GSE141174

Genome-wide analysis of colorectal cancer gene expression by using primary tumors, normal colon and lymph nodes

Whole-study status Needs manual review

Scores are usable, but sample metadata contains review-only concerns.

Whole-study downloads — these do not apply your sample requirements.

Selected cohort requirements

Samples meeting selected requirements: 0 cases / 0 controls

View matching samples

8 case / 8 control samples elsewhere in the study have incomplete or conflicting evidence; they are not included above

Patient pairs verified in indexed sample metadata: 0

A case/control comparison meeting these requirements is not confirmed.

Counts describe samples, not independent patients. Pair verification uses explicit subject identifiers in indexed sample metadata. Zero verified pairs does not establish that the study is unpaired; reported matched-normal design alone is insufficient.

Source: GEO
Assay: microarray
Organism: Homo sapiens
Whole-study samples: 16 samples
Specimen: Tissue
Reported/interpreted study design: Tumor vs normal; consult patient linkage Design classification does not establish patient pairs.

Comparison type: Tumor vs normal
Contributors: Hammarström S, Hammarström M, Olsson L
Contact name: Marie-Louise Hammarström
Submission date: 2019-11-29
Last update: 2020-02-13
Organization: Umeå universitet
Department: Clinical Microbiology
Public date: 2020-02-13
Experiment types: Expression profiling by array
Platforms: GPL6104 Illumina humanRef-8 v2.0 expression beadchip
Series type: Series
SubSeries: Not available
BioProject: PRJNA592547

Summary

Analysis of the difference in gene expression between colorectal cancer samples and control samples

Overall design

Total RNA was extracted from colorectal cancer primary tumors and lymph nodes metastasis and compared to RNA extracted from lymph nodes and colon tissue of control patients

Source Evidence

4 sources

Source	Contribution	Status
GEO	Original dataset metadata, sample metadata, source links, and GEO data availability flags. Sample records 16 GSM samples	Primary source
recount3	Planned trusted source for processed count availability.	No match found
Expression Atlas	Planned source for curated expression experiment links.	No match found
PubMed	Primary GEO citations and related PubMed articles that mention this dataset. 4 linked publications 4 DOIs Primary publication Allocating colorectal cancer patients to different risk categories by using a five-biomarker mRNA combination in lymph node analysis. PloS one, 2020 PubMed DOI Related publications E3 Ubiquitination Ligase MYLIP Mediates the NKRF/SLC25A34 Axis to Suppress Malignant Progression in Colorectal Cancer. Digestive diseases and sciences, 2025 PubMed DOI ITLN1 suppresses colorectal cancer progression by inhibiting Wnt/β-catenin-mediated EMT and reprogramming macrophage polarization. International immunopharmacology, 2026 PubMed DOI SPINK4 modulates inhibition of glycolysis against colorectal cancer progression. Biomolecules & biomedicine, 2024 PubMed DOI	Available

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: Anatomical source 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.

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

Verify the proposed sample assignments and case-versus-control comparison against the GEO metadata before using them in DESeq2 or another differential-expression tool.
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.

Review the grouping table for biologically meaningful differences that the automated checks may not detect.

Exclusion decisions recorded

Ready

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

Record any manual exclusions in the downstream analysis notes.

Source traceability preserved

Ready

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

Keep GEO accessions with exported metadata.

Bioinformatician Review

Bioinformatician review required

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

Assay context may require expert handling before DESeq2-style analysis.

Why This Is Ranked Here

Tumor vs normal

Needs manual review Scores are usable, but sample metadata contains review-only concerns.

Applied Review Decisions

No active review decisions affect this ranking.

Derived Classifications

Assay differs from search intent Microarray Search intent expects bulk RNA-seq. Assay came from Normalization rules.
Disease context Crohn's disease, colorectal cancer, ulcerative colitis Disease context came from Normalization rules.
Likely case group Colorectal cancer 8 samples
Likely control group Control 8 samples

Intent Interpretation

Downgrade or exclusion reason Downgraded assay: microarray cohorts are separated from the RNA-seq intent. Derived from current-intent ranking reasons.

