Ranking Candidate Genes for Bphs Phenotype

The positional candidate genes were ranked based on their predicted association with seven functional terms related to the Bphs phenotype: Cardiac, G-protein coupled receptor, Histamine, Pertussis toxin, Type I hypersensitivity, Vascular Permeability, and ER/EMC/ERAD. Gene Weaver^{74 (link)} was used to identify genes annotated with each term. Each term was entered the Gene Weaver homepage (https://geneweaver.org) and search restricted to human, rat, and mouse genes, and to curated lists only. Mouse homologs for each gene were retrieved using the batch query tool in MGI (http://www.informatics.jax.org/batch_data.shtml). In addition, using the Gene Expression Omnibus (GEO) and PubMed, additional gene expression data sets were retrieved for each phenotype term. Final gene lists consisted of the unique set of genes associated with each process term.

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Raza A., Diehl S.A., Krementsov D.N., Case L.K., Li D., Kost J., Ball R.L., Chesler E.J., Philip V.M., Huang R., Chen Y., Ma R., Tyler A.L., Mahoney J.M., Blankenhorn E.P, & Teuscher C. (2023). A genetic locus complements resistance to Bordetella pertussis-induced histamine sensitization. Communications Biology, 6, 244.

Publication 2023

Bphs Cardiac G protein coupled receptor Gene expression Genes Histamine Human Mouse Pertussis toxin Phenotype Type i hypersensitivity Vascular permeability

Corresponding Organization : University of Vermont

Other organizations : Jackson Laboratory, Florida Atlantic University, Catalytic Materials (United States), University of Chinese Academy of Sciences, Drexel University

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Variable analysis

independent variables

Gene annotations for seven functional terms related to the Bphs phenotype: Cardiac, G-protein coupled receptor, Histamine, Pertussis toxin, Type I hypersensitivity, Vascular Permeability, and ER/EMC/ERAD

dependent variables

Ranking of positional candidate genes based on their predicted association with the seven functional terms

control variables

Search was restricted to human, rat, and mouse genes
Search was restricted to curated lists only
Mouse homologs for each gene were retrieved using the batch query tool in MGI
Additional gene expression data sets were retrieved for each phenotype term from the Gene Expression Omnibus (GEO) and PubMed

controls

No positive or negative controls were explicitly mentioned

Annotations

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