A PoCo is a set of genomic loci that collectively “cover” a larger fraction of case samples while minimally covering control samples.
Since our aim is to find sets of variants that are related to each other in their association with a phenotype, utilizing interaction data can be a powerful tool to provide a functional context for PoCos.
To identify NetPocos, in addition to GWAS data, we utilize a heterogeneous network represents the functional relationships among genomic loci. The network has two types of nodes, proteins and loci.
The interaction in a network comes from protein-protein interaction network, region of interest of genes and expression quantitative trait loci data.
PoCos can be utilize for different context such as prioritizing locus pairs for testing epistasis and also risk assessment.
The source code for identification of PoCos is implemented in MATLAB.