Siftome Phase 3L

GSE29580

RNA-seq of two paired normal and cancer tissues in two stage III colorectal cancer patients

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
2011-05-27
Last update
2019-05-15
Organization
Chang Gung University
Department
Graduate Institute of Biomedical Sciences, Division of Medical Biotechnology
Public date
2011-05-28
Experiment types
Expression profiling by high throughput sequencing
Platforms
GPL9052 Illumina Genome Analyzer (Homo sapiens)
Series type
Series
SubSeries
Not available
BioProject
PRJNA141411
Supplementary files
TAR: GSE29580_RAW.tar
Organism
Homo sapiens
Assay
bulk RNA-seq
Samples
4
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
97% 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

10/10 pts

Metadata quality is high enough to support downstream handoff.

Blockers

No readiness blockers detected.

Next Steps

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

Analysis Preparation Checklist

5/6 ready

Group labels reviewed

Needs review

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

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

Minimum sample count met

Ready

Both groups meet the minimum of 2 samples.

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

Processed counts available

Ready

Processed data availability is marked true in the GEO index.

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

Ambiguous samples handled

Ready

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

Still scan the grouping table for biology-specific ambiguity.

Exclusion decisions recorded

Ready

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

Record any manual exclusions in the downstream analysis notes.

Source links preserved

Ready

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

Keep GEO dataset and sample links with exported metadata.

Bioinformatician Review

Bioinformatician review required

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

  • Small cohort warning is present.

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 100% 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. 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: 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 fewer than six samples are too small for top-ranked cohort confidence.

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 2 samples
  • Likely control group normal tissue 2 samples

Warnings

  • SMALL_COHORT_NEEDS_REVIEW warning Dataset has fewer than six samples and should not be treated as a high-confidence cohort without manual review.

Intent Interpretation

  • Active intent Patient tissue tumor-vs-normal Ranks human colorectal tissue or biopsy cohorts where tumor samples can be compared with normal controls.
  • Organism expectation Homo sapiens Dataset organism is interpreted as Homo sapiens.
  • Assay expectation bulk RNA-seq Dataset assay is interpreted as bulk RNA-seq.
  • Specimen assumption patient tissue or biopsy Derived specimen/source is Tissue.
  • Control-group assumption matched normal, adjacent normal, paired normal, healthy tissue control, or otherwise normal tissue control Derived study design is Tumor vs unmatched normal; likely groups are tumor sample vs normal tissue.
  • Score caps Applied when matching conditions are present non-human datasets stay below the primary recommendation band, missing colorectal/colon/rectal/CRC context stays below the primary recommendation band, biofluid and model-system datasets cannot reach Recommended by default, microarray and secondary assays are capped unless explicitly enabled, or small cohorts are capped below high-confidence recommendations
  • Warning rules 1 active warning missing or unclear control group, unclear disease context, unclear tissue source, mixed sample types, model-system markers, secondary assay context, missing processed data, or small cohort size
  • Downgrade or exclusion reason 1 warning 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 unmatched normal · Tissue · suitability 100%. 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 1 warning require review. Contributed to match or upgrade 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 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 fewer than six samples are too small for top-ranked cohort confidence. 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
GSE29580
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
GSE29580
  • 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
GSE29580
  • 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
GSE29580
  • 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: GSE29580
dataset_title: RNA-seq of two paired normal and cancer tissues in two stage III colorectal cancer patients
organism: Homo sapiens
assay_type: bulk RNA-seq
processed_data_available: true
raw_data_available: true
submission_date: 2011-05-27
last_update_date: 2019-05-15
organization_name: Chang Gung University
department: Graduate Institute of Biomedical Sciences, Division of Medical Biotechnology
public_date: 2011-05-28
experiment_types: Expression profiling by high throughput sequencing
platforms: GPL9052 Illumina Genome Analyzer (Homo sapiens)
sub_series: Not available
bioproject: PRJNA141411
supplementary_files: TAR: GSE29580_RAW.tar
series_type: Series

Why It Matched

  • Tumor vs unmatched normal · Tissue · suitability 100%.
  • 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.
  • 1 warning require review.

Why It May Not Be Suitable

  • Dataset has fewer than six samples and should not be treated as a high-confidence cohort without manual review.
  • Missing or unclear metadata: Treatment clarity: No unclear treatment split detected in the sample metadata.
  • Overall score capped because fewer than six samples are too small for top-ranked cohort confidence.

Warnings

  • warning SMALL_COHORT_NEEDS_REVIEW Dataset has fewer than six samples and should not be treated as a high-confidence cohort without manual review.

