Siftome Phase 3L

GSE43550

Small RNA Solexa sequencing of colorectal tumor and adjancent normal tissues

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
2013-01-16
Last update
2019-05-15
Organization
Yunnan Agricultural University
Department
Not available
Public date
2014-01-15
Experiment types
Non-coding RNA profiling by high throughput sequencing
Platforms
GPL11154 Illumina HiSeq 2000 (Homo sapiens)
Series type
Series
SubSeries
Not available
BioProject
PRJNA186684
Supplementary files
TAR: GSE43550_RAW.tar; TXT: GSE43550_processed-mir-frequency.txt.gz
Organism
Homo sapiens
Assay
bulk RNA-seq
Samples
4
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

Review before analysis
85% DE readiness

Contrast completeness

25/25 pts

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

Minimum group size

20/20 pts

Each contrast group has at least 2 samples.

Processed data availability

20/20 pts

Processed data is marked available in the GEO index.

Sample decision clarity

3/15 pts

Unassigned or review-needed samples remain before analysis.

Blocking warnings

7/10 pts

Warnings are present, but none are critical blockers.

Metadata normalization

10/10 pts

Metadata quality is high enough to support downstream handoff.

Blockers

  • 4 samples need manual grouping review.
  • Secondary RNA assay context should be analyzed separately from ordinary bulk RNA-seq.

Next Steps

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

Analysis Preparation Checklist

4/6 ready

Group labels reviewed

Needs review

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

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

Minimum sample count met

Ready

Both groups meet the minimum of 2 samples.

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

Processed counts available

Ready

Processed data availability is marked true in the GEO index.

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

Ambiguous samples handled

Needs review

4 review-needed samples and 0 unassigned samples remain.

Resolve ambiguous and unassigned samples before finalizing the contrast.

Exclusion decisions recorded

Ready

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

Record any manual exclusions in the downstream analysis notes.

Source links preserved

Ready

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

Keep GEO dataset and sample links with exported metadata.

Bioinformatician Review

Bioinformatician review required

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

  • Analysis readiness has blockers that must be resolved before DE.
  • One or more samples were flagged for manual review.
  • Small cohort warning is present.
  • Assay context may require expert handling before DESeq2-style analysis.

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 100% Disease or condition metadata normalized. Organism normalized. Assay type normalized. Tissue metadata normalized.
  • comparison suitability 55% 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. Small RNA, miRNA, circRNA, or extracellular-vesicle RNA context downgraded for primary mRNA tissue ranking. Colorectal, colon, rectal, or CRC disease context boosted for 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: Treatment status metadata normalized where treatment is part of the comparison. 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 fewer than six samples are too small for top-ranked cohort confidence. Overall score capped because secondary RNA assays are not primary mRNA tissue RNA-seq.

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 2 samples
  • Likely control group normal tissue 2 samples

Warnings

  • TREATED_SAMPLES_NEED_REVIEW info Treated samples may need review depending on the comparison.
  • SMALL_COHORT_NEEDS_REVIEW warning Dataset has fewer than six samples and should not be treated as a high-confidence cohort without manual review.
  • SECONDARY_ASSAY_CONTEXT warning Secondary RNA assay context such as small RNA, miRNA, circRNA, or non-coding RNA was detected.

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 3 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 3 warnings require review. Derived from current-intent ranking reasons and warnings.

Applied Review Decisions

No active review decisions affect this ranking.

