Siftome Phase 3L

GSE236991

miRNA expression profile in 3 sporadic young-onset and 2 late-onset Indian colorectal carcinoma 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
2023-07-10
Last update
2025-03-14
Organization
Netaji Subhash Chandra Bose Cancer Research Institute
Department
Molecular Biology
Public date
2023-07-26
Experiment types
Non-coding RNA profiling by high throughput sequencing
Platforms
GPL18573 Illumina NextSeq 500 (Homo sapiens)
Series type
Series
SubSeries
Not available
BioProject
PRJNA993265
Supplementary files
TXT: GSE236991_normalized_count_matrix.txt.gz; TXT: GSE236991_raw_count_matrix.txt.gz
Organism
Homo sapiens
Assay
bulk RNA-seq
Samples
10
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

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 50% 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. 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: 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 50% 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 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 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 5 samples
  • Likely control group normal tissue 5 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 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 50%. 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 Small RNA, miRNA, circRNA, or extracellular-vesicle RNA context downgraded for primary mRNA tissue ranking. 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 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
GSE236991
Sample records
10 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
GSE236991
  • 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
GSE236991
  • 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
GSE236991
  • 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: GSE236991
dataset_title: miRNA expression profile in 3 sporadic young-onset and 2 late-onset Indian colorectal carcinoma patients
organism: Homo sapiens
assay_type: bulk RNA-seq
processed_data_available: true
raw_data_available: true
submission_date: 2023-07-10
last_update_date: 2025-03-14
organization_name: Netaji Subhash Chandra Bose Cancer Research Institute
department: Molecular Biology
public_date: 2023-07-26
experiment_types: Non-coding RNA profiling by high throughput sequencing
platforms: GPL18573 Illumina NextSeq 500 (Homo sapiens)
sub_series: Not available
bioproject: PRJNA993265
supplementary_files: TXT: GSE236991_normalized_count_matrix.txt.gz; TXT: GSE236991_raw_count_matrix.txt.gz
series_type: Series

Why It Matched

  • Tumor vs unmatched normal · Tissue · suitability 50%.
  • 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.
  • Small RNA, miRNA, circRNA, or extracellular-vesicle RNA context downgraded for primary mRNA tissue ranking.
  • 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 secondary RNA assays are not primary mRNA tissue RNA-seq.
  • Comparison suitability score is below the Phase 1 recommended threshold.

