group.

Blocking warnings

7/10 pts

Warnings are present, but none are critical blockers.

Metadata normalization

7/10 pts

Metadata quality is usable, but still deserves review.

Blockers

No readiness blockers detected.

Next Steps

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

Analysis Preparation Checklist

5/6 ready

Group labels reviewed

Needs review

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

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

Minimum sample count met

Ready

Both groups meet the minimum of 2 samples.

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

Processed counts available

Ready

Processed data availability is marked true in the GEO index.

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

Ambiguous samples handled

Ready

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

Still scan the grouping table for biology-specific ambiguity.

Exclusion decisions recorded

Ready

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

Record any manual exclusions in the downstream analysis notes.

Source links preserved

Ready

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

Keep GEO dataset and sample links with exported metadata.

Bioinformatician Review

Standard analyst review

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

No expert-review triggers were detected by Siftome.

Why This Is Ranked Here

Patient tissue tumor-vs-normal
Exploratory only Dataset can inform exploration but is not strong enough for primary analysis.

Score Components

  • relevance 50% Organism normalized. Assay type normalized.
  • comparison suitability 5% 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. Missing colorectal disease context downgraded for tumor-vs-normal tissue ranking.
  • metadata quality 70% Sample source clarity: All samples have source metadata and clear GSE/GSM accessions. Group clarity: Rule-based grouping found both case and control samples. Disease clarity: Disease or condition metadata was not normalized. Tissue clarity: Tissue metadata was not normalized. Treatment clarity: No unclear treatment split detected in the sample metadata. Replicate clarity: No pooled sample or technical replicate flags detected. Data availability clarity: Dataset-level processed or raw data availability is explicit.
  • data availability 100% Processed data available. Raw data available.
  • overall 45% Weighted score: 30% relevance, 30% comparison suitability, 25% metadata quality, 15% data availability. Overall score capped because comparison suitability is weak for the selected search intent. Overall score capped because colorectal/CRC disease context is not explicit.

Derived Classifications

  • Organism Homo sapiens Organism remains rule-derived: Homo sapiens.
  • Assay bulk RNA-seq Assay remains rule-derived: bulk RNA-seq.
  • Study design Tumor vs 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 7 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 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 2 active warnings missing or unclear control group, unclear disease context, unclear tissue source, mixed sample types, model-system markers, secondary assay context, missing processed data, or small cohort size
  • Downgrade or exclusion reason Downgraded disease context: colorectal/GI relevance is unclear. Derived from current-intent ranking reasons and warnings.

Applied Review Decisions

No active review decisions affect this ranking.

Ranking Facts

  • Recommendation Exploratory only Dataset can inform exploration but is not strong enough for primary analysis.
  • Supporting fact Tumor vs unmatched normal · Tissue · suitability 5%. Contributed to match or upgrade evidence.
  • Supporting fact Prioritized assay: bulk RNA-seq is the active assay expectation. Contributed to match or upgrade evidence.
  • Supporting fact Downgraded disease context: colorectal/GI relevance is unclear. Contributed to match or upgrade evidence.
  • Supporting fact Processed data is available for downstream review. Contributed to match or upgrade evidence.
  • Supporting fact 2 warnings require review. Contributed to match or upgrade evidence.
  • Caution fact Disease or condition label could not be normalized. Contributed to downgrade or manual-review evidence.
  • Caution fact Tissue or cell type could not be normalized. Contributed to downgrade or manual-review evidence.
  • Caution fact Missing colorectal disease context downgraded for tumor-vs-normal tissue ranking. Contributed to downgrade or manual-review evidence.
  • Caution fact Missing or unclear metadata: Missing colorectal disease context downgraded for tumor-vs-normal tissue ranking. Contributed to downgrade or manual-review evidence.
  • Caution fact Missing or unclear metadata: Disease clarity: Disease or condition metadata was not normalized. Contributed to downgrade or manual-review evidence.
  • Caution fact Missing or unclear metadata: Tissue clarity: Tissue metadata was not normalized. Contributed to downgrade or manual-review evidence.
  • Caution fact Missing or unclear metadata: Treatment clarity: No unclear treatment split detected in the sample metadata. Contributed to downgrade or manual-review evidence.
  • Caution fact Overall score capped because comparison suitability is weak for the selected search intent. Contributed to downgrade or manual-review evidence.
  • Caution fact Overall score capped because colorectal/CRC disease context is not explicit. Contributed to downgrade or manual-review evidence.
  • Caution fact Downgraded disease context: colorectal/GI relevance is unclear. Contributed to downgrade or manual-review evidence.
  • Caution fact Missing or unclear metadata: Downgraded disease context: colorectal/GI relevance is unclear. Contributed to downgrade or manual-review evidence.
  • Caution fact Comparison suitability score is below the Phase 1 recommended threshold. Contributed to downgrade or manual-review evidence.