Ranking Facts

  • Recommendation Exploratory only Dataset can inform exploration but is not strong enough for primary analysis.
  • Supporting fact Tumor vs matched normal · Tissue · suitability 55%. 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 Prioritized disease context: colorectal, colon, rectal, or CRC metadata detected. Contributed to match or upgrade evidence.
  • Supporting fact Processed data is available for downstream review. Contributed to match or upgrade evidence.
  • Supporting fact 3 warnings require review. Contributed to match or upgrade evidence.
  • Caution fact Treated samples may need review depending on the comparison. Contributed to downgrade or manual-review evidence.
  • Caution fact Dataset has fewer than six samples and should not be treated as a high-confidence cohort without manual review. Contributed to downgrade or manual-review evidence.
  • Caution fact Secondary RNA assay context such as small RNA, miRNA, circRNA, or non-coding RNA was detected. Contributed to downgrade or manual-review evidence.
  • Caution fact Small RNA, miRNA, circRNA, or extracellular-vesicle RNA context downgraded for primary mRNA tissue ranking. 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 fewer than six samples are too small for top-ranked cohort confidence. Contributed to downgrade or manual-review evidence.
  • Caution fact Overall score capped because secondary RNA assays are not primary mRNA tissue RNA-seq. 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
GSE43550
Sample records
4 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
GSE43550
  • 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
GSE43550
  • 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
GSE43550
  • 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: GSE43550
dataset_title: Small RNA Solexa sequencing of colorectal tumor and adjancent normal tissues
organism: Homo sapiens
assay_type: bulk RNA-seq
processed_data_available: true
raw_data_available: true
submission_date: 2013-01-16
last_update_date: 2019-05-15
organization_name: Yunnan Agricultural University
department: Not available
public_date: 2014-01-15
experiment_types: Non-coding RNA profiling by high throughput sequencing
platforms: GPL11154 Illumina HiSeq 2000 (Homo sapiens)
sub_series: Not available
bioproject: PRJNA186684
supplementary_files: TAR: GSE43550_RAW.tar; TXT: GSE43550_processed-mir-frequency.txt.gz
series_type: Series

Why It Matched

  • Tumor vs matched normal · Tissue · suitability 55%.
  • Prioritized for patient tissue tumor-vs-normal triage.
  • Prioritized assay: bulk RNA-seq is the active assay expectation.
  • Prioritized disease context: colorectal, colon, rectal, or CRC metadata detected.
  • Processed data is available for downstream review.
  • 3 warnings require review.

Why It May Not Be Suitable

  • Treated samples may need review depending on the comparison.
  • Dataset has fewer than six samples and should not be treated as a high-confidence cohort without manual review.
  • Secondary RNA assay context such as small RNA, miRNA, circRNA, or non-coding RNA was detected.
  • Small RNA, miRNA, circRNA, or extracellular-vesicle RNA context downgraded for primary mRNA tissue ranking.
  • Overall score capped because comparison suitability is weak for the selected search intent.
  • Overall score capped because fewer than six samples are too small for top-ranked cohort confidence.
  • Overall score capped because secondary RNA assays are not primary mRNA tissue RNA-seq.
  • Comparison suitability score is below the Phase 1 recommended threshold.

Warnings

  • info TREATED_SAMPLES_NEED_REVIEW Treated samples may need review depending on the comparison.
  • warning SMALL_COHORT_NEEDS_REVIEW Dataset has fewer than six samples and should not be treated as a high-confidence cohort without manual review.
  • warning SECONDARY_ASSAY_CONTEXT Secondary RNA assay context such as small RNA, miRNA, circRNA, or non-coding RNA was detected.

