Fig. 1

Biological concept of the PATOWAS pipeline and biological insight of an example association mapping resulting from PATOWAS. a Three types of omic markers to phenotype association mappings, e.g., (1) genome-wide sequence/genotype variation to phenotypic variation mapping (G2P or GWAS), (2) transcriptome-wide gene expression variation to phenotypic variation mapping (T2P or TWAS), and (3) metabolome-wide metabolite abundance variation to phenotypic variation mapping (M2P or MWAS), can be analyzed using the unified linear mixed model in PATOWAS. b PATOWAS needs 2D omics marker matrix data and 1D phenotypic trait data as input. Specific PATOWAS results include (1) variance component analysis result showing two biologically meaningful components: additive, additive–additive, and residual; (2) 1D association mapping for the Additive component; and (3) 2D association mapping for the Additive–Additive component, and further, the significant omics marker pairs extracted by thresholding