Table 3 Summary of research approaches: Analytical strategies
From: Pathway-based analyses
Contribution | Pathway assembly | Probe/variant filters | Source of annotations/ biological significance | Analytical tools |
|---|---|---|---|---|
Brunel | Annotated to BP genes and interactors | Ontology, protein-protein interaction | Gene Ontology, other (unspecified) | Independent components analysis, GWAS in GenABEL |
Kos | Synthetic | Nonsynonymous or stop codon gain/loss | KEGG, Biocarta, Pathway Interaction Database, Reactome | SOLAR measured genotype association |
Lo | Annotated to type 2 diabetes genes and interactors | Not applicable | OMIM, GeneMania | Bespoke method to detect SNP-SNP interaction |
Quillen | Synthetic | Not applicable | Ariadne Pathway Studio 8.0 | Empirical similarity matrices, variance decomposition |
Tayo | Annotated to genes in specific pathway | BP-related pathway of interest | KEGG | PLINK association |
Valcarcel | Synthetic | Not reported | ANNOVAR | SKAT, burden tests |
Ziyatdinov | Associated with BP | Heritability | Gene Ontology | Linear mixed models |