Warnings

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

Normalized Fields

39 fields
Field Value Source Origin Confidence Evidence Reason
assay_type bulk RNA-seq dataset GSE236991 Runtime Siftome inference GEO:dataset:GSE236991:c355d30c5a99af20e1b987887ac001d3437e694e33e47c7d01a257604e5d6faa high confidence bulk rna-seq dataset_accession: GSE236991 dataset_title: miRNA expression profile in 3 sporadic young-onset and 2 late-onset Indian colorectal carcinoma patients organism: Homo sapiens assay... keyword match keyword match: bulk rna-seq
disease colorectal cancer dataset GSE236991 Runtime Siftome inference GEO:dataset:GSE236991:c355d30c5a99af20e1b987887ac001d3437e694e33e47c7d01a257604e5d6faa high confidence colorectal carcinoma dataset_accession: GSE236991 dataset_title: miRNA expression profile in 3 sporadic young-onset and 2 late-onset Indian colorectal carcinoma patients organism: Homo sapiens assay... controlled vocabulary controlled vocabulary disease match: colorectal carcinoma
disease colorectal cancer sample GSM7592739 Runtime Siftome inference GEO:sample:GSM7592739:9efb7aada5d12416ca43c429d36d1249f6555dc3bf38c83bc9cb5b454459d4ae high confidence colorectal carcinoma sample_accession: GSM7592739 sample_title: Colorectal Carcinoma patient 39 years old, Normal colonic mucosa source_name: Normal colonic mucosa characteristics: tissue: Normal co... controlled vocabulary controlled vocabulary disease match: colorectal carcinoma
disease colorectal cancer sample GSM7592740 Runtime Siftome inference GEO:sample:GSM7592740:9b5e1d3ecd254ecc718ae79d6b7a534d431e4bb7cd5671d4cc78a2f6afe6bac6 high confidence colorectal carcinoma sample_accession: GSM7592740 sample_title: Colorectal Carcinoma patient 39 years old, Tumor tissue source_name: Tumor tissue characteristics: tissue: Tumor tissue; Sex: female; ... controlled vocabulary controlled vocabulary disease match: colorectal carcinoma
disease colorectal cancer sample GSM7592741 Runtime Siftome inference GEO:sample:GSM7592741:b4d04e9a4dcd4d0367ea364168d2c26b326e544d9f5d1efdd057fddad637c34c high confidence colorectal carcinoma sample_accession: GSM7592741 sample_title: Colorectal Carcinoma patient 44 years old, Normal colonic mucosa source_name: Normal colonic mucosa characteristics: tissue: Normal co... controlled vocabulary controlled vocabulary disease match: colorectal carcinoma
disease colorectal cancer sample GSM7592742 Runtime Siftome inference GEO:sample:GSM7592742:8c02ed50d0f3476b927091a3cd4c5454a57868e41998c2d2844cabdb6337a2d0 high confidence colorectal carcinoma sample_accession: GSM7592742 sample_title: Colorectal Carcinoma patient 44 years old, Tumor tissue source_name: Tumor tissue characteristics: tissue: Tumor tissue; Sex: female; ... controlled vocabulary controlled vocabulary disease match: colorectal carcinoma
disease colorectal cancer sample GSM7592743 Runtime Siftome inference GEO:sample:GSM7592743:9d42c7b493822d7f2b6d8f8f381a2666eb55fabd23afef36489dd2300d16d2e9 high confidence colorectal carcinoma sample_accession: GSM7592743 sample_title: Colorectal Carcinoma patient 47 years old, Normal colonic mucosa source_name: Normal colonic mucosa characteristics: tissue: Normal co... controlled vocabulary controlled vocabulary disease match: colorectal carcinoma
disease colorectal cancer sample GSM7592744 Runtime Siftome inference GEO:sample:GSM7592744:100dd4a34f465add34795ca6532d90d449c526af9a916ca148211dc08347b4f0 high confidence colorectal carcinoma sample_accession: GSM7592744 sample_title: Colorectal Carcinoma patient 47 years old, Tumor tissue source_name: Tumor tissue characteristics: tissue: Tumor tissue; Sex: male; tu... controlled vocabulary controlled vocabulary disease match: colorectal carcinoma
disease colorectal cancer sample GSM7592745 Runtime Siftome inference GEO:sample:GSM7592745:1a67ee67e95bb898f07bf782570252184b82419c3982858d6561d05da17e297d high confidence colorectal carcinoma sample_accession: GSM7592745 sample_title: Colorectal Carcinoma patient 66 years old, Normal colonic mucosa source_name: Normal colonic mucosa characteristics: tissue: Normal co... controlled vocabulary controlled vocabulary disease match: colorectal carcinoma
