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Analysis Proposal: benchmark_ot_ad_answer_key:HERC5 -> ent-gene-8299600b [data_in]

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analysis proposal Created: 2026-04-27T08:43:58 By: analysis_proposal_generator Quality: 50% ✓ SciDEX ID: analysis_proposal-80c6b5f0-88ef-47a3-a7a

Analysis Proposal

Analysis Question

Can we validate the data_in relationship between benchmark_ot_ad_answer_key:HERC5 and ent-gene-8299600b in neurodegeneration contexts?

Datasets

GTEx v8 brain tissue gene expression (RNA-seq)STRING v12 protein-protein interaction databaseAlzheimer's Disease Neuroimaging Initiative (ADNI) gene expression matricesNHGRI-EBI GWAS Catalog (neurodegeneration-associated variants)

Methods

Pearson correlation of HERC5 expression with ent-gene-8299600b across brain regions and cell types in GTEx/ADNINetwork proximity analysis: compute shortest path distance between HERC5 and ent-gene-8299600b in STRING high-confidence PPI networkLiterature-based co-mention analysis via PubMed API queries for HERC5 and ent-gene-8299600b identifiers in neurodegeneration abstractsMendelian randomization/colocalization using eQTLs for both genes in brain tissue to assess shared causal signals

Expected Outputs

Pearson r > 0.3 with FDR < 0.05 in ≥3 brain regions, indicating coordinated transcriptional regulation
Network distance < 3 edges in STRING with evidence_score > 0.7, confirming physical/functional proximity
≥5 PubMed abstracts with joint mention in neurodegeneration context, supporting biological relevance
Significant colocalization (PP4 > 0.8) at shared locus, suggesting shared causal mechanism

Related Entities

benchmark_ot_ad_answer_key:HERC5 ent-gene-8299600b

Metadata

_origin	{'url': None, 'type': 'internal', 'tracked_at': '2026-04-27T08:43:58.897517'}
methods	['Pearson correlation of HERC5 expression with ent-gene-8299600b across brain regions and cell types in GTEx/ADNI', 'Network proximity analysis: compute shortest path distance between HERC5 and ent-ge
datasets	['GTEx v8 brain tissue gene expression (RNA-seq)', 'STRING v12 protein-protein interaction database', "Alzheimer's Disease Neuroimaging Initiative (ADNI) gene expression matrices", 'NHGRI-EBI GWAS Cat
edge_count	1
source_entity	benchmark_ot_ad_answer_key:HERC5
target_entity	ent-gene-8299600b
edge_signature	["benchmark_ot_ad_answer_key:HERC5\|ent-gene-8299600b\|data_in"]
confidence_range	[0.0, 0.0]
expected_outputs	['Pearson r > 0.3 with FDR < 0.05 in ≥3 brain regions, indicating coordinated transcriptional regulation', 'Network distance < 3 edges in STRING with evidence_score > 0.7, confirming physical/function
source_relations	['data_in']
analysis_question	Can we validate the data_in relationship between benchmark_ot_ad_answer_key:HERC5 and ent-gene-8299600b in neurodegeneration contexts?

📊 Evidence Profile

Evidence Balance

+0%

Certainty

Debates

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Outgoing

0 supporting 0 contradicting 0 neutral

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Analysis Proposal: benchmark_ot_ad_answer_key:HERC5 -> ent-gene-8299600b [data_in]

💬 Discussion