Siftome Phase 3L

GSE104178

RNA-Sequencing approach for the identification of novel long non-coding RNA biomarkers in colorectal cancer

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
2017-09-25
Last update
2023-03-16
Organization
Baylor Research Institute
Department
Not available
Public date
2018-02-14
Experiment types
Expression profiling by high throughput sequencing
Platforms
GPL11154 Illumina HiSeq 2000 (Homo sapiens)
Series type
Series
SubSeries
Not available
BioProject
PRJNA411984
Supplementary files
CSV: GSE104178_Differentially_expressed_lncRNAs_Wei_s_analysis_11052014.csv.gz
Organism
Homo sapiens
Assay
bulk RNA-seq
Samples
6
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
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

  • Secondary RNA assay context should be analyzed separately from ordinary bulk RNA-seq.

Next Steps

  • Review blockers and update sample grouping or dataset selection before analysis.

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.

  • Analysis readiness has blockers that must be resolved before DE.
  • 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 100% Case and control sample groups detected: colorectal cancer vs normal tissue. 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. 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 55% Weighted score: 30% relevance, 30% comparison suitability, 25% metadata quality, 15% data availability. Overall score capped because fewer than ten samples limit 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 matched normal Study design remains rule-derived: Tumor vs matched normal.
  • Specimen/source Tissue Specimen/source remains rule-derived: Tissue.
  • Likely case group colorectal cancer 3 samples
  • Likely control group normal tissue 3 samples

Warnings

  • 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 colorectal cancer 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 matched normal · Tissue · suitability 100%. 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 1 warning require review. Contributed to match or upgrade 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 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 ten samples limit 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
GSE104178
Sample records
6 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
GSE104178
  • 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
GSE104178
  • 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
GSE104178
  • 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: GSE104178
dataset_title: RNA-Sequencing approach for the identification of novel long non-coding RNA biomarkers in colorectal cancer
organism: Homo sapiens
assay_type: bulk RNA-seq
processed_data_available: true
raw_data_available: true
submission_date: 2017-09-25
last_update_date: 2023-03-16
organization_name: Baylor Research Institute
department: Not available
public_date: 2018-02-14
experiment_types: Expression profiling by high throughput sequencing
platforms: GPL11154 Illumina HiSeq 2000 (Homo sapiens)
sub_series: Not available
bioproject: PRJNA411984
supplementary_files: CSV: GSE104178_Differentially_expressed_lncRNAs_Wei_s_analysis_11052014.csv.gz
series_type: Series

Why It Matched

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

Why It May Not Be Suitable

  • Secondary RNA assay context such as small RNA, miRNA, circRNA, or non-coding RNA was detected.
  • Missing or unclear metadata: Treatment clarity: No unclear treatment split detected in the sample metadata.
  • Overall score capped because fewer than ten samples limit cohort confidence.

Warnings

  • warning SECONDARY_ASSAY_CONTEXT Secondary RNA assay context such as small RNA, miRNA, circRNA, or non-coding RNA was detected.