Manual Corrections

0 active

Source Evidence

4 sources

GEO

Primary source

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

Dataset accession
GSE228376
Sample records
19 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
GSE228376
  • 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
GSE228376
  • 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
GSE228376
  • 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: GSE228376
dataset_title: Gene expression profiling study to identify molecular markers exhibiting distinct characteristics of Pseudomyxoma Peritonei [Fresh Frozen]
organism: Homo sapiens
assay_type: bulk RNA-seq
processed_data_available: true
raw_data_available: true
submission_date: 2023-03-28
last_update_date: 2025-02-24
organization_name: Korea Research Institute of Bioscience and Biotechnology
department: Not available
public_date: 2024-10-09
experiment_types: Expression profiling by high throughput sequencing
platforms: GPL24676 Illumina NovaSeq 6000 (Homo sapiens)
sub_series: Not available
bioproject: PRJNA949593
supplementary_files: XLSX: GSE228376_PMP_fresh_sample_log2CPM.xlsx; XLSX: GSE228376_Pseudomyxoma_Peritonei_Fresh_Frozen_clinical_information.xlsx; TAR: GSE228376_RAW.tar
series_type: Series

Why It Matched

  • Tumor vs unmatched normal · Tissue · suitability 5%.
  • Prioritized assay: bulk RNA-seq is the active assay expectation.
  • Downgraded disease context: colorectal/GI relevance is unclear.
  • Processed data is available for downstream review.
  • 2 warnings require review.

