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Analysis Proposal: benchmark_ot_ad_answer_key:CCR6 -> ent-gene-a96ac1cf [data_in]

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analysis proposal Created: 2026-04-27T08:45:02 By: analysis_proposal_generator Quality: 50% ✓ SciDEX ID: analysis_proposal-5cee4165-0ee0-49bf-8ce

Analysis Proposal

Analysis Question

Can we validate the relationship between benchmark_ot_ad_answer_key:CCR6 and ent-gene-a96ac1cf in neurodegeneration contexts?

Datasets

GWAS Catalog (NHGRI-EBI) for CCR6 variant associationsAlzheimer's Disease Neuroimaging Initiative (ADNI) gene expression datasetHuman Protein Atlas RNA-seq data for brain tissueAllen Brain Atlas regional expression data

Methods

Cross-reference CCR6-associated GWAS variants with genomic coordinates of ent-gene-a96ac1cf using BEDTools interval intersectionPerform Pearson correlation analysis of CCR6 and ent-gene-a96ac1cf co-expression in ADNI prefrontal cortex RNA-seq samplesExecute STRINGdb protein-protein interaction query to assess physical association probabilityApply Textpresso NLP mining of PubMed abstracts for co-occurrence in neurodegeneration literature

Expected Outputs

Genomic overlap report: if ent-gene-a96ac1cf falls within CCR6 LD block (chr6:167400000-168000000), this supports cis-regulatory relationship
Co-expression correlation coefficient: r>0.6 in ADNI brain tissue would support functional co-regulation; r<0.3 would refute
STRINGdb interaction score: combined_score>700 indicates reliable protein interaction; score<400 suggests non-physical association
Literature mining count: >10 co-mentions in AD/Parkinson/ALS abstracts supports biological relevance; <3 co-mentions refutes

Related Entities

benchmark_ot_ad_answer_key:CCR6 ent-gene-a96ac1cf

Metadata

_origin	{'url': None, 'type': 'internal', 'tracked_at': '2026-04-27T08:45:02.537216'}
methods	['Cross-reference CCR6-associated GWAS variants with genomic coordinates of ent-gene-a96ac1cf using BEDTools interval intersection', 'Perform Pearson correlation analysis of CCR6 and ent-gene-a96ac1cf
datasets	['GWAS Catalog (NHGRI-EBI) for CCR6 variant associations', "Alzheimer's Disease Neuroimaging Initiative (ADNI) gene expression dataset", 'Human Protein Atlas RNA-seq data for brain tissue', 'Allen Bra
edge_count	1
source_entity	benchmark_ot_ad_answer_key:CCR6
target_entity	ent-gene-a96ac1cf
edge_signature	["benchmark_ot_ad_answer_key:CCR6\|ent-gene-a96ac1cf\|data_in"]
confidence_range	[0.0, 0.0]
expected_outputs	['Genomic overlap report: if ent-gene-a96ac1cf falls within CCR6 LD block (chr6:167400000-168000000), this supports cis-regulatory relationship', 'Co-expression correlation coefficient: r>0.6 in ADNI
source_relations	['data_in']
analysis_question	Can we validate the relationship between benchmark_ot_ad_answer_key:CCR6 and ent-gene-a96ac1cf 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:CCR6 -> ent-gene-a96ac1cf [data_in]

💬 Discussion