Ranking Facts

Supporting evidence

Comparison: Tumor vs unmatched normal. Specimen: Tissue. Comparison suitability: 100%.
Interpreted disease metadata: Colorectal cancer, Crohn's disease, Ulcerative colitis.
Processed data is available for downstream review.
External evidence: PubMed links 4 publications; 4 DOIs available: PMID 32049988, PMID 38747892, PMID 39661280, PMID 41747601.
Publication context: Allocating colorectal cancer patients to different risk categories by using a five-biomarker mRNA combination in lymph node analysis.. PloS one, 2020. PMID 32049988. DOI 10.1371/journal.pone.0229007.
Publication context: SPINK4 modulates inhibition of glycolysis against colorectal cancer progression.. Biomolecules & biomedicine, 2024. PMID 38747892. DOI 10.17305/bb.2024.10338.
Publication context: E3 Ubiquitination Ligase MYLIP Mediates the NKRF/SLC25A34 Axis to Suppress Malignant Progression in Colorectal Cancer.. Digestive diseases and sciences, 2025. PMID 39661280. DOI 10.1007/s10620-024-08735-9.
Publication context: 1 additional linked PubMed publications are available.

Cautions

Downgraded assay: microarray cohorts are separated from the RNA-seq intent.

Dataset Warnings

Microarray expression context was detected; compare separately from RNA-seq cohorts.
Multiple disease or phenotype arms were detected. The displayed grouping summarizes the full dataset; select the requested disease-specific contrast before analysis.
Microarray datasets are downgraded in the patient-tissue tumor-normal intent unless secondary assays are explicitly enabled.

Normalized Fields

46 fields

Field Value Source Derived by Confidence Evidence Reason

anatomical_source colon GSM4196531 Runtime Siftome inference UNRESOLVED / UNREVIEWED medium confidence colorectal sample_title: Colorectal cancer lymph node no1 sample-anatomical-source-v1 sample-local anatomical source

anatomical_source colon GSM4196532 Runtime Siftome inference UNRESOLVED / UNREVIEWED medium confidence colorectal sample_title: Colorectal cancer lymph node no1_2 sample-anatomical-source-v1 sample-local anatomical source

anatomical_source colon GSM4196533 Runtime Siftome inference UNRESOLVED / UNREVIEWED medium confidence colorectal sample_title: Colorectal cancer lymph node no2 sample-anatomical-source-v1 sample-local anatomical source

anatomical_source colon GSM4196537 Runtime Siftome inference UNRESOLVED / UNREVIEWED medium confidence colorectal sample_title: Colorectal cancer primary tumor no1 sample-anatomical-source-v1 sample-local anatomical source

anatomical_source colon GSM4196538 Runtime Siftome inference UNRESOLVED / UNREVIEWED high confidence colon source_name: Normal colon sample-anatomical-source-v1 sample-local anatomical source

anatomical_source colon GSM4196539 Runtime Siftome inference UNRESOLVED / UNREVIEWED medium confidence colorectal sample_title: Colorectal cancer lymph node no3 sample-anatomical-source-v1 sample-local anatomical source

anatomical_source colon GSM4196540 Runtime Siftome inference UNRESOLVED / UNREVIEWED medium confidence colorectal sample_title: Colorectal cancer lymph node no4 sample-anatomical-source-v1 sample-local anatomical source

anatomical_source colon GSM4196543 Runtime Siftome inference UNRESOLVED / UNREVIEWED medium confidence colorectal sample_title: Colorectal cancer primary tumor no2 sample-anatomical-source-v1 sample-local anatomical source

anatomical_source colon GSM4196544 Runtime Siftome inference UNRESOLVED / UNREVIEWED medium confidence colorectal sample_title: Colorectal cancer primary tumor no3 sample-anatomical-source-v1 sample-local anatomical source

anatomical_source colon GSM4196545 Runtime Siftome inference UNRESOLVED / UNREVIEWED high confidence colon source_name: Normal colon sample-anatomical-source-v1 sample-local anatomical source

anatomical_source colon GSM4196546 Runtime Siftome inference UNRESOLVED / UNREVIEWED high confidence colon source_name: Normal colon sample-anatomical-source-v1 sample-local anatomical source