Why It May Not Be Suitable

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

Warnings

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

Normalized Fields

21 fields
Field Value Source Origin Confidence Evidence Reason
assay_type bulk RNA-seq dataset GSE228376 Runtime Siftome inference GEO:dataset:GSE228376:0115dff9c530686539788ffa2767fdaaedd41820eaf0ba55bb3e38cadd5cf848 high confidence bulk rna-seq dataset_accession: GSE228376 dataset_title: Gene expression profiling study to identify molecular markers exhibiting distinct characteristics of Pseudomyxoma Peritonei [Fresh Fr... keyword match keyword match: bulk rna-seq
organism Homo sapiens dataset GSE228376 Runtime Siftome inference GEO:dataset:GSE228376:0115dff9c530686539788ffa2767fdaaedd41820eaf0ba55bb3e38cadd5cf848 high confidence homo sapiens dataset_accession: GSE228376 dataset_title: Gene expression profiling study to identify molecular markers exhibiting distinct characteristics of Pseudomyxoma Peritonei [Fresh Fr... keyword match keyword match: homo sapiens
sample_type normal tissue sample GSM7119880 Runtime Siftome inference GEO:sample:GSM7119880:567b14f4533b46dbe46cb2aa1ab976e22f3a70fb04fa426a8c3e0b2112ec2ec8 low confidence normal sample_accession: GSM7119880 sample_title: PMP-1N_RNA-seq source_name: Normal characteristics: histologic type: Normal; source of healthy tissue: peritoneum PMP-1N_RNA-seq controlled vocabulary controlled vocabulary sample type match: normal
sample_type normal tissue sample GSM7119881 Runtime Siftome inference GEO:sample:GSM7119881:15cc0c16957161e4692a88832561a67edcc40f03726e62a71afe2522c428ef7b low confidence normal sample_accession: GSM7119881 sample_title: PMP-3N_RNA-seq source_name: Normal characteristics: histologic type: Normal; source of healthy tissue: peritoneum PMP-3N_RNA-seq controlled vocabulary controlled vocabulary sample type match: normal
sample_type normal tissue sample GSM7119882 Runtime Siftome inference GEO:sample:GSM7119882:20ca13aa8e54e3a304c791818e7ced382ff12e8c449b6668a1ae5bab002eb78b low confidence normal sample_accession: GSM7119882 sample_title: PMP-4N_RNA-seq source_name: Normal characteristics: histologic type: Normal; source of healthy tissue: peritoneum PMP-4N_RNA-seq controlled vocabulary controlled vocabulary sample type match: normal
sample_type normal tissue sample GSM7119883 Runtime Siftome inference GEO:sample:GSM7119883:283a30320f2fe7b7d46a83af4128a819ae731c3ba85ee0a9a1edcf4cadac2fa6 low confidence normal sample_accession: GSM7119883 sample_title: PMP-5N_RNA-seq source_name: Normal characteristics: histologic type: Normal; source of healthy tissue: peritoneum PMP-5N_RNA-seq controlled vocabulary controlled vocabulary sample type match: normal
sample_type normal tissue sample GSM7119884 Runtime Siftome inference GEO:sample:GSM7119884:69a633e398826c878fd1db2ceaf3404dce7fc572e3148bf6d970e86c30aa15a0 low confidence normal sample_accession: GSM7119884 sample_title: PMP-6N_RNA-seq source_name: Normal characteristics: histologic type: Normal; source of healthy tissue: peritoneum PMP-6N_RNA-seq controlled vocabulary controlled vocabulary sample type match: normal
sample_type normal tissue sample GSM7119885 Runtime Siftome inference GEO:sample:GSM7119885:17c709a860498179c6fcedcc1c5b01e7d13d856b12f5b61865444e9f63dc4f9f low confidence normal sample_accession: GSM7119885 sample_title: PMP-7N_RNA-seq source_name: Normal characteristics: histologic type: Normal; source of healthy tissue: peritoneum PMP-7N_RNA-seq controlled vocabulary controlled vocabulary sample type match: normal
sample_type normal tissue sample GSM7119886 Runtime Siftome inference GEO:sample:GSM7119886:c7ab225b49fe7dc568b207d3149552d47497c8e55f04a8702fc8cdfe299ff53c low confidence normal sample_accession: GSM7119886 sample_title: PMP-9N_RNA-seq source_name: Normal characteristics: histologic type: Normal; source of healthy tissue: peritoneum PMP-9N_RNA-seq controlled vocabulary controlled vocabulary sample type match: normal
sample_type tumor sample sample GSM7119887 Runtime Siftome inference GEO:sample:GSM7119887:73c85a067f20e61783119216869b4bb7571f23ce8b044649f2539be3ca1d7542 low confidence tumor sample_accession: GSM7119887 sample_title: PMP-1_RNA-seq source_name: Pseudomyxoma Peritonei characteristics: histologic type: Pseudomyxoma Peritonei; source of tumor tissue: Pe... controlled vocabulary controlled vocabulary sample type match: tumor
