The Pig RNA Atlas

The Pig RNA atlas is based on transcriptomics data representing the whole pig body. 350 individual tissue samples, representing 98 different tissues in the pig, were sampled from 4 Bama minipigs (2 male and 2 female).

A selection of the transcriptomics-based analysis are described in more detail in the individual summary pages:

The tissue specific proteome

The tissue specificity proteome describes the gene classification based on RNA abundance in the 44 organ/tissue types where genes are categorized according to their expression pattern across all tissue types. In total, 13372 genes are classified as elevated in one or a group of tissues, defined as having a four-fold higher expression in one or several tissues compared to the rest. The brain holds the highest number of genes classified as tissue elevated (2930) while the testis includes most genes categorized as tissue enriched (1004) with four-fold higher expression in testis compared to the second highest tissue.

Within- tissue variation

Out of the 44 organ/tissue types used for gene classification, 15 organ/tissue types consist of grouped tissues with similar function or cellular composition. To complement the whole-body classification these tissues were further investigated based on the expression variation within the grouped tissue types. For example, by comparing the expression profile of kidney cortex to kidney medulla, 916 genes are highlighted as significantly variable between the two.

14 organ system chapters

Each of the organ system is described in individual chapters, where expression overview, tables of enriched genes and short introductions are included. For example, learn more about how you can explore the differences between joint and ear cartilage in the database here, explore the long list of brain elevated genes or find out what genes are only expressed by the testis.

UMAP gene clustering

Genes were clustered based on their expression in all samples in order to stratify them into groups with related expression pattern and function, such that global transcriptomic structures can easily be navigated. The clustering of genes resulted in 84 clusters, annotated based on tissue specificity, function and expression levels. This enables a holistic view of the pig expression landscape.

The different clusters are visualized in the UMAP summary page and the UMAP cluster is listed on each individual gene summary pages.

The pig in biomedical research

An educational summary page is included, that describes the background of using pig as a model in biomedical research. Different human disease genes are described based on the organ system they are related to. The Pig RNA Atlas is a resource that can be used for studying the body-wide expression similarity and specificity to human in order to evaluate pig as a disease model.

The pig tissue dictionary

The tissue dictionary enables study of the pig tissue morphology. This is especially interesting since this is shown for the tissue adjacent to the tissue samples used for RNAsequencing, i.e., you can compare the detailed expression information with histological information. The Pig tissue dictionary is based on the similar dictionary available for human tissues at the HPA, enabling comparison between human and pig histology.