assay_type microarray GSE141174 Runtime Siftome inference UNRESOLVED / UNREVIEWED high confidence microarray dataset_accession: GSE141174 dataset_title: Genome-wide analysis of colorectal cancer gene expression by using primary tumors, normal colon and lymph nodes organism: Homo sapien... keyword match keyword match: microarray

disease colorectal cancer GSE141174 Runtime Siftome inference UNRESOLVED / UNREVIEWED high confidence colorectal cancer dataset_accession: GSE141174 dataset_title: Genome-wide analysis of colorectal cancer gene expression by using primary tumors, normal colon and lymph nodes organism: Homo sapien... controlled vocabulary controlled vocabulary disease match: colorectal cancer

disease colorectal cancer GSM4196531 Runtime Siftome inference UNRESOLVED / UNREVIEWED high confidence colorectal cancer Colorectal cancer lymph node no1 Lymph node disease state: stage III controlled vocabulary controlled vocabulary disease match: colorectal cancer

disease colorectal cancer GSM4196532 Runtime Siftome inference UNRESOLVED / UNREVIEWED high confidence colorectal cancer Colorectal cancer lymph node no1_2 Lymph node disease state: stage III controlled vocabulary controlled vocabulary disease match: colorectal cancer

disease colorectal cancer GSM4196533 Runtime Siftome inference UNRESOLVED / UNREVIEWED high confidence colorectal cancer Colorectal cancer lymph node no2 Lymph node disease state: stage III controlled vocabulary controlled vocabulary disease match: colorectal cancer

disease ulcerative colitis GSM4196534 Runtime Siftome inference UNRESOLVED / UNREVIEWED high confidence ulcerative colitis Control lymph node no1 UC Lymph node disease state: ulcerative colitis controlled vocabulary controlled vocabulary disease match: ulcerative colitis

disease colorectal cancer GSM4196537 Runtime Siftome inference UNRESOLVED / UNREVIEWED high confidence colorectal cancer Colorectal cancer primary tumor no1 Primary tumor disease state: stage III controlled vocabulary controlled vocabulary disease match: colorectal cancer

disease colorectal cancer GSM4196539 Runtime Siftome inference UNRESOLVED / UNREVIEWED high confidence colorectal cancer Colorectal cancer lymph node no3 Lymph node disease state: stage III controlled vocabulary controlled vocabulary disease match: colorectal cancer

disease colorectal cancer GSM4196540 Runtime Siftome inference UNRESOLVED / UNREVIEWED high confidence colorectal cancer Colorectal cancer lymph node no4 Lymph node disease state: stage III controlled vocabulary controlled vocabulary disease match: colorectal cancer

disease ulcerative colitis GSM4196541 Runtime Siftome inference UNRESOLVED / UNREVIEWED high confidence ulcerative colitis Control lymph node no3 Lymph node disease state: ulcerative colitis controlled vocabulary controlled vocabulary disease match: ulcerative colitis

disease Crohn's disease GSM4196542 Runtime Siftome inference UNRESOLVED / UNREVIEWED high confidence Crohn's disease Control lymph node no4 Lymph node disease state: Crohn's disease controlled vocabulary controlled vocabulary disease match: Crohn's disease

disease colorectal cancer GSM4196543 Runtime Siftome inference UNRESOLVED / UNREVIEWED high confidence colorectal cancer Colorectal cancer primary tumor no2 Primary tumor disease state: stage III controlled vocabulary controlled vocabulary disease match: colorectal cancer

disease colorectal cancer GSM4196544 Runtime Siftome inference UNRESOLVED / UNREVIEWED high confidence colorectal cancer Colorectal cancer primary tumor no3 Primary tumor disease state: stage III controlled vocabulary controlled vocabulary disease match: colorectal cancer

organism Homo sapiens GSE141174 Runtime Siftome inference UNRESOLVED / UNREVIEWED high confidence homo sapiens dataset_accession: GSE141174 dataset_title: Genome-wide analysis of colorectal cancer gene expression by using primary tumors, normal colon and lymph nodes organism: Homo sapien... keyword match keyword match: homo sapiens