disease colorectal cancer sample GSM7592746 Runtime Siftome inference GEO:sample:GSM7592746:29d1098d997fdc23da5dc34801039a87594436f402db18e8d0bf75018b0488ae high confidence colorectal carcinoma sample_accession: GSM7592746 sample_title: Colorectal Carcinoma patient 66 years old, Tumor tissue source_name: Tumor tissue characteristics: tissue: Tumor tissue; Sex: male; tu... controlled vocabulary controlled vocabulary disease match: colorectal carcinoma
disease colorectal cancer sample GSM7592747 Runtime Siftome inference GEO:sample:GSM7592747:597a0534cae5d622cc5d747f5be39d9f469db8a5cdec1023ceec5f1530210c18 high confidence colorectal carcinoma sample_accession: GSM7592747 sample_title: Colorectal Carcinoma patient 60 years old, Normal colonic mucosa source_name: Normal colonic mucosa characteristics: tissue: Normal co... controlled vocabulary controlled vocabulary disease match: colorectal carcinoma
disease colorectal cancer sample GSM7592748 Runtime Siftome inference GEO:sample:GSM7592748:d648c4652f57dddd5856e1fe209865269b08bd1c8af27ecad2c824067f53a2fe high confidence colorectal carcinoma sample_accession: GSM7592748 sample_title: Colorectal Carcinoma patient 60 years old, Tumor tissue source_name: Tumor tissue characteristics: tissue: Tumor tissue; Sex: female; ... controlled vocabulary controlled vocabulary disease match: colorectal carcinoma
organism Homo sapiens dataset GSE236991 Runtime Siftome inference GEO:dataset:GSE236991:c355d30c5a99af20e1b987887ac001d3437e694e33e47c7d01a257604e5d6faa high confidence homo sapiens dataset_accession: GSE236991 dataset_title: miRNA expression profile in 3 sporadic young-onset and 2 late-onset Indian colorectal carcinoma patients organism: Homo sapiens assay... keyword match keyword match: homo sapiens
sample_type normal tissue sample GSM7592739 Runtime Siftome inference GEO:sample:GSM7592739:9efb7aada5d12416ca43c429d36d1249f6555dc3bf38c83bc9cb5b454459d4ae low confidence normal sample_accession: GSM7592739 sample_title: Colorectal Carcinoma patient 39 years old, Normal colonic mucosa source_name: Normal colonic mucosa characteristics: tissue: Normal co... controlled vocabulary controlled vocabulary sample type match: normal
sample_type tumor sample sample GSM7592739 Runtime Siftome inference GEO:sample:GSM7592739:9efb7aada5d12416ca43c429d36d1249f6555dc3bf38c83bc9cb5b454459d4ae medium confidence carcinoma sample_accession: GSM7592739 sample_title: Colorectal Carcinoma patient 39 years old, Normal colonic mucosa source_name: Normal colonic mucosa characteristics: tissue: Normal co... controlled vocabulary controlled vocabulary sample type match: carcinoma
sample_type tumor sample sample GSM7592740 Runtime Siftome inference GEO:sample:GSM7592740:9b5e1d3ecd254ecc718ae79d6b7a534d431e4bb7cd5671d4cc78a2f6afe6bac6 low confidence tumor sample_accession: GSM7592740 sample_title: Colorectal Carcinoma patient 39 years old, Tumor tissue source_name: Tumor tissue characteristics: tissue: Tumor tissue; Sex: female; ... controlled vocabulary controlled vocabulary sample type match: tumor
sample_type normal tissue sample GSM7592741 Runtime Siftome inference GEO:sample:GSM7592741:b4d04e9a4dcd4d0367ea364168d2c26b326e544d9f5d1efdd057fddad637c34c low confidence normal sample_accession: GSM7592741 sample_title: Colorectal Carcinoma patient 44 years old, Normal colonic mucosa source_name: Normal colonic mucosa characteristics: tissue: Normal co... controlled vocabulary controlled vocabulary sample type match: normal
sample_type tumor sample sample GSM7592741 Runtime Siftome inference GEO:sample:GSM7592741:b4d04e9a4dcd4d0367ea364168d2c26b326e544d9f5d1efdd057fddad637c34c medium confidence carcinoma sample_accession: GSM7592741 sample_title: Colorectal Carcinoma patient 44 years old, Normal colonic mucosa source_name: Normal colonic mucosa characteristics: tissue: Normal co... controlled vocabulary controlled vocabulary sample type match: carcinoma
sample_type tumor sample sample GSM7592742 Runtime Siftome inference GEO:sample:GSM7592742:8c02ed50d0f3476b927091a3cd4c5454a57868e41998c2d2844cabdb6337a2d0 low confidence tumor sample_accession: GSM7592742 sample_title: Colorectal Carcinoma patient 44 years old, Tumor tissue source_name: Tumor tissue characteristics: tissue: Tumor tissue; Sex: female; ... controlled vocabulary controlled vocabulary sample type match: tumor
