GSE20941

Mediators in Crohn’s disease influence the gene expression profiles of mesenchymal progenitor cells differentiated into the osteoblastic lineage.

Whole-study status Not suitable

Dataset does not meet the current suitability threshold.

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

Selected cohort requirements

Samples meeting selected requirements: 0 cases / 0 controls

View matching samples

12 case / 0 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
12 samples
Specimen
Tissue
Reported/interpreted study design
Unclear study design Design classification does not establish patient pairs.
Comparison type
Tumor vs normal
Contributors
Blaschke M, Cortis J, Baums MH, Köpp R, Raddatz D, Schuetze N, Miosge N, Salinas-Riester G, Siggelkow H, Salinas G
Contact name
Gabriela Salinas
Submission date
2010-03-18
Last update
2018-02-22
Organization
Universitaetsmedizin Goettingen
Department
Department of Pathology
Public date
2012-03-16
Experiment types
Expression profiling by array
Platforms
GPL4133 Agilent-014850 Whole Human Genome Microarray 4x44K G4112F (Feature Number version)
Series type
Series
SubSeries
Not available
BioProject
PRJNA124421

Summary

Crohn’s disease (CD) is associated with a higher prevalence of osteoporosis, a complication that is increasingly recognised as a significant cause of morbidity. Its pathogenesis is still controversial, but activity of CD is thought to be one contributing factor.

Overall design

Two-Color DRLL-IS-Design [Landgrebe et.al 2004: Efficient two-sample designs for microarray experiments with biological replications. In Silico Biology 4] including 12 Arrays, osteoporosis samples from 4 mc patients, control samples from 3 mc patients without osteoporosis

Source Evidence

4 sources
Source Contribution Status
GEO

Original dataset metadata, sample metadata, source links, and GEO data availability flags.

Sample records
12 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

Publication context when PubMed identifiers are already known.

 No match found

Metadata Quality Components

Persisted metadata quality

78 pts
Clarity
78%
Weight
100 pts

Sample source clarity: All samples have source metadata and clear GSE/GSM accessions. Group clarity: Only one side of the comparison is clearly grouped. Disease clarity: Disease or condition metadata normalized. Tissue clarity: Tissue metadata was not 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

Not ready
52% DE readiness

Contrast completeness

10/25 pts

Only one side of the contrast is present; downstream DE needs both groups.

Minimum group size

0/20 pts

Minimum group size cannot be evaluated until a complete contrast exists.

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

0/10 pts

Critical warnings must be resolved before downstream analysis.

Metadata normalization

7/10 pts

Metadata quality is usable, but still deserves review.

Blockers

  • No complete case/control contrast is available.
  • Critical dataset warnings must be resolved.

Next Steps

  • Resolve critical warnings before downstream analysis.

Analysis Preparation Checklist

4/6 ready

Group labels reviewed

Blocked

No complete case/control grouping exists yet.

Review the sample grouping table and assign both case and control groups.

Minimum sample count met

Blocked

At least one group has fewer than 2 samples.

Choose a larger dataset or merge only scientifically valid groups.

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.

Analysis readiness has blockers that must be resolved before DE.

Analysis preparation checklist contains blocked items.

No complete case/control or treatment/control contrast is available.

At least one comparison group has fewer than two samples.

Critical dataset warnings are present.

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

Study design is model-system or unclear and should be reviewed before analysis.

Why This Is Ranked Here

Tumor vs normal
Not suitable Dataset does not meet the current suitability threshold.

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 Disease context came from Normalization rules.
  • Likely case group Tumor sample 12 samples
  • Likely control group No control group detected 0 samples

Intent Interpretation

  • Downgrade or exclusion reason Comparison: Unclear study design. Specimen: Tissue. Comparison suitability: 0%. Derived from current-intent ranking reasons.

Ranking Facts

Supporting evidence

  • Interpreted disease metadata: Crohn's disease.
  • Processed data is available for downstream review.