sample_type tumor sample GSM4196537 Runtime Siftome inference UNRESOLVED / UNREVIEWED high confidence source_name: Primary tumor source_name: Primary tumor reported-sample-specimen-v1 explicit sample-local specimen label

sample_type normal tissue GSM4196538 Runtime Siftome inference UNRESOLVED / UNREVIEWED low confidence normal Normal colon no1 Normal colon disease state: normal colon controlled vocabulary controlled vocabulary sample type match: normal

sample_type tumor sample GSM4196543 Runtime Siftome inference UNRESOLVED / UNREVIEWED high confidence source_name: Primary tumor source_name: Primary tumor reported-sample-specimen-v1 explicit sample-local specimen label

sample_type tumor sample GSM4196544 Runtime Siftome inference UNRESOLVED / UNREVIEWED high confidence source_name: Primary tumor source_name: Primary tumor reported-sample-specimen-v1 explicit sample-local specimen label

sample_type normal tissue GSM4196545 Runtime Siftome inference UNRESOLVED / UNREVIEWED low confidence normal Normal colon no2 Normal colon disease state: normal colon controlled vocabulary controlled vocabulary sample type match: normal

sample_type normal tissue GSM4196546 Runtime Siftome inference UNRESOLVED / UNREVIEWED low confidence normal Normal colon no3 Normal colon disease state: normal colon controlled vocabulary controlled vocabulary sample type match: normal

tissue colon GSE141174 Runtime Siftome inference UNRESOLVED / UNREVIEWED low confidence colon dataset_accession: GSE141174 dataset_title: Genome-wide analysis of colorectal cancer gene expression by using primary tumors, normal colon and lymph nodes organism: Homo sapien... controlled vocabulary controlled vocabulary tissue match: colon

tissue colon GSM4196531 Runtime Siftome inference UNRESOLVED / UNREVIEWED medium confidence colorectal Colorectal cancer lymph node no1 Lymph node disease state: stage III controlled vocabulary controlled vocabulary tissue match: colorectal

tissue colon GSM4196532 Runtime Siftome inference UNRESOLVED / UNREVIEWED medium confidence colorectal Colorectal cancer lymph node no1_2 Lymph node disease state: stage III controlled vocabulary controlled vocabulary tissue match: colorectal

tissue colon GSM4196533 Runtime Siftome inference UNRESOLVED / UNREVIEWED medium confidence colorectal Colorectal cancer lymph node no2 Lymph node disease state: stage III controlled vocabulary controlled vocabulary tissue match: colorectal

tissue colon GSM4196537 Runtime Siftome inference UNRESOLVED / UNREVIEWED medium confidence colorectal Colorectal cancer primary tumor no1 Primary tumor disease state: stage III controlled vocabulary controlled vocabulary tissue match: colorectal

tissue colon GSM4196538 Runtime Siftome inference UNRESOLVED / UNREVIEWED low confidence colon Normal colon no1 Normal colon disease state: normal colon controlled vocabulary controlled vocabulary tissue match: colon

tissue colon GSM4196539 Runtime Siftome inference UNRESOLVED / UNREVIEWED medium confidence colorectal Colorectal cancer lymph node no3 Lymph node disease state: stage III controlled vocabulary controlled vocabulary tissue match: colorectal

tissue colon GSM4196540 Runtime Siftome inference UNRESOLVED / UNREVIEWED medium confidence colorectal Colorectal cancer lymph node no4 Lymph node disease state: stage III controlled vocabulary controlled vocabulary tissue match: colorectal

tissue colon GSM4196543 Runtime Siftome inference UNRESOLVED / UNREVIEWED medium confidence colorectal Colorectal cancer primary tumor no2 Primary tumor disease state: stage III controlled vocabulary controlled vocabulary tissue match: colorectal

tissue colon GSM4196544 Runtime Siftome inference UNRESOLVED / UNREVIEWED medium confidence colorectal Colorectal cancer primary tumor no3 Primary tumor disease state: stage III controlled vocabulary controlled vocabulary tissue match: colorectal

tissue colon GSM4196545 Runtime Siftome inference UNRESOLVED / UNREVIEWED low confidence colon Normal colon no2 Normal colon disease state: normal colon controlled vocabulary controlled vocabulary tissue match: colon