sample_type normal tissue sample GSM7592743 Runtime Siftome inference GEO:sample:GSM7592743:9d42c7b493822d7f2b6d8f8f381a2666eb55fabd23afef36489dd2300d16d2e9 low confidence normal sample_accession: GSM7592743 sample_title: Colorectal Carcinoma patient 47 years old, Normal colonic mucosa source_name: Normal colonic mucosa characteristics: tissue: Normal co... controlled vocabulary controlled vocabulary sample type match: normal
sample_type tumor sample sample GSM7592743 Runtime Siftome inference GEO:sample:GSM7592743:9d42c7b493822d7f2b6d8f8f381a2666eb55fabd23afef36489dd2300d16d2e9 medium confidence carcinoma sample_accession: GSM7592743 sample_title: Colorectal Carcinoma patient 47 years old, Normal colonic mucosa source_name: Normal colonic mucosa characteristics: tissue: Normal co... controlled vocabulary controlled vocabulary sample type match: carcinoma
sample_type tumor sample sample GSM7592744 Runtime Siftome inference GEO:sample:GSM7592744:100dd4a34f465add34795ca6532d90d449c526af9a916ca148211dc08347b4f0 low confidence tumor sample_accession: GSM7592744 sample_title: Colorectal Carcinoma patient 47 years old, Tumor tissue source_name: Tumor tissue characteristics: tissue: Tumor tissue; Sex: male; tu... controlled vocabulary controlled vocabulary sample type match: tumor
sample_type normal tissue sample GSM7592745 Runtime Siftome inference GEO:sample:GSM7592745:1a67ee67e95bb898f07bf782570252184b82419c3982858d6561d05da17e297d low confidence normal sample_accession: GSM7592745 sample_title: Colorectal Carcinoma patient 66 years old, Normal colonic mucosa source_name: Normal colonic mucosa characteristics: tissue: Normal co... controlled vocabulary controlled vocabulary sample type match: normal
sample_type tumor sample sample GSM7592745 Runtime Siftome inference GEO:sample:GSM7592745:1a67ee67e95bb898f07bf782570252184b82419c3982858d6561d05da17e297d medium confidence carcinoma sample_accession: GSM7592745 sample_title: Colorectal Carcinoma patient 66 years old, Normal colonic mucosa source_name: Normal colonic mucosa characteristics: tissue: Normal co... controlled vocabulary controlled vocabulary sample type match: carcinoma
sample_type tumor sample sample GSM7592746 Runtime Siftome inference GEO:sample:GSM7592746:29d1098d997fdc23da5dc34801039a87594436f402db18e8d0bf75018b0488ae low confidence tumor sample_accession: GSM7592746 sample_title: Colorectal Carcinoma patient 66 years old, Tumor tissue source_name: Tumor tissue characteristics: tissue: Tumor tissue; Sex: male; tu... controlled vocabulary controlled vocabulary sample type match: tumor
sample_type normal tissue sample GSM7592747 Runtime Siftome inference GEO:sample:GSM7592747:597a0534cae5d622cc5d747f5be39d9f469db8a5cdec1023ceec5f1530210c18 low confidence normal sample_accession: GSM7592747 sample_title: Colorectal Carcinoma patient 60 years old, Normal colonic mucosa source_name: Normal colonic mucosa characteristics: tissue: Normal co... controlled vocabulary controlled vocabulary sample type match: normal
sample_type tumor sample sample GSM7592747 Runtime Siftome inference GEO:sample:GSM7592747:597a0534cae5d622cc5d747f5be39d9f469db8a5cdec1023ceec5f1530210c18 medium confidence carcinoma sample_accession: GSM7592747 sample_title: Colorectal Carcinoma patient 60 years old, Normal colonic mucosa source_name: Normal colonic mucosa characteristics: tissue: Normal co... controlled vocabulary controlled vocabulary sample type match: carcinoma
sample_type tumor sample sample GSM7592748 Runtime Siftome inference GEO:sample:GSM7592748:d648c4652f57dddd5856e1fe209865269b08bd1c8af27ecad2c824067f53a2fe low confidence tumor sample_accession: GSM7592748 sample_title: Colorectal Carcinoma patient 60 years old, Tumor tissue source_name: Tumor tissue characteristics: tissue: Tumor tissue; Sex: female; ... controlled vocabulary controlled vocabulary sample type match: tumor
tissue colon dataset GSE236991 Runtime Siftome inference GEO:dataset:GSE236991:c355d30c5a99af20e1b987887ac001d3437e694e33e47c7d01a257604e5d6faa medium confidence colorectal dataset_accession: GSE236991 dataset_title: miRNA expression profile in 3 sporadic young-onset and 2 late-onset Indian colorectal carcinoma patients organism: Homo sapiens assay... controlled vocabulary controlled vocabulary tissue match: colorectal