Cautions

  • Comparison: Unclear study design. Specimen: Tissue. Comparison suitability: 0%.
  • Downgraded for tissue search because study design or specimen source is unclear.
  • Downgraded assay: microarray cohorts are separated from the RNA-seq intent.
  • Unclear study design downgraded for patient tissue tumor-vs-normal search intent.
  • Missing or unclear metadata. Unclear study design downgraded for patient tissue tumor-vs-normal search intent.
  • Microarray expression context downgraded below primary bulk RNA-seq for the default tissue ranking.
  • Missing or unclear metadata. Tissue clarity - Tissue metadata was not normalized.
  • Overall score capped because comparison suitability is weak for the selected search intent.
  • Overall score capped because microarray cohorts should be compared separately from RNA-seq cohorts.
  • Missing or unclear metadata. Comparison - Unclear study design. Specimen - Tissue. Comparison suitability: 0%.
  • Missing or unclear metadata. Downgraded for tissue search because study design or specimen source is unclear.
  • Comparison suitability score is below the Phase 1 recommended threshold.

Dataset Warnings

Normalized Fields

27 fields

Sample Group Preview

12 rows shown Show Hide
Study totals: Case 12 | Control 0 | Unassigned 0 | Excluded 0 | Ambiguous 0 12 rows shown
Group Role Accession Title Source / characteristics Reason
Tumor sample Case GSM523728 Replicate 1 OP1 Tissue: Bone spongiosa; Cell type: Mesenchymal progenitor cells (human MSCs); Disease status: Metastatic Crohn's disease with osteoporosis Case marker detected.
Tumor sample Case GSM523729 Replicate 2 C2 Tissue: Bone spongiosa; Cell type: Mesenchymal progenitor cells (human MSCs); Disease status: Metastatic Crohn's disease without osteoporosis Case marker detected.
Tumor sample Case GSM523730 Replicate 3 OP3 Tissue: Bone spongiosa; Cell type: Mesenchymal progenitor cells (human MSCs); Disease status: Metastatic Crohn's disease with osteoporosis Case marker detected.
Tumor sample Case GSM523731 Replicate 4 C1 Tissue: Bone spongiosa; Cell type: Mesenchymal progenitor cells (human MSCs); Disease status: Metastatic Crohn's disease without osteoporosis Case marker detected.
Tumor sample Case GSM523732 Replicate 5 OP1 Tissue: Bone spongiosa; Cell type: Mesenchymal progenitor cells (human MSCs); Disease status: Metastatic Crohn's disease with osteoporosis Case marker detected.
Tumor sample Case GSM523733 Replicate 6 C1 Tissue: Bone spongiosa; Cell type: Mesenchymal progenitor cells (human MSCs); Disease status: Metastatic Crohn's disease without osteoporosis Case marker detected.
Tumor sample Case GSM523734 Replicate 7 OP2 Tissue: Bone spongiosa; Cell type: Mesenchymal progenitor cells (human MSCs); Disease status: Metastatic Crohn's disease with osteoporosis Case marker detected.
Tumor sample Case GSM523735 Replicate 8 C2 Tissue: Bone spongiosa; Cell type: Mesenchymal progenitor cells (human MSCs); Disease status: Metastatic Crohn's disease without osteoporosis Case marker detected.
Tumor sample Case GSM523736 Replicate 9 OP3 Tissue: Bone spongiosa; Cell type: Mesenchymal progenitor cells (human MSCs); Disease status: Metastatic Crohn's disease with osteoporosis Case marker detected.
Tumor sample Case GSM523737 Replicate 10 C3 Tissue: Bone spongiosa; Cell type: Mesenchymal progenitor cells (human MSCs); Disease status: Metastatic Crohn's disease without osteoporosis Case marker detected.
Tumor sample Case GSM523738 Replicate 11 OP4 Tissue: Bone spongiosa; Cell type: Mesenchymal progenitor cells (human MSCs); Disease status: Metastatic Crohn's disease with osteoporosis Case marker detected.
Tumor sample Case GSM523739 Replicate 12 C1 Tissue: Bone spongiosa; Cell type: Mesenchymal progenitor cells (human MSCs); Disease status: Metastatic Crohn's disease without osteoporosis Case 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.