tissue colon GSM4196546 Runtime Siftome inference UNRESOLVED / UNREVIEWED low confidence colon Normal colon no3 Normal colon disease state: normal colon controlled vocabulary controlled vocabulary tissue match: colon

tumor_type primary tumor GSM4196537 Runtime Siftome inference UNRESOLVED / UNREVIEWED high confidence primary tumor Colorectal cancer primary tumor no1 Primary tumor disease state: stage III controlled vocabulary controlled vocabulary tumor type match: primary tumor

tumor_type primary tumor GSM4196543 Runtime Siftome inference UNRESOLVED / UNREVIEWED high confidence primary tumor Colorectal cancer primary tumor no2 Primary tumor disease state: stage III controlled vocabulary controlled vocabulary tumor type match: primary tumor

tumor_type primary tumor GSM4196544 Runtime Siftome inference UNRESOLVED / UNREVIEWED high confidence primary tumor Colorectal cancer primary tumor no3 Primary tumor disease state: stage III controlled vocabulary controlled vocabulary tumor type match: primary tumor

Sample Group Preview

16 rows shown Show Hide

Study totals: Case 8 | Control 8 | Unassigned 0 | Excluded 0 | Ambiguous 0 16 rows shown

Group	Role	Accession	Title	Source / characteristics	Reason
Colorectal cancer	Case	GSM4196531	Colorectal cancer lymph node no1	Lymph node Disease state: Stage III	Case marker detected.
Colorectal cancer	Case	GSM4196532	Colorectal cancer lymph node no1_2	Lymph node Disease state: Stage III	Case marker detected.
Colorectal cancer	Case	GSM4196533	Colorectal cancer lymph node no2	Lymph node Disease state: Stage III	Case marker detected.
Tumor sample	Case	GSM4196537	Colorectal cancer primary tumor no1	Primary tumor Disease state: Stage III	Explicit sample label case marker detected.
Colorectal cancer	Case	GSM4196539	Colorectal cancer lymph node no3	Lymph node Disease state: Stage III	Case marker detected.
Colorectal cancer	Case	GSM4196540	Colorectal cancer lymph node no4	Lymph node Disease state: Stage III	Case marker detected.
Tumor sample	Case	GSM4196543	Colorectal cancer primary tumor no2	Primary tumor Disease state: Stage III	Explicit sample label case marker detected.
Tumor sample	Case	GSM4196544	Colorectal cancer primary tumor no3	Primary tumor Disease state: Stage III	Explicit sample label case marker detected.
Control	Control	GSM4196534	Control lymph node no1 UC	Lymph node Disease state: Ulcerative colitis	Sample-local control marker detected.
Control	Control	GSM4196535	Control lymph node no2	Lymph node Disease state: Lipoma	Sample-local control marker detected.
Control	Control	GSM4196536	Control lymph node no2_2	Lymph node Disease state: Lipoma	Sample-local control marker detected.
Normal tissue	Control	GSM4196538	Normal colon no1	Normal colon Disease state: Normal colon	Sample-local control marker detected.
Control	Control	GSM4196541	Control lymph node no3	Lymph node Disease state: Ulcerative colitis	Sample-local control marker detected.
Control	Control	GSM4196542	Control lymph node no4	Lymph node Disease state: Crohn's disease	Sample-local control marker detected.
Normal tissue	Control	GSM4196545	Normal colon no2	Normal colon Disease state: Normal colon	Sample-local control marker detected.
Normal tissue	Control	GSM4196546	Normal colon no3	Normal colon Disease state: Normal colon	Sample-local control marker detected.

Use as Discovery Cohort

External Validation Finder

Carry Siftome's disease, organism, specimen, assay, data type, and accession into a validation project. Uncertain fields remain Unknown.

Summary

Overall design

Source Evidence

Primary publication

Related publications

Metadata Quality Components

Analysis Readiness

Blockers

Next Steps

Analysis Preparation Checklist

Bioinformatician Review

Why This Is Ranked Here

Applied Review Decisions

Derived Classifications

Intent Interpretation

Ranking Facts

Supporting evidence

Cautions

Dataset Warnings

Normalized Fields

Sample Group Preview

Use as Discovery Cohort