Liver & Gallbladder

The liver plays a central role in metabolism, detoxification and the production of bile, while the gallbladder stores and concentrates bile where this organ is present. Although liver functions are highly conserved across mammals, differences in liver anatomy and lobular organization may contribute to variation in tissue-level gene expression.

Liver tissue is available for all four species, with two separate liver lobes sampled in macaque, rat and mouse, whereas pig is represented by a single general liver sample. For the tissue specificity analysis, samples from different liver lobes are combined into one main tissue type, liver, although potential differences between lobes can be explored at the individual sample level. Gallbladder samples are available for macaque, pig and mouse, while rats anatomically lack a gallbladder, representing a genuine species difference rather than missing sampling.

Figure 1. Tissue sample overview and the hierarchy of grouped tissues representing liver & gallbladder

Comparative transcriptomics of the mammalian liver and gallbladder

The transcriptomic data is used to identify genes with elevated expression in individual tissues or groups of tissues, classified into three categories:

Tissue enriched: Genes with elevated expression in a single tissue compared with all other tissues.
Group enriched: Genes with elevated expression in a limited group of tissues compared with the remaining tissues.
Tissue enhanced: Genes with elevated expression in one or more tissues compared with the average expression across tissues (gap ratio ≥2)

Tissue specificity is evaluated at two levels: first, within each species using all available tissue types, and second, using only tissues that can be directly compared between the species and human. This distinction makes it possible to explore both tissue-specific expression within each species and the conservation of expression patterns across evolution.

The results can be explored for individual genes on the gene summary pages or searched to identify genes with specific expression patterns. To assess evolutionary conservation, pairwise overlap analysis compares each species individually with human, identifying genes that share the same tissue specificity classification in corresponding tissues and quantifying the extent of overlap between species.

Tissue	Species	Elevated	Human elevated overlap
Tissue	Species	Elevated	Complete overlap	Partial overlap
Gallbladder	Macaque	146	1	22
	Mouse	112	2	11
	Pig	60	2	12
Liver	Macaque	491	243	148
	Mouse	650	215	197
	Rat	484	186	138
	Pig	508	173	174

Liver

The liver has a broadly conserved lobular organization across mammals, with hepatocytes performing metabolic and synthetic functions and specialized non-parenchymal cells supporting vascular, immune and biliary processes. However, the organization of connective tissue surrounding hepatic lobules differs, being particularly distinct in pigs, where prominent interlobular septa make the lobular boundaries easier to identify than in humans and rodents.

Species coverage

Gallbladder

The gallbladder stores and concentrates bile produced by the liver, and its epithelial cells contribute to fluid and electrolyte transport. It is present in humans, macaques, pigs and mice but absent in rats, which deliver bile directly to the intestine. Even among species with a gallbladder, differences in epithelial folding, wall organization and bile composition may influence gene expression.