Fig. 1.

Overview of integrated genomics with various other ‘omics’ platforms/data types created via array-based or spectrometry or NGS technologies and systems genomics analyses. a Collection of multiple types of ‘omics’ datasets in farm or companion animals in controlled experimental conditions or in field experiments. b Systems genomics involves analysis of single-layer (vertical arrows) and multi-layer ‘omic’ datasets (horizontal arrow) ranging from GWAS, differential expression or methylation analyses through proteomic/metabolomic datasets to eQTL/mQTL/pQTL and network analyses. c Typical results of systems genomics involve single- and multi-layer analyses from GWAS Manhattan plots, genome-wide epistatic heat plots, variant detection or transcript counts in NGS data and gene expression heat plots through eQTL maps, gene regulatory or co-expression networks of eQTL or protein–protein interaction (PPI) networks to networks of differentially connected genes. The eSNP/eQTL box plot is taken from Kogelman et al. [115]. The remaining images in this panel are from the authors’ own unpublished material. d Potential applications of such approaches involve identification of causal genes or pathways, biomarkers, drug targets, various networks for a specific trait level or disease state and individualized genomic predictions of performance or disease risk