Normalized Fields

23 fields
Field Value Source Origin Confidence Evidence Reason
assay_type bulk RNA-seq dataset GSE43550 Runtime Siftome inference GEO:dataset:GSE43550:95d199dbad79fe1f616917eab605f555fb246924730ec3e4f0d2f110ded54d3b high confidence bulk rna-seq dataset_accession: GSE43550 dataset_title: Small RNA Solexa sequencing of colorectal tumor and adjancent normal tissues organism: Homo sapiens assay_type: bulk RNA-seq processed... keyword match keyword match: bulk rna-seq
disease colorectal cancer sample GSM1065163 Runtime Siftome inference GEO:sample:GSM1065163:b15054bca54e600bbd0cf92554f318b75e80baad327940e306ac2888b05f928d high confidence colorectal cancer sample_accession: GSM1065163 sample_title: adjacent normal tissue without Transcatheter Arterial Infusion chemotherapy source_name: adjacent normal tissue of stage III CRC tumor... controlled vocabulary controlled vocabulary disease match: colorectal cancer
disease colorectal cancer sample GSM1065164 Runtime Siftome inference GEO:sample:GSM1065164:79894f6273eea9535a63ae097fafdf996eff7ae98b7d9b47ff0764be31bb97b3 high confidence colorectal cancer sample_accession: GSM1065164 sample_title: tumor tissue without Transcatheter Arterial Infusion chemotherapy source_name: tumor tissue of stage III CRC characteristics: country/... controlled vocabulary controlled vocabulary disease match: colorectal cancer
disease colorectal cancer sample GSM1065165 Runtime Siftome inference GEO:sample:GSM1065165:e48340645516fb30e80e79a2bce46acccf9cf98ef92ff9dd7359306a740a4ac2 high confidence colorectal cancer sample_accession: GSM1065165 sample_title: adjacent normal tissue with Transcatheter Arterial Infusion chemotherapy source_name: adjacent normal tissue of stage III CRC patient ... controlled vocabulary controlled vocabulary disease match: colorectal cancer
disease colorectal cancer sample GSM1065166 Runtime Siftome inference GEO:sample:GSM1065166:3d0057b8faca636612220e9ba9ec805c7ca88202540133462e96988be87d5bee high confidence colorectal cancer sample_accession: GSM1065166 sample_title: tumor tissue with Transcatheter Arterial Infusion chemotherapy source_name: tumor tissue of stage III CRC patient who received Transca... controlled vocabulary controlled vocabulary disease match: colorectal cancer
normal_tissue_type adjacent normal sample GSM1065163 Runtime Siftome inference GEO:sample:GSM1065163:b15054bca54e600bbd0cf92554f318b75e80baad327940e306ac2888b05f928d high confidence adjacent normal sample_accession: GSM1065163 sample_title: adjacent normal tissue without Transcatheter Arterial Infusion chemotherapy source_name: adjacent normal tissue of stage III CRC tumor... controlled vocabulary controlled vocabulary normal tissue type match: adjacent normal
normal_tissue_type adjacent normal sample GSM1065165 Runtime Siftome inference GEO:sample:GSM1065165:e48340645516fb30e80e79a2bce46acccf9cf98ef92ff9dd7359306a740a4ac2 high confidence adjacent normal sample_accession: GSM1065165 sample_title: adjacent normal tissue with Transcatheter Arterial Infusion chemotherapy source_name: adjacent normal tissue of stage III CRC patient ... controlled vocabulary controlled vocabulary normal tissue type match: adjacent normal
organism Homo sapiens dataset GSE43550 Runtime Siftome inference GEO:dataset:GSE43550:95d199dbad79fe1f616917eab605f555fb246924730ec3e4f0d2f110ded54d3b high confidence homo sapiens dataset_accession: GSE43550 dataset_title: Small RNA Solexa sequencing of colorectal tumor and adjancent normal tissues organism: Homo sapiens assay_type: bulk RNA-seq processed... keyword match keyword match: homo sapiens
sample_type normal tissue sample GSM1065163 Runtime Siftome inference GEO:sample:GSM1065163:b15054bca54e600bbd0cf92554f318b75e80baad327940e306ac2888b05f928d high confidence adjacent normal sample_accession: GSM1065163 sample_title: adjacent normal tissue without Transcatheter Arterial Infusion chemotherapy source_name: adjacent normal tissue of stage III CRC tumor... controlled vocabulary controlled vocabulary sample type match: adjacent normal
sample_type tumor sample sample GSM1065163 Runtime Siftome inference GEO:sample:GSM1065163:b15054bca54e600bbd0cf92554f318b75e80baad327940e306ac2888b05f928d low confidence tumor sample_accession: GSM1065163 sample_title: adjacent normal tissue without Transcatheter Arterial Infusion chemotherapy source_name: adjacent normal tissue of stage III CRC tumor... controlled vocabulary controlled vocabulary sample type match: tumor
sample_type tumor sample sample GSM1065164 Runtime Siftome inference GEO:sample:GSM1065164:79894f6273eea9535a63ae097fafdf996eff7ae98b7d9b47ff0764be31bb97b3 low confidence tumor sample_accession: GSM1065164 sample_title: tumor tissue without Transcatheter Arterial Infusion chemotherapy source_name: tumor tissue of stage III CRC characteristics: country/... controlled vocabulary controlled vocabulary sample type match: tumor