Normalized Fields

16 fields
Field Value Source Origin Confidence Evidence Reason
assay_type bulk RNA-seq dataset GSE29580 Runtime Siftome inference GEO:dataset:GSE29580:9bf7919585c531b2b63ef51dd218e5a6dc690cf31e25f6f78e893b6d03e04413 high confidence bulk rna-seq dataset_accession: GSE29580 dataset_title: RNA-seq of two paired normal and cancer tissues in two stage III colorectal cancer patients organism: Homo sapiens assay_type: bulk RN... keyword match keyword match: bulk rna-seq
disease colorectal cancer dataset GSE29580 Runtime Siftome inference GEO:dataset:GSE29580:9bf7919585c531b2b63ef51dd218e5a6dc690cf31e25f6f78e893b6d03e04413 high confidence colorectal cancer dataset_accession: GSE29580 dataset_title: RNA-seq of two paired normal and cancer tissues in two stage III colorectal cancer patients organism: Homo sapiens assay_type: bulk RN... controlled vocabulary controlled vocabulary disease match: colorectal cancer
disease colorectal cancer sample GSM732315 Runtime Siftome inference GEO:sample:GSM732315:cb0ce2f2fb2f7312aaad4f6fe479cbbfc22176d3cbab789e9fde14709ec8d232 high confidence colorectal cancer sample_accession: GSM732315 sample_title: RNA_seq_P1N source_name: normal tissue characteristics: tissue type: normal bowel tissue; disease status: stage III colorectal cancer p... controlled vocabulary controlled vocabulary disease match: colorectal cancer
disease colorectal cancer sample GSM732316 Runtime Siftome inference GEO:sample:GSM732316:b66031b52989bf16ae20185074008c6d77cf3fbd9023c4031097b0e2d8735657 high confidence colorectal cancer sample_accession: GSM732316 sample_title: RNA_seq_P1T source_name: colorectal tumor tissue characteristics: tissue type: Bowel adenocarcinoma tissue; disease status: stage III c... controlled vocabulary controlled vocabulary disease match: colorectal cancer
disease colorectal cancer sample GSM732317 Runtime Siftome inference GEO:sample:GSM732317:41088998fd218a40e7b57d5568bb808a47b023b8e0c3447fc51249c49a60dda3 high confidence colorectal cancer sample_accession: GSM732317 sample_title: RNA_seq_P2N source_name: normal tissue characteristics: tissue type: normal bowel tissue; disease status: stage III colorectal cancer p... controlled vocabulary controlled vocabulary disease match: colorectal cancer
disease colorectal cancer sample GSM732318 Runtime Siftome inference GEO:sample:GSM732318:1311a5d297d6c800f27aeca16d9721069cec9c073bce01d7b953e54cc4f6ca41 high confidence colorectal cancer sample_accession: GSM732318 sample_title: RNA_seq_P2T source_name: colorectal tumor tissue characteristics: tissue type: Bowel adenocarcinoma tissue; disease status: stage III c... controlled vocabulary controlled vocabulary disease match: colorectal cancer
organism Homo sapiens dataset GSE29580 Runtime Siftome inference GEO:dataset:GSE29580:9bf7919585c531b2b63ef51dd218e5a6dc690cf31e25f6f78e893b6d03e04413 high confidence homo sapiens dataset_accession: GSE29580 dataset_title: RNA-seq of two paired normal and cancer tissues in two stage III colorectal cancer patients organism: Homo sapiens assay_type: bulk RN... keyword match keyword match: homo sapiens
sample_type normal tissue sample GSM732315 Runtime Siftome inference GEO:sample:GSM732315:cb0ce2f2fb2f7312aaad4f6fe479cbbfc22176d3cbab789e9fde14709ec8d232 low confidence normal sample_accession: GSM732315 sample_title: RNA_seq_P1N source_name: normal tissue characteristics: tissue type: normal bowel tissue; disease status: stage III colorectal cancer p... controlled vocabulary controlled vocabulary sample type match: normal
sample_type tumor sample sample GSM732316 Runtime Siftome inference GEO:sample:GSM732316:b66031b52989bf16ae20185074008c6d77cf3fbd9023c4031097b0e2d8735657 low confidence tumor sample_accession: GSM732316 sample_title: RNA_seq_P1T source_name: colorectal tumor tissue characteristics: tissue type: Bowel adenocarcinoma tissue; disease status: stage III c... controlled vocabulary controlled vocabulary sample type match: tumor
sample_type normal tissue sample GSM732317 Runtime Siftome inference GEO:sample:GSM732317:41088998fd218a40e7b57d5568bb808a47b023b8e0c3447fc51249c49a60dda3 low confidence normal sample_accession: GSM732317 sample_title: RNA_seq_P2N source_name: normal tissue characteristics: tissue type: normal bowel tissue; disease status: stage III colorectal cancer p... controlled vocabulary controlled vocabulary sample type match: normal
sample_type tumor sample sample GSM732318 Runtime Siftome inference GEO:sample:GSM732318:1311a5d297d6c800f27aeca16d9721069cec9c073bce01d7b953e54cc4f6ca41 low confidence tumor sample_accession: GSM732318 sample_title: RNA_seq_P2T source_name: colorectal tumor tissue characteristics: tissue type: Bowel adenocarcinoma tissue; disease status: stage III c... controlled vocabulary controlled vocabulary sample type match: tumor
tissue colon dataset GSE29580 Runtime Siftome inference GEO:dataset:GSE29580:9bf7919585c531b2b63ef51dd218e5a6dc690cf31e25f6f78e893b6d03e04413 medium confidence colorectal dataset_accession: GSE29580 dataset_title: RNA-seq of two paired normal and cancer tissues in two stage III colorectal cancer patients organism: Homo sapiens assay_type: bulk RN... controlled vocabulary controlled vocabulary tissue match: colorectal
tissue colon sample GSM732315 Runtime Siftome inference GEO:sample:GSM732315:cb0ce2f2fb2f7312aaad4f6fe479cbbfc22176d3cbab789e9fde14709ec8d232 medium confidence colorectal sample_accession: GSM732315 sample_title: RNA_seq_P1N source_name: normal tissue characteristics: tissue type: normal bowel tissue; disease status: stage III colorectal cancer p... controlled vocabulary controlled vocabulary tissue match: colorectal
tissue colon sample GSM732316 Runtime Siftome inference GEO:sample:GSM732316:b66031b52989bf16ae20185074008c6d77cf3fbd9023c4031097b0e2d8735657 medium confidence colorectal sample_accession: GSM732316 sample_title: RNA_seq_P1T source_name: colorectal tumor tissue characteristics: tissue type: Bowel adenocarcinoma tissue; disease status: stage III c... controlled vocabulary controlled vocabulary tissue match: colorectal
tissue colon sample GSM732317 Runtime Siftome inference GEO:sample:GSM732317:41088998fd218a40e7b57d5568bb808a47b023b8e0c3447fc51249c49a60dda3 medium confidence colorectal sample_accession: GSM732317 sample_title: RNA_seq_P2N source_name: normal tissue characteristics: tissue type: normal bowel tissue; disease status: stage III colorectal cancer p... controlled vocabulary controlled vocabulary tissue match: colorectal
tissue colon sample GSM732318 Runtime Siftome inference GEO:sample:GSM732318:1311a5d297d6c800f27aeca16d9721069cec9c073bce01d7b953e54cc4f6ca41 medium confidence colorectal sample_accession: GSM732318 sample_title: RNA_seq_P2T source_name: colorectal tumor tissue characteristics: tissue type: Bowel adenocarcinoma tissue; disease status: stage III c... controlled vocabulary controlled vocabulary tissue match: colorectal

