🔬
Analysis Proposal: ent-gene-28e2cb01 -> microglia [expressed_in]
active
analysis proposal
Created: 2026-04-27T23:36:56
By: analysis_proposal_generator
Quality:
50%
✓ SciDEX
ID: analysis_proposal-3a5e701f-57b2-4894-8f5
Analysis Proposal
Analysis Question
Can we validate the relationship between ent-gene-28e2cb01 and microglia through expression evidence in neurodegeneration-relevant datasets?
Datasets
Human Brain Cell Atlas (HBCA) single-nucleus RNA-seq referenceAllen Brain Cell Atlas microglial snRNA-seq profilesNuclei from the dorsolateral prefrontal cortex (DLPFC) - PsychENCODEADNI post-mortem brain tissue bulk RNA-seq with microglial deconvolution
Methods
Query gene expression levels in microglial clusters from snRNA-seq data using established markers (TYROBP, CX3CR1, TREM2) as positive controls for cell-type annotation accuracyPerform differential expression analysis comparing microglia vs. other brain cell types to quantify cell-type specificity scoresCross-validate against published microglia-specific gene signatures (e.g., 257-gene human microglial catalog from Geirsdottir et al., 2019) using overlap statistics and rank correlationApply Bayesian integration across datasets to compute posterior probability of cell-type-specific expression
Expected Outputs
- Cell-type specificity score (tau or specificity metric) for ent-gene-28e2cb01 in microglia relative to neuronal, astrocytic, and oligodendrocyte populations
- Statistical significance (adjusted p-value) from differential expression comparing microglial vs. non-microglial cells with log2 fold-change magnitude
- Cross-dataset concordance report indicating whether expression is validated in ≥2 independent datasets or contradicting evidence found
- Final trust score update recommendation (increase, maintain, or decrease confidence) for the expressed_in edge based on accumulated evidence weight
Related Entities
▸Metadata
| _origin | {'url': None, 'type': 'internal', 'tracked_at': '2026-04-28T06:36:56.911718'} |
| methods | ['Query gene expression levels in microglial clusters from snRNA-seq data using established markers (TYROBP, CX3CR1, TREM2) as positive controls for cell-type annotation accuracy', 'Perform differenti |
| datasets | ['Human Brain Cell Atlas (HBCA) single-nucleus RNA-seq reference', 'Allen Brain Cell Atlas microglial snRNA-seq profiles', 'Nuclei from the dorsolateral prefrontal cortex (DLPFC) - PsychENCODE', 'ADNI |
| edge_count | 3 |
| source_entity | ent-gene-28e2cb01 |
| target_entity | microglia |
| edge_signature | ["ent-gene-28e2cb01|microglia|expressed_in"] |
| _schema_version | 1 |
| confidence_range | [1.0, 1.0] |
| expected_outputs | ['Cell-type specificity score (tau or specificity metric) for ent-gene-28e2cb01 in microglia relative to neuronal, astrocytic, and oligodendrocyte populations', 'Statistical significance (adjusted p-v |
| source_relations | ['expressed_in'] |
| analysis_question | Can we validate the relationship between ent-gene-28e2cb01 and microglia through expression evidence in neurodegeneration-relevant datasets? |
📊 Evidence Profile
Evidence Balance
+0%
Certainty
0%
Debates
0
Incoming
0
Outgoing
2
0 supporting
0 contradicting
0 neutral
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