sample_type tumor sample sample GSM7119888 Runtime Siftome inference GEO:sample:GSM7119888:e0b97c4fd49af9a2ba6143473b465043456405372020e594721941b4685ede72 low confidence tumor sample_accession: GSM7119888 sample_title: PMP-2_RNA-seq source_name: Pseudomyxoma Peritonei characteristics: histologic type: Pseudomyxoma Peritonei; source of tumor tissue: Pe... controlled vocabulary controlled vocabulary sample type match: tumor
sample_type tumor sample sample GSM7119889 Runtime Siftome inference GEO:sample:GSM7119889:c33365f34bc904fd3b27a08a72ccce7284fd7e406d836b17f08d5661d07ede81 low confidence tumor sample_accession: GSM7119889 sample_title: PMP-3_RNA-seq source_name: Pseudomyxoma Peritonei characteristics: histologic type: Pseudomyxoma Peritonei; source of tumor tissue: Pe... controlled vocabulary controlled vocabulary sample type match: tumor
sample_type tumor sample sample GSM7119890 Runtime Siftome inference GEO:sample:GSM7119890:349d96eb4f7e56a7c22532155c266571deed5a901faa272a2dc4a362eb817499 low confidence tumor sample_accession: GSM7119890 sample_title: PMP-4_RNA-seq source_name: Pseudomyxoma Peritonei characteristics: histologic type: Pseudomyxoma Peritonei; source of tumor tissue: Pe... controlled vocabulary controlled vocabulary sample type match: tumor
sample_type tumor sample sample GSM7119891 Runtime Siftome inference GEO:sample:GSM7119891:ea1c09813b54ab426acb1af474d3f5814e6bd7904fbebe0f47932c1f03cf96e6 low confidence tumor sample_accession: GSM7119891 sample_title: PMP-5_RNA-seq source_name: Pseudomyxoma Peritonei characteristics: histologic type: Pseudomyxoma Peritonei; source of tumor tissue: Pe... controlled vocabulary controlled vocabulary sample type match: tumor
sample_type tumor sample sample GSM7119892 Runtime Siftome inference GEO:sample:GSM7119892:8e5acc943cff1c1df38d91d6401f9929d0cf07e08b5f57da5e072f33917c10a8 low confidence tumor sample_accession: GSM7119892 sample_title: PMP-6_RNA-seq source_name: Pseudomyxoma Peritonei characteristics: histologic type: Pseudomyxoma Peritonei; source of tumor tissue: Pe... controlled vocabulary controlled vocabulary sample type match: tumor
sample_type tumor sample sample GSM7119893 Runtime Siftome inference GEO:sample:GSM7119893:b3461cf35d50b4aeac6aff3862e203050ca5bd5ad3a96c7194be8a6f8c4b9800 low confidence tumor sample_accession: GSM7119893 sample_title: PMP-7_RNA-seq source_name: Pseudomyxoma Peritonei characteristics: histologic type: Pseudomyxoma Peritonei; source of tumor tissue: Pe... controlled vocabulary controlled vocabulary sample type match: tumor
sample_type tumor sample sample GSM7119894 Runtime Siftome inference GEO:sample:GSM7119894:e8467b7548a09e62c75fa6261becef7170793429c81124d3934492409bb2d73c low confidence tumor sample_accession: GSM7119894 sample_title: PMP-8_RNA-seq source_name: Pseudomyxoma Peritonei characteristics: histologic type: Pseudomyxoma Peritonei; source of tumor tissue: Pe... controlled vocabulary controlled vocabulary sample type match: tumor
sample_type tumor sample sample GSM7119895 Runtime Siftome inference GEO:sample:GSM7119895:d613e5afce10716e1f4d246ae7c934d99342ac4858ffde397e9684b4e741bd3a low confidence tumor sample_accession: GSM7119895 sample_title: PMP-9_RNA-seq source_name: Pseudomyxoma Peritonei characteristics: histologic type: Pseudomyxoma Peritonei; source of tumor tissue: Pe... controlled vocabulary controlled vocabulary sample type match: tumor
sample_type tumor sample sample GSM7119896 Runtime Siftome inference GEO:sample:GSM7119896:0d5371b0b42afb75459be01a2b3150778f51913e11606842bea3a30b2369cc12 low confidence tumor sample_accession: GSM7119896 sample_title: PMP-10_RNA-seq source_name: Pseudomyxoma Peritonei characteristics: histologic type: Pseudomyxoma Peritonei; source of tumor tissue: P... controlled vocabulary controlled vocabulary sample type match: tumor
sample_type tumor sample sample GSM7119897 Runtime Siftome inference GEO:sample:GSM7119897:66f9ad953e96c3cc1d6f32e44060c5293feacf3ce17dc9a1d22eab10177c2985 low confidence tumor sample_accession: GSM7119897 sample_title: PMP-11_RNA-seq source_name: Pseudomyxoma Peritonei characteristics: histologic type: Pseudomyxoma Peritonei; source of tumor tissue: P... controlled vocabulary controlled vocabulary sample type match: tumor
sample_type tumor sample sample GSM7119898 Runtime Siftome inference GEO:sample:GSM7119898:3d0e339598c8df1328b4db519b2ed88ee67105a42bd30710780697758c864d3d low confidence tumor sample_accession: GSM7119898 sample_title: PMP-12_RNA-seq source_name: Pseudomyxoma Peritonei characteristics: histologic type: Pseudomyxoma Peritonei; source of tumor tissue: P... controlled vocabulary controlled vocabulary sample type match: tumor