Normalized Fields

16 fields
Field Value Source Origin Confidence Evidence Reason
assay_type bulk RNA-seq dataset GSE104178 Runtime Siftome inference GEO:dataset:GSE104178:8431a2a20e0868955cdd0b5bf70e9f1060cf34915d8dd25dc587b7f2c80cb721 high confidence bulk rna-seq dataset_accession: GSE104178 dataset_title: RNA-Sequencing approach for the identification of novel long non-coding RNA biomarkers in colorectal cancer organism: Homo sapiens as... keyword match keyword match: bulk rna-seq
disease colorectal cancer dataset GSE104178 Runtime Siftome inference GEO:dataset:GSE104178:8431a2a20e0868955cdd0b5bf70e9f1060cf34915d8dd25dc587b7f2c80cb721 high confidence colorectal cancer dataset_accession: GSE104178 dataset_title: RNA-Sequencing approach for the identification of novel long non-coding RNA biomarkers in colorectal cancer organism: Homo sapiens as... controlled vocabulary controlled vocabulary disease match: colorectal cancer
disease colorectal cancer sample GSM2791405 Runtime Siftome inference GEO:sample:GSM2791405:285fe93f4c1ed25ba43497663df8e588db41b2fee8f0a6aa87221a2fcb242985 high confidence colorectal cancer sample_accession: GSM2791405 sample_title: CXIR56SE6-CRC: colorectal cancer source_name: frozen mucosal tissue characteristics: tissue: frozen mucosal tissue; tissue type: CRC: ... controlled vocabulary controlled vocabulary disease match: colorectal cancer
disease colorectal cancer sample GSM2791406 Runtime Siftome inference GEO:sample:GSM2791406:80d95b6ec1fc1614e99431fe59e652cbd1fc7dca8332d7c7dcb48821a3eefa0d high confidence colorectal cancer sample_accession: GSM2791406 sample_title: CXIR60OC4-CRC: colorectal cancer source_name: frozen mucosal tissue characteristics: tissue: frozen mucosal tissue; tissue type: CRC: ... controlled vocabulary controlled vocabulary disease match: colorectal cancer
disease colorectal cancer sample GSM2791407 Runtime Siftome inference GEO:sample:GSM2791407:edbb0ec706dda1e010809837bc1d493316878cb130c46481408986eedfde6aaf high confidence colorectal cancer sample_accession: GSM2791407 sample_title: CXIR66OC21-CRC: colorectal cancer source_name: frozen mucosal tissue characteristics: tissue: frozen mucosal tissue; tissue type: CRC:... controlled vocabulary controlled vocabulary disease match: colorectal cancer
normal_tissue_type adjacent normal sample GSM2791408 Runtime Siftome inference GEO:sample:GSM2791408:73783eff0013d54c5db0cc911065e07299b9f05fef559b8c8311836f047f90cb high confidence matched normal sample_accession: GSM2791408 sample_title: CXIR56SE6-matched normal mucosa (NM) source_name: frozen mucosal tissue characteristics: tissue: frozen mucosal tissue; tissue type: m... controlled vocabulary controlled vocabulary normal tissue type match: matched normal
normal_tissue_type adjacent normal sample GSM2791409 Runtime Siftome inference GEO:sample:GSM2791409:f4a468b0dd086a2edf5aea1693ac01d92861084653bfde3eca9fdb07b587ec8f high confidence matched normal sample_accession: GSM2791409 sample_title: CXIR60OC4-matched normal mucosa (NM) source_name: frozen mucosal tissue characteristics: tissue: frozen mucosal tissue; tissue type: m... controlled vocabulary controlled vocabulary normal tissue type match: matched normal
normal_tissue_type adjacent normal sample GSM2791410 Runtime Siftome inference GEO:sample:GSM2791410:ed2e6bfc9f1ea1d3e8524b1ee53e46fc63ff8b938e0d35200d503c08c9236a27 high confidence matched normal sample_accession: GSM2791410 sample_title: CXIR66OC21-matched normal mucosa (NM) source_name: frozen mucosal tissue characteristics: tissue: frozen mucosal tissue; tissue type: ... controlled vocabulary controlled vocabulary normal tissue type match: matched normal
organism Homo sapiens dataset GSE104178 Runtime Siftome inference GEO:dataset:GSE104178:8431a2a20e0868955cdd0b5bf70e9f1060cf34915d8dd25dc587b7f2c80cb721 high confidence homo sapiens dataset_accession: GSE104178 dataset_title: RNA-Sequencing approach for the identification of novel long non-coding RNA biomarkers in colorectal cancer organism: Homo sapiens as... keyword match keyword match: homo sapiens
sample_type normal tissue sample GSM2791408 Runtime Siftome inference GEO:sample:GSM2791408:73783eff0013d54c5db0cc911065e07299b9f05fef559b8c8311836f047f90cb low confidence normal sample_accession: GSM2791408 sample_title: CXIR56SE6-matched normal mucosa (NM) source_name: frozen mucosal tissue characteristics: tissue: frozen mucosal tissue; tissue type: m... controlled vocabulary controlled vocabulary sample type match: normal
sample_type normal tissue sample GSM2791409 Runtime Siftome inference GEO:sample:GSM2791409:f4a468b0dd086a2edf5aea1693ac01d92861084653bfde3eca9fdb07b587ec8f low confidence normal sample_accession: GSM2791409 sample_title: CXIR60OC4-matched normal mucosa (NM) source_name: frozen mucosal tissue characteristics: tissue: frozen mucosal tissue; tissue type: m... controlled vocabulary controlled vocabulary sample type match: normal
sample_type normal tissue sample GSM2791410 Runtime Siftome inference GEO:sample:GSM2791410:ed2e6bfc9f1ea1d3e8524b1ee53e46fc63ff8b938e0d35200d503c08c9236a27 low confidence normal sample_accession: GSM2791410 sample_title: CXIR66OC21-matched normal mucosa (NM) source_name: frozen mucosal tissue characteristics: tissue: frozen mucosal tissue; tissue type: ... controlled vocabulary controlled vocabulary sample type match: normal
tissue colon dataset GSE104178 Runtime Siftome inference GEO:dataset:GSE104178:8431a2a20e0868955cdd0b5bf70e9f1060cf34915d8dd25dc587b7f2c80cb721 medium confidence colorectal dataset_accession: GSE104178 dataset_title: RNA-Sequencing approach for the identification of novel long non-coding RNA biomarkers in colorectal cancer organism: Homo sapiens as... controlled vocabulary controlled vocabulary tissue match: colorectal
tissue colon sample GSM2791405 Runtime Siftome inference GEO:sample:GSM2791405:285fe93f4c1ed25ba43497663df8e588db41b2fee8f0a6aa87221a2fcb242985 medium confidence colorectal sample_accession: GSM2791405 sample_title: CXIR56SE6-CRC: colorectal cancer source_name: frozen mucosal tissue characteristics: tissue: frozen mucosal tissue; tissue type: CRC: ... controlled vocabulary controlled vocabulary tissue match: colorectal
tissue colon sample GSM2791406 Runtime Siftome inference GEO:sample:GSM2791406:80d95b6ec1fc1614e99431fe59e652cbd1fc7dca8332d7c7dcb48821a3eefa0d medium confidence colorectal sample_accession: GSM2791406 sample_title: CXIR60OC4-CRC: colorectal cancer source_name: frozen mucosal tissue characteristics: tissue: frozen mucosal tissue; tissue type: CRC: ... controlled vocabulary controlled vocabulary tissue match: colorectal
tissue colon sample GSM2791407 Runtime Siftome inference GEO:sample:GSM2791407:edbb0ec706dda1e010809837bc1d493316878cb130c46481408986eedfde6aaf medium confidence colorectal sample_accession: GSM2791407 sample_title: CXIR66OC21-CRC: colorectal cancer source_name: frozen mucosal tissue characteristics: tissue: frozen mucosal tissue; tissue type: CRC:... controlled vocabulary controlled vocabulary tissue match: colorectal

