The tissue specific proteome

All (22342) protein-coding pig genes are classified according to their expression across 44 different organ/tissue types. In total, 98 different tissues (350 samples) were sampled from Bama minipig and analyzed by RNA sequencing. The tissues were grouped into 44 different organ/tissue types used for gene classification based on expression distribution and abundance in the different tissue types. You can learn more about sampling method and details in the about section.

Figure 1. Illustrative overview of the tissue types included in the tissue specific classification strategy.

The brain (2930) and testis (2718) are the two tissues with most genes categorized as tissue elevated. In the table below the 44 different tissue types, used for gene classification, are listed with the respective number of genes classified as tissue elevated.

Table 1. The 44 tissues and the number of genes classified as elevated in respective tissue type.

Tissue specificity and tissue distribution

To complement the tissue specificity category, all genes are classified based on detection above cut off (NX=1). The tissue distribution category visualizes how many genes that have, or do not have, detectable levels (NX=1) of transcribed mRNA molecules and includes 4 categories:

• Detected in single - Detected in a single tissue
• Detected in some - Detected in more than one but less than one third of tissues
• Detected in many - Detected in at least one third but not in all tissues
• Detected in all - Detected in all tissues

The combination of tissue specificity and tissue distribution provides an overview of the tissue expression across all genes and tissues, shown in table 2.

Table 2. Number of genes in the subdivided categories of tissue specificity and tissue distribution, based on the 44 tissue types.

Genes with tissue enriched expression

The 3085 genes classified as tissue enriched represents genes with high expression in one tissue compared to all other tissues. In table 3 the top 10 genes with highest Tissue Specificity (TS) score are shown.

Table 3. The 10 genes with the highest level of enriched expression. Tissue specificity score (TS) corresponds to the fold-change between the expression level in the tissue with highest expression level and the tissue with the second highest expression level.

As observed, the lens accounts for all genes with highly abundant expression, and this is due to the unique expression of crystallines.

The antibody resource within the HPA project was utilized to detect proteins in pig tissues, and verifying the tissue specificity on protein level (further described here). Figure 2 shows five example genes, all classified as tissue enriched, where the protein product has been localized in pig tissues. MOG codes for a glycoprotein involved in nerve myelination and is almost exclusively expressed by the brain. ASGR1 is a transmembrane protein mediating the endocytosis, classified as liver enriched and is a potential target for liver-specific drugs. The testis enriched CRISP2 is rather uncharacterized but is potentially associated with male infertility in humans. TNNT1 is a well-studied protein expressed by the slow skeletal muscle. The skin enriched DSC1 codes for a calcium-dependent glycoprotein important for cell-cell junctions.

Figure 2. Immunohistochemical images of genes classified as tissue enriched in pig. The antibodies used are MOG - HPA021873, ASGR1 - HPA012852, CRISP2 - HPA031248, TNNT1 - HPA058448 and DSC1 - HPA075379

Expression variation within organ/tissues

For the whole-body classification strategy, we used 44 tissue types as representation where the highest expression value among the grouped tissues were used as representation for a certain tissue/organ type. In total, 15 organ/tissue types include grouped tissues, which enable further expression analysis into more detailed tissue profiling based on expression variation within the respective organ/tissue type.

Significantly differentially expressed genes (4-fold expression difference) are found within grouped tissue types for all tissues except for lung, where the expression profile of lung and bronchus are too similar. Brain includes most genes highlighted as variable, which is expected since brain have 30 different sub regions included in the analysis.

• brain - including 30 different sub regions, further described here and 4635 genes are highlighted as variable within the brain.
• upper respiratory system - includes olfactory epithelium, nasopharynx epithelium, trachea and larynx. 765 genes show variable expression within the upper respiratory system.
• lung - bronchus and lung was samples separately, however there was not significant variation in expression between the two.
• mouth - tongue, oral mucosa and lip represents the mouth and 240 genes are highlighted as variable within the mouth.
• stomach - upper and lower stomach was sampled and resulted in 390 genes with variable expression.
• small intestine - duodenum, jejunum and ilium was sampled from the small intestine, expression comparison showed that 117 genes are variable between the tissues.
• large intestine - cecum, colon and rectum comparison highlighted 113 genes with variable expression.
• kidney - comparing kidney cortex and medulla, highlights 916 genes as kidney variable.
• male glands - prostate, urethral gland, seminal vesicle and bulbourethral gland, comparison resulted in 3366 genes classified as male gland variable.
• heart - ventricle wall, atrium wall and mitral valve analysis indicated 332 genes as hear variable
• adipose tissues - orbital, abdominal and subcutaneous, highlight 382 genes with variable expression in adipose tissue.
• mesothelial tissues - pleura and peritoneum, showed 58 genes with variable expression.
• cartilage - ear and joint cartilage comparison resulted in 1362 genes with variable expression profile.
• skin - groin and back skin expression analysis showed that 100 genes are variable expressed between the two.
• lymphoid tissues - lymph node, tonsil, thymus and spleen highlights 3143 genes with variable expression.