sample_type normal tissue sample GSM1065165 Runtime Siftome inference GEO:sample:GSM1065165:e48340645516fb30e80e79a2bce46acccf9cf98ef92ff9dd7359306a740a4ac2 high confidence adjacent normal sample_accession: GSM1065165 sample_title: adjacent normal tissue with Transcatheter Arterial Infusion chemotherapy source_name: adjacent normal tissue of stage III CRC patient ... controlled vocabulary controlled vocabulary sample type match: adjacent normal
sample_type tumor sample sample GSM1065165 Runtime Siftome inference GEO:sample:GSM1065165:e48340645516fb30e80e79a2bce46acccf9cf98ef92ff9dd7359306a740a4ac2 low confidence tumor sample_accession: GSM1065165 sample_title: adjacent normal tissue with Transcatheter Arterial Infusion chemotherapy source_name: adjacent normal tissue of stage III CRC patient ... controlled vocabulary controlled vocabulary sample type match: tumor
sample_type tumor sample sample GSM1065166 Runtime Siftome inference GEO:sample:GSM1065166:3d0057b8faca636612220e9ba9ec805c7ca88202540133462e96988be87d5bee low confidence tumor sample_accession: GSM1065166 sample_title: tumor tissue with Transcatheter Arterial Infusion chemotherapy source_name: tumor tissue of stage III CRC patient who received Transca... controlled vocabulary controlled vocabulary sample type match: tumor
tissue colon dataset GSE43550 Runtime Siftome inference GEO:dataset:GSE43550:95d199dbad79fe1f616917eab605f555fb246924730ec3e4f0d2f110ded54d3b medium confidence colorectal dataset_accession: GSE43550 dataset_title: Small RNA Solexa sequencing of colorectal tumor and adjancent normal tissues organism: Homo sapiens assay_type: bulk RNA-seq processed... controlled vocabulary controlled vocabulary tissue match: colorectal
tissue colon sample GSM1065163 Runtime Siftome inference GEO:sample:GSM1065163:b15054bca54e600bbd0cf92554f318b75e80baad327940e306ac2888b05f928d medium confidence colorectal sample_accession: GSM1065163 sample_title: adjacent normal tissue without Transcatheter Arterial Infusion chemotherapy source_name: adjacent normal tissue of stage III CRC tumor... controlled vocabulary controlled vocabulary tissue match: colorectal
tissue colon sample GSM1065164 Runtime Siftome inference GEO:sample:GSM1065164:79894f6273eea9535a63ae097fafdf996eff7ae98b7d9b47ff0764be31bb97b3 medium confidence colorectal sample_accession: GSM1065164 sample_title: tumor tissue without Transcatheter Arterial Infusion chemotherapy source_name: tumor tissue of stage III CRC characteristics: country/... controlled vocabulary controlled vocabulary tissue match: colorectal
tissue colon sample GSM1065165 Runtime Siftome inference GEO:sample:GSM1065165:e48340645516fb30e80e79a2bce46acccf9cf98ef92ff9dd7359306a740a4ac2 medium confidence colorectal sample_accession: GSM1065165 sample_title: adjacent normal tissue with Transcatheter Arterial Infusion chemotherapy source_name: adjacent normal tissue of stage III CRC patient ... controlled vocabulary controlled vocabulary tissue match: colorectal
tissue colon sample GSM1065166 Runtime Siftome inference GEO:sample:GSM1065166:3d0057b8faca636612220e9ba9ec805c7ca88202540133462e96988be87d5bee medium confidence colorectal sample_accession: GSM1065166 sample_title: tumor tissue with Transcatheter Arterial Infusion chemotherapy source_name: tumor tissue of stage III CRC patient who received Transca... controlled vocabulary controlled vocabulary tissue match: colorectal
treatment_status treated sample GSM1065163 Runtime Siftome inference GEO:sample:GSM1065163:b15054bca54e600bbd0cf92554f318b75e80baad327940e306ac2888b05f928d low confidence therapy sample_accession: GSM1065163 sample_title: adjacent normal tissue without Transcatheter Arterial Infusion chemotherapy source_name: adjacent normal tissue of stage III CRC tumor... controlled vocabulary controlled vocabulary treatment status match: therapy
treatment_status treated sample GSM1065164 Runtime Siftome inference GEO:sample:GSM1065164:79894f6273eea9535a63ae097fafdf996eff7ae98b7d9b47ff0764be31bb97b3 low confidence therapy sample_accession: GSM1065164 sample_title: tumor tissue without Transcatheter Arterial Infusion chemotherapy source_name: tumor tissue of stage III CRC characteristics: country/... controlled vocabulary controlled vocabulary treatment status match: therapy
treatment_status treated sample GSM1065165 Runtime Siftome inference GEO:sample:GSM1065165:e48340645516fb30e80e79a2bce46acccf9cf98ef92ff9dd7359306a740a4ac2 low confidence therapy sample_accession: GSM1065165 sample_title: adjacent normal tissue with Transcatheter Arterial Infusion chemotherapy source_name: adjacent normal tissue of stage III CRC patient ... controlled vocabulary controlled vocabulary treatment status match: therapy
treatment_status treated sample GSM1065166 Runtime Siftome inference GEO:sample:GSM1065166:3d0057b8faca636612220e9ba9ec805c7ca88202540133462e96988be87d5bee low confidence therapy sample_accession: GSM1065166 sample_title: tumor tissue with Transcatheter Arterial Infusion chemotherapy source_name: tumor tissue of stage III CRC patient who received Transca... controlled vocabulary controlled vocabulary treatment status match: therapy

