Body fat content and the partition of lipid stores in the different tissues of the carcasses are important phenotypic traits to be considered for the sustainability of farm animal production. Indeed, fatty animals are generally less efficient in the conversion of feed during rearing period, and detrimental costs are associated to trimming of visible fats when butchering the carcasses. However, the fat content of meat and meat-processed products is generally linked to better scores of sensory quality traits. Both genetics and non-genetic factors are able to modify body fatness of animals, through their actions on lipid metabolism that occurs in key tissues. Energy input from nutrients is indeed partly stored in various organs and tissues into lipids that will be re-mobilized to cope with low energy intake periods, physiological transitions or stress situations. Thus, flexibility of lipid metabolism may influence the adaptation of animals to cope with various environments, including the distribution of diets formulated under the optimal requirements. To answer the question of elucidating key regulators of lipid metabolism associated to variations in body fat content and partition, we propose a systemic approach to unravel the flexibility of lipid metabolism into a generic frame. This systemic approach is based on acquisition of transcriptomics and lipidomics data in key tissues and the whole blood from genetic lines divergent for body fatness, and on statistical, bioinformatics and phylogenetics approaches to analyse the tissues- and species-specificities of the key actors. Complementary skills of teams gathering physiologists, (phylo)-geneticians, statisticians and bioinformaticians are mobilized. A coordinated diet (isoenergetic low vs high fat diets) x genotype (lines with divergence in body fatness) will be performed in growing animals of two phylogenetically-distant farm species (pigs and chickens). The FatInteger project proposes first to acquire new transcriptional data in 4 tissues (the liver, two fat pads, and one skeletal muscle) playing key roles in various aspects of lipid metabolism and in the whole blood integrating organs communication. Second, sets of differentially-expressed genes will be provided. Each gene-set will be analyzed more deeply by gene-network statistical approaches to identify modules in which genes are likely co-regulated by a same mechanism. Third, the key regulators in these gene-modules will be proposed by bioinformatics and promotology. To identify tissues- or species- specificities versus genericities, some of these genes and regulators will be compared between tissues and species, respectively, and the differences will be analyzed by the gene evolution of corresponding paralog (for tissue differences) and ortholog (for species-differences) genes. Fourth, phenotypic changes in pathways that are suggested to be correlated to the gene-sets, and having or not a priori links to lipid metabolism, will be checked in experimental animals or cell line cultures. Taken together, the FatInteger project will provide relevant answers and novel hypotheses related to the plasticity of body fatness and lipid metabolism in pigs and chickens, to offer clues for next feeding or genetic schemes. It will participate in developing statistical, bioinformatical and phylogenetical tools that could serve a wide community interested in analyzing transcriptomic data from various experimental settings.