tissue colon sample GSM7592739 Runtime Siftome inference GEO:sample:GSM7592739:9efb7aada5d12416ca43c429d36d1249f6555dc3bf38c83bc9cb5b454459d4ae low confidence colon sample_accession: GSM7592739 sample_title: Colorectal Carcinoma patient 39 years old, Normal colonic mucosa source_name: Normal colonic mucosa characteristics: tissue: Normal co... controlled vocabulary controlled vocabulary tissue match: colon
tissue colon sample GSM7592740 Runtime Siftome inference GEO:sample:GSM7592740:9b5e1d3ecd254ecc718ae79d6b7a534d431e4bb7cd5671d4cc78a2f6afe6bac6 low confidence colon sample_accession: GSM7592740 sample_title: Colorectal Carcinoma patient 39 years old, Tumor tissue source_name: Tumor tissue characteristics: tissue: Tumor tissue; Sex: female; ... controlled vocabulary controlled vocabulary tissue match: colon
tissue colon sample GSM7592741 Runtime Siftome inference GEO:sample:GSM7592741:b4d04e9a4dcd4d0367ea364168d2c26b326e544d9f5d1efdd057fddad637c34c low confidence colon sample_accession: GSM7592741 sample_title: Colorectal Carcinoma patient 44 years old, Normal colonic mucosa source_name: Normal colonic mucosa characteristics: tissue: Normal co... controlled vocabulary controlled vocabulary tissue match: colon
tissue colon sample GSM7592742 Runtime Siftome inference GEO:sample:GSM7592742:8c02ed50d0f3476b927091a3cd4c5454a57868e41998c2d2844cabdb6337a2d0 low confidence colon sample_accession: GSM7592742 sample_title: Colorectal Carcinoma patient 44 years old, Tumor tissue source_name: Tumor tissue characteristics: tissue: Tumor tissue; Sex: female; ... controlled vocabulary controlled vocabulary tissue match: colon
tissue colon sample GSM7592743 Runtime Siftome inference GEO:sample:GSM7592743:9d42c7b493822d7f2b6d8f8f381a2666eb55fabd23afef36489dd2300d16d2e9 low confidence colon sample_accession: GSM7592743 sample_title: Colorectal Carcinoma patient 47 years old, Normal colonic mucosa source_name: Normal colonic mucosa characteristics: tissue: Normal co... controlled vocabulary controlled vocabulary tissue match: colon
tissue colon sample GSM7592744 Runtime Siftome inference GEO:sample:GSM7592744:100dd4a34f465add34795ca6532d90d449c526af9a916ca148211dc08347b4f0 low confidence colon sample_accession: GSM7592744 sample_title: Colorectal Carcinoma patient 47 years old, Tumor tissue source_name: Tumor tissue characteristics: tissue: Tumor tissue; Sex: male; tu... controlled vocabulary controlled vocabulary tissue match: colon
tissue colon sample GSM7592745 Runtime Siftome inference GEO:sample:GSM7592745:1a67ee67e95bb898f07bf782570252184b82419c3982858d6561d05da17e297d low confidence colon sample_accession: GSM7592745 sample_title: Colorectal Carcinoma patient 66 years old, Normal colonic mucosa source_name: Normal colonic mucosa characteristics: tissue: Normal co... controlled vocabulary controlled vocabulary tissue match: colon
tissue colon sample GSM7592746 Runtime Siftome inference GEO:sample:GSM7592746:29d1098d997fdc23da5dc34801039a87594436f402db18e8d0bf75018b0488ae medium confidence colorectal sample_accession: GSM7592746 sample_title: Colorectal Carcinoma patient 66 years old, Tumor tissue source_name: Tumor tissue characteristics: tissue: Tumor tissue; Sex: male; tu... controlled vocabulary controlled vocabulary tissue match: colorectal
tissue colon sample GSM7592747 Runtime Siftome inference GEO:sample:GSM7592747:597a0534cae5d622cc5d747f5be39d9f469db8a5cdec1023ceec5f1530210c18 low confidence colon sample_accession: GSM7592747 sample_title: Colorectal Carcinoma patient 60 years old, Normal colonic mucosa source_name: Normal colonic mucosa characteristics: tissue: Normal co... controlled vocabulary controlled vocabulary tissue match: colon
tissue colon sample GSM7592748 Runtime Siftome inference GEO:sample:GSM7592748:d648c4652f57dddd5856e1fe209865269b08bd1c8af27ecad2c824067f53a2fe medium confidence colorectal sample_accession: GSM7592748 sample_title: Colorectal Carcinoma patient 60 years old, Tumor tissue source_name: Tumor tissue characteristics: tissue: Tumor tissue; Sex: female; ... controlled vocabulary controlled vocabulary tissue match: colorectal