Sample Group Preview

Possible case samples

Samples currently treated as the comparison case group.

2
  • GSM732316 RNA_seq_P1T tumor sample Case marker detected. colorectal tumor tissue tissue type: Bowel adenocarcinoma tissue; disease status: stage III colorectal cancer patients
  • GSM732318 RNA_seq_P2T tumor sample Case marker detected. colorectal tumor tissue tissue type: Bowel adenocarcinoma tissue; disease status: stage III colorectal cancer patients

Possible control samples

Samples currently treated as controls or baseline.

2
  • GSM732315 RNA_seq_P1N normal tissue Control marker detected. normal tissue tissue type: normal bowel tissue; disease status: stage III colorectal cancer patients
  • GSM732317 RNA_seq_P2N normal tissue Control marker detected. normal tissue tissue type: normal bowel tissue; disease status: stage III colorectal cancer patients

Unassigned samples

Samples with no explicit case or control marker.

0

No samples

Excluded samples

Samples excluded from grouping by hard exclusion rules.

0

No samples

Ambiguous samples

Samples that need manual review before trusting grouping.

0

No samples

Metadata Quality Components

Persisted metadata quality

100 pts
Clarity
100%
Weight
100 pts

Sample source clarity: All samples have source metadata and clear GSE/GSM accessions. Group clarity: Rule-based grouping found both case and control samples. Disease clarity: Disease or condition metadata normalized. Tissue clarity: Tissue metadata normalized. Treatment clarity: No unclear treatment split detected in the sample metadata. Replicate clarity: No pooled sample or technical replicate flags detected. Data availability clarity: Dataset-level processed or raw data availability is explicit.

Detected Sample Groups

normal tissue

2 samples
  • GSM732315 RNA_seq_P1N normal tissue tissue type: normal bowel tissue; disease status: stage III colorectal cancer patients
  • GSM732317 RNA_seq_P2N normal tissue tissue type: normal bowel tissue; disease status: stage III colorectal cancer patients

tumor sample

2 samples
  • GSM732316 RNA_seq_P1T colorectal tumor tissue tissue type: Bowel adenocarcinoma tissue; disease status: stage III colorectal cancer patients
  • GSM732318 RNA_seq_P2T colorectal tumor tissue tissue type: Bowel adenocarcinoma tissue; disease status: stage III colorectal cancer patients

Score Breakdown

100%

relevance

  • Disease or condition metadata normalized.
  • Organism normalized.
  • Assay type normalized.
  • Tissue metadata normalized.
100%

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.
  • 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: 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 fewer than six samples are too small for top-ranked cohort confidence.

Sample Links

4 samples

Review Audit Trail

0 decisions

No review decisions have been stored for this dataset.