Sample Group Preview

Possible case samples

Samples currently treated as the comparison case group.

12
  • GSM7119887 PMP-1_RNA-seq tumor sample Case marker detected. Pseudomyxoma Peritonei histologic type: Pseudomyxoma Peritonei; source of tumor tissue: Peritoneal implant
  • GSM7119888 PMP-2_RNA-seq tumor sample Case marker detected. Pseudomyxoma Peritonei histologic type: Pseudomyxoma Peritonei; source of tumor tissue: Peritoneal implant
  • GSM7119889 PMP-3_RNA-seq tumor sample Case marker detected. Pseudomyxoma Peritonei histologic type: Pseudomyxoma Peritonei; source of tumor tissue: Peritoneal implant
  • GSM7119890 PMP-4_RNA-seq tumor sample Case marker detected. Pseudomyxoma Peritonei histologic type: Pseudomyxoma Peritonei; source of tumor tissue: Peritoneal implant
  • GSM7119891 PMP-5_RNA-seq tumor sample Case marker detected. Pseudomyxoma Peritonei histologic type: Pseudomyxoma Peritonei; source of tumor tissue: Peritoneal implant
  • GSM7119892 PMP-6_RNA-seq tumor sample Case marker detected. Pseudomyxoma Peritonei histologic type: Pseudomyxoma Peritonei; source of tumor tissue: Peritoneal implant
  • GSM7119893 PMP-7_RNA-seq tumor sample Case marker detected. Pseudomyxoma Peritonei histologic type: Pseudomyxoma Peritonei; source of tumor tissue: Peritoneal implant
  • GSM7119894 PMP-8_RNA-seq tumor sample Case marker detected. Pseudomyxoma Peritonei histologic type: Pseudomyxoma Peritonei; source of tumor tissue: Peritoneal implant
  • GSM7119895 PMP-9_RNA-seq tumor sample Case marker detected. Pseudomyxoma Peritonei histologic type: Pseudomyxoma Peritonei; source of tumor tissue: Peritoneal implant
  • GSM7119896 PMP-10_RNA-seq tumor sample Case marker detected. Pseudomyxoma Peritonei histologic type: Pseudomyxoma Peritonei; source of tumor tissue: Peritoneal implant
  • GSM7119897 PMP-11_RNA-seq tumor sample Case marker detected. Pseudomyxoma Peritonei histologic type: Pseudomyxoma Peritonei; source of tumor tissue: Peritoneal implant
  • GSM7119898 PMP-12_RNA-seq tumor sample Case marker detected. Pseudomyxoma Peritonei histologic type: Pseudomyxoma Peritonei; source of tumor tissue: Peritoneal implant

Possible control samples

Samples currently treated as controls or baseline.

7
  • GSM7119880 PMP-1N_RNA-seq normal tissue Control marker detected. Normal histologic type: Normal; source of healthy tissue: peritoneum
  • GSM7119881 PMP-3N_RNA-seq normal tissue Control marker detected. Normal histologic type: Normal; source of healthy tissue: peritoneum
  • GSM7119882 PMP-4N_RNA-seq normal tissue Control marker detected. Normal histologic type: Normal; source of healthy tissue: peritoneum
  • GSM7119883 PMP-5N_RNA-seq normal tissue Control marker detected. Normal histologic type: Normal; source of healthy tissue: peritoneum
  • GSM7119884 PMP-6N_RNA-seq normal tissue Control marker detected. Normal histologic type: Normal; source of healthy tissue: peritoneum
  • GSM7119885 PMP-7N_RNA-seq normal tissue Control marker detected. Normal histologic type: Normal; source of healthy tissue: peritoneum
  • GSM7119886 PMP-9N_RNA-seq normal tissue Control marker detected. Normal histologic type: Normal; source of healthy tissue: peritoneum

Unassigned samples

Samples with no explicit case or control marker.