Sample Group Preview

Possible case samples

Samples currently treated as the comparison case group.

5
  • GSM7592740 Colorectal Carcinoma patient 39 years old, Tumor tissue tumor sample Case marker detected. Tumor tissue tissue: Tumor tissue; Sex: female; tumor stage: T3N2bMx; tumor grade: G2; histopathological type: adenocarcinoma; location: Junction of ascending and transverse colon
  • GSM7592742 Colorectal Carcinoma patient 44 years old, Tumor tissue tumor sample Case marker detected. Tumor tissue tissue: Tumor tissue; Sex: female; tumor stage: T4aN0; tumor grade: G2; histopathological type: adenocarcinoma; location: Rectosigmoid colon
  • GSM7592744 Colorectal Carcinoma patient 47 years old, Tumor tissue tumor sample Case marker detected. Tumor tissue tissue: Tumor tissue; Sex: male; tumor stage: T2N0; tumor grade: G2; histopathological type: adenocarcinoma; location: Ascending colon and cecum
  • GSM7592746 Colorectal Carcinoma patient 66 years old, Tumor tissue tumor sample Case marker detected. Tumor tissue tissue: Tumor tissue; Sex: male; tumor stage: T3N2b; tumor grade: G2; histopathological type: adenocarcinoma; location: Rectum
  • GSM7592748 Colorectal Carcinoma patient 60 years old, Tumor tissue tumor sample Case marker detected. Tumor tissue tissue: Tumor tissue; Sex: female; tumor stage: T1N0; tumor grade: G1; histopathological type: adenocarcinoma; location: Rectum

Possible control samples

Samples currently treated as controls or baseline.