Sample Group Preview

Possible case samples

Samples currently treated as the comparison case group.

2
  • GSM1065164 tumor tissue without Transcatheter Arterial Infusion chemotherapy tumor sample treated sample: Treated sample may need exclusion outside treatment comparisons. tumor tissue of stage III CRC country/location: Chinese in eastern China; tissue: tumor tissue of colorectal cancer; tumor stage: stage III; therapy: no therapy
  • GSM1065166 tumor tissue with Transcatheter Arterial Infusion chemotherapy tumor sample treated sample: Treated sample may need exclusion outside treatment comparisons. tumor tissue of stage III CRC patient who received Transcatheter Arterial Infusion chemotherapy one week before surgical resection country/location: Chinese in eastern China; tissue: tumor tissue of colorectal cancer; tumor stage: stage III; therapy: Transcatheter Arterial Infusion chemotherapy one week before surgical resection

Possible control samples

Samples currently treated as controls or baseline.

2
  • GSM1065163 adjacent normal tissue without Transcatheter Arterial Infusion chemotherapy normal tissue treated sample: Treated sample may need exclusion outside treatment comparisons. adjacent normal tissue of stage III CRC tumor country/location: Chinese in eastern China; tissue: adjacent normal tissue of colorectal cancer; tumor stage: stage III; therapy: no therapy
  • GSM1065165 adjacent normal tissue with Transcatheter Arterial Infusion chemotherapy normal tissue treated sample: Treated sample may need exclusion outside treatment comparisons. adjacent normal tissue of stage III CRC patient who received Transcatheter Arterial Infusion chemotherapy one week before surgical resection country/location: Chinese in eastern China; tissue: adjacent normal tissue of colorectal cancer; tumor stage: stage III; therapy: Transcatheter Arterial Infusion chemotherapy one week before surgical resection

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: Treatment status metadata normalized where treatment is part of the comparison. 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

2 samples
  • GSM1065163 adjacent normal tissue without Transcatheter Arterial Infusion chemotherapy adjacent normal tissue of stage III CRC tumor country/location: Chinese in eastern China; tissue: adjacent normal tissue of colorectal cancer; tumor stage: stage III; therapy: no therapy
  • GSM1065165 adjacent normal tissue with Transcatheter Arterial Infusion chemotherapy adjacent normal tissue of stage III CRC patient who received Transcatheter Arterial Infusion chemotherapy one week before surgical resection country/location: Chinese in eastern China; tissue: adjacent normal tissue of colorectal cancer; tumor stage: stage III; therapy: Transcatheter Arterial Infusion chemotherapy one week before surgical resection

tumor sample

2 samples
  • GSM1065164 tumor tissue without Transcatheter Arterial Infusion chemotherapy tumor tissue of stage III CRC country/location: Chinese in eastern China; tissue: tumor tissue of colorectal cancer; tumor stage: stage III; therapy: no therapy
  • GSM1065166 tumor tissue with Transcatheter Arterial Infusion chemotherapy tumor tissue of stage III CRC patient who received Transcatheter Arterial Infusion chemotherapy one week before surgical resection country/location: Chinese in eastern China; tissue: tumor tissue of colorectal cancer; tumor stage: stage III; therapy: Transcatheter Arterial Infusion chemotherapy one week before surgical resection

Score Breakdown

100%

relevance

  • Disease or condition metadata normalized.
  • Organism normalized.
  • Assay type normalized.
  • Tissue metadata normalized.
55%

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.
  • Small RNA, miRNA, circRNA, or extracellular-vesicle RNA context downgraded for primary mRNA tissue ranking.
  • Colorectal, colon, rectal, or CRC disease context boosted for 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: Treatment status metadata normalized where treatment is part of the comparison.
  • 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 fewer than six samples are too small for top-ranked cohort confidence.
  • Overall score capped because secondary RNA assays are not primary mRNA tissue RNA-seq.

Sample Links

4 samples

Review Audit Trail

0 decisions

No review decisions have been stored for this dataset.