0

No samples

Excluded samples

Samples excluded from grouping by hard exclusion rules.

0

No samples

Ambiguous samples

Samples that need manual review before trusting grouping.

0

No samples

Metadata Quality Components

Persisted metadata quality

70 pts
Clarity
70%
Weight
100 pts

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

Detected Sample Groups

normal tissue

7 samples
  • GSM7119880 PMP-1N_RNA-seq Normal histologic type: Normal; source of healthy tissue: peritoneum
  • GSM7119881 PMP-3N_RNA-seq Normal histologic type: Normal; source of healthy tissue: peritoneum
  • GSM7119882 PMP-4N_RNA-seq Normal histologic type: Normal; source of healthy tissue: peritoneum
  • GSM7119883 PMP-5N_RNA-seq Normal histologic type: Normal; source of healthy tissue: peritoneum
  • GSM7119884 PMP-6N_RNA-seq Normal histologic type: Normal; source of healthy tissue: peritoneum
  • GSM7119885 PMP-7N_RNA-seq Normal histologic type: Normal; source of healthy tissue: peritoneum
  • GSM7119886 PMP-9N_RNA-seq Normal histologic type: Normal; source of healthy tissue: peritoneum

tumor sample

12 samples
  • GSM7119887 PMP-1_RNA-seq Pseudomyxoma Peritonei histologic type: Pseudomyxoma Peritonei; source of tumor tissue: Peritoneal implant
  • GSM7119888 PMP-2_RNA-seq Pseudomyxoma Peritonei histologic type: Pseudomyxoma Peritonei; source of tumor tissue: Peritoneal implant
  • GSM7119889 PMP-3_RNA-seq Pseudomyxoma Peritonei histologic type: Pseudomyxoma Peritonei; source of tumor tissue: Peritoneal implant
  • GSM7119890 PMP-4_RNA-seq Pseudomyxoma Peritonei histologic type: Pseudomyxoma Peritonei; source of tumor tissue: Peritoneal implant
  • GSM7119891 PMP-5_RNA-seq Pseudomyxoma Peritonei histologic type: Pseudomyxoma Peritonei; source of tumor tissue: Peritoneal implant
  • GSM7119892 PMP-6_RNA-seq Pseudomyxoma Peritonei histologic type: Pseudomyxoma Peritonei; source of tumor tissue: Peritoneal implant
  • GSM7119893 PMP-7_RNA-seq Pseudomyxoma Peritonei histologic type: Pseudomyxoma Peritonei; source of tumor tissue: Peritoneal implant
  • GSM7119894 PMP-8_RNA-seq Pseudomyxoma Peritonei histologic type: Pseudomyxoma Peritonei; source of tumor tissue: Peritoneal implant
  • GSM7119895 PMP-9_RNA-seq Pseudomyxoma Peritonei histologic type: Pseudomyxoma Peritonei; source of tumor tissue: Peritoneal implant
  • GSM7119896 PMP-10_RNA-seq Pseudomyxoma Peritonei histologic type: Pseudomyxoma Peritonei; source of tumor tissue: Peritoneal implant
  • GSM7119897 PMP-11_RNA-seq Pseudomyxoma Peritonei histologic type: Pseudomyxoma Peritonei; source of tumor tissue: Peritoneal implant
  • GSM7119898 PMP-12_RNA-seq Pseudomyxoma Peritonei histologic type: Pseudomyxoma Peritonei; source of tumor tissue: Peritoneal implant

Score Breakdown

50%

relevance

  • Organism normalized.
  • Assay type normalized.
5%

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.
  • Missing colorectal disease context downgraded for tumor-vs-normal tissue ranking.
70%

metadata quality

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

data availability

  • Processed data available.
  • Raw data available.
45%

overall

  • Weighted score: 30% relevance, 30% comparison suitability, 25% metadata quality, 15% data availability.
  • Overall score capped because comparison suitability is weak for the selected search intent.
  • Overall score capped because colorectal/CRC disease context is not explicit.

Sample Links

19 samples

Review Audit Trail

0 decisions

No review decisions have been stored for this dataset.