5
  • GSM7592739 Colorectal Carcinoma patient 39 years old, Normal colonic mucosa normal tissue Control marker detected. Normal colonic mucosa tissue: Normal colonic mucosa; Sex: female; histopathological type: normal colonic mucosa; location: Junction of ascending and transverse colon
  • GSM7592741 Colorectal Carcinoma patient 44 years old, Normal colonic mucosa normal tissue Control marker detected. Normal colonic mucosa tissue: Normal colonic mucosa; Sex: female; histopathological type: normal colonic mucosa; location: Rectosigmoid colon
  • GSM7592743 Colorectal Carcinoma patient 47 years old, Normal colonic mucosa normal tissue Control marker detected. Normal colonic mucosa tissue: Normal colonic mucosa; Sex: male; histopathological type: normal colonic mucosa; location: Ascending colon and cecum
  • GSM7592745 Colorectal Carcinoma patient 66 years old, Normal colonic mucosa normal tissue Control marker detected. Normal colonic mucosa tissue: Normal colonic mucosa; Sex: male; histopathological type: normal colonic mucosa; location: Rectum
  • GSM7592747 Colorectal Carcinoma patient 60 years old, Normal colonic mucosa normal tissue Control marker detected. Normal colonic mucosa tissue: Normal colonic mucosa; Sex: female; histopathological type: normal colonic mucosa; location: Rectum

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

5 samples
  • GSM7592739 Colorectal Carcinoma patient 39 years old, Normal colonic mucosa Normal colonic mucosa tissue: Normal colonic mucosa; Sex: female; histopathological type: normal colonic mucosa; location: Junction of ascending and transverse colon
  • GSM7592741 Colorectal Carcinoma patient 44 years old, Normal colonic mucosa Normal colonic mucosa tissue: Normal colonic mucosa; Sex: female; histopathological type: normal colonic mucosa; location: Rectosigmoid colon
  • GSM7592743 Colorectal Carcinoma patient 47 years old, Normal colonic mucosa Normal colonic mucosa tissue: Normal colonic mucosa; Sex: male; histopathological type: normal colonic mucosa; location: Ascending colon and cecum
  • GSM7592745 Colorectal Carcinoma patient 66 years old, Normal colonic mucosa Normal colonic mucosa tissue: Normal colonic mucosa; Sex: male; histopathological type: normal colonic mucosa; location: Rectum
  • GSM7592747 Colorectal Carcinoma patient 60 years old, Normal colonic mucosa Normal colonic mucosa tissue: Normal colonic mucosa; Sex: female; histopathological type: normal colonic mucosa; location: Rectum

tumor sample

5 samples
  • GSM7592740 Colorectal Carcinoma patient 39 years old, Tumor tissue Tumor tissue tissue: Tumor tissue; Sex: female; tumor stage: T3N2bMx; tumor grade: G2; histopathological type: adenocarcinoma; location: Junction of ascending and transverse colon
  • GSM7592742 Colorectal Carcinoma patient 44 years old, Tumor tissue Tumor tissue tissue: Tumor tissue; Sex: female; tumor stage: T4aN0; tumor grade: G2; histopathological type: adenocarcinoma; location: Rectosigmoid colon
  • GSM7592744 Colorectal Carcinoma patient 47 years old, Tumor tissue Tumor tissue tissue: Tumor tissue; Sex: male; tumor stage: T2N0; tumor grade: G2; histopathological type: adenocarcinoma; location: Ascending colon and cecum
  • GSM7592746 Colorectal Carcinoma patient 66 years old, Tumor tissue Tumor tissue tissue: Tumor tissue; Sex: male; tumor stage: T3N2b; tumor grade: G2; histopathological type: adenocarcinoma; location: Rectum
  • GSM7592748 Colorectal Carcinoma patient 60 years old, Tumor tissue Tumor tissue tissue: Tumor tissue; Sex: female; tumor stage: T1N0; tumor grade: G1; histopathological type: adenocarcinoma; location: Rectum

Score Breakdown

100%

relevance

  • Disease or condition metadata normalized.
  • Organism normalized.
  • Assay type normalized.
  • Tissue metadata normalized.
50%

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.
  • 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: 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.
50%

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 secondary RNA assays are not primary mRNA tissue RNA-seq.

Sample Links

10 samples

Review Audit Trail

0 decisions

No review decisions have been stored for this dataset.