Sample Group Preview

Possible case samples

Samples currently treated as the comparison case group.

3
  • GSM2791405 CXIR56SE6-CRC: colorectal cancer colorectal cancer Case marker detected. frozen mucosal tissue tissue: frozen mucosal tissue; tissue type: CRC: colorectal cancer; source id: CXIR56SE6
  • GSM2791406 CXIR60OC4-CRC: colorectal cancer colorectal cancer Case marker detected. frozen mucosal tissue tissue: frozen mucosal tissue; tissue type: CRC: colorectal cancer; source id: CXIR60OC4
  • GSM2791407 CXIR66OC21-CRC: colorectal cancer colorectal cancer Case marker detected. frozen mucosal tissue tissue: frozen mucosal tissue; tissue type: CRC: colorectal cancer; source id: CXIR66OC21

Possible control samples

Samples currently treated as controls or baseline.

3
  • GSM2791408 CXIR56SE6-matched normal mucosa (NM) normal tissue Control marker detected. frozen mucosal tissue tissue: frozen mucosal tissue; tissue type: matched normal mucosa (NM); source id: CXIR56SE6
  • GSM2791409 CXIR60OC4-matched normal mucosa (NM) normal tissue Control marker detected. frozen mucosal tissue tissue: frozen mucosal tissue; tissue type: matched normal mucosa (NM); source id: CXIR60OC4
  • GSM2791410 CXIR66OC21-matched normal mucosa (NM) normal tissue Control marker detected. frozen mucosal tissue tissue: frozen mucosal tissue; tissue type: matched normal mucosa (NM); source id: CXIR66OC21

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

colorectal cancer

3 samples
  • GSM2791405 CXIR56SE6-CRC: colorectal cancer frozen mucosal tissue tissue: frozen mucosal tissue; tissue type: CRC: colorectal cancer; source id: CXIR56SE6
  • GSM2791406 CXIR60OC4-CRC: colorectal cancer frozen mucosal tissue tissue: frozen mucosal tissue; tissue type: CRC: colorectal cancer; source id: CXIR60OC4
  • GSM2791407 CXIR66OC21-CRC: colorectal cancer frozen mucosal tissue tissue: frozen mucosal tissue; tissue type: CRC: colorectal cancer; source id: CXIR66OC21

normal tissue

3 samples
  • GSM2791408 CXIR56SE6-matched normal mucosa (NM) frozen mucosal tissue tissue: frozen mucosal tissue; tissue type: matched normal mucosa (NM); source id: CXIR56SE6
  • GSM2791409 CXIR60OC4-matched normal mucosa (NM) frozen mucosal tissue tissue: frozen mucosal tissue; tissue type: matched normal mucosa (NM); source id: CXIR60OC4
  • GSM2791410 CXIR66OC21-matched normal mucosa (NM) frozen mucosal tissue tissue: frozen mucosal tissue; tissue type: matched normal mucosa (NM); source id: CXIR66OC21

Score Breakdown

100%

relevance

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

comparison suitability

  • Case and control sample groups detected: colorectal cancer vs normal tissue.
  • 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.
  • 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.
55%

overall

  • Weighted score: 30% relevance, 30% comparison suitability, 25% metadata quality, 15% data availability.
  • Overall score capped because fewer than ten samples limit cohort confidence.

Sample Links

6 samples

Review Audit Trail

0 decisions

No review decisions have been stored for this dataset.