Female tissues

Histological image of the tissues used in the analysis can be found in the pig tissue dictionary.

Ovary

The ovary is a paired organ and is an important component of the sow genitalia system. The main function is to produce and release mature oocytes and produce hormones that are needed for reproduction. The released oocyte travels down the fallopian tube into the uterus. In the ovary, oocytes mature in fluid-filled follicles that changes during the maturation process. After rupture of the follicle and release of the mature oocyte, the follicle changes into a corpus luteum, secreting steroid hormones.

Gene expression in ovary is categorized based on two gene classification strategies, tissue detection and tissue specificity. Figure 3 summarizes the number of genes in respective category. In total, 14772 genes are detected above cut of (1NX) in pig ovary. The tissue distribution category highlights 5 genes only detected in ovary while 343 genes are classified as ovary elevated compared to other tissues. Table 1 shows the overlap for the ovary elevated genes and tissue distribution category.

Figure 3, (A) The distribution of all genes across the five categories based on transcript specificity in ovary as well as in all other tissues. (B) The distribution of all genes across the six categories, based on transcript detection (NX≥1) in ovary as well as in all other tissues. The combination of the two categories is shown in table 1.

Table 1, Number of genes in the subdivided categories of elevated expression and tissue distribution in ovary

Ovary enriched expression

In the list of genes classified as ovary enriched in pig, there are several genes with different expression profiles in human and pig. In fact, most of the top 10 enriched - genes in pig ovary is not expressed or expressed at much lower levels in the human ovary. For example, BMP15 show ovary enriched expression in pig but is not detected in the human ovary. TMEM56 is classified as ovary enriched in pig but liver enriched in human, SERPINE1 is highly expressed in the human placenta (not included in the pig dataset) and human ovary only show low expression, compared to the pig ovary expression enrichment. The prorelaxin precursor (RLN2) is only detected in the pig ovary, while in human show high expression in nucleus accumbens of the basal ganglia in brain.

Table 2, The 10 genes with the highest level of enriched expression in ovary. "mRNA (tissue)" shows the transcript level in ovary as NX values. "Tissue specificity score (TS)" corresponds to the fold-change between the expression level in ovary and the tissue with second highest expression level.

Fallopian tube

The fallopian tubes, also called oviducts, are the tubes in which the oocytes transports through from the ovary to the uterus. The inside of the fallopian tube is lined with simple columned epithelium with ciliated cells. Gene expression in fallopian tube is categorized based on two gene classification strategies, tissue detection and tissue specificity. Figure 4 summarizes the number of genes in respective category. In total, 15717 genes are detected above cut of (1NX) in pig fallopian tube. The tissue distribution category highlights 4 genes only detected in fallopian tube while 432 genes are classified as fallopian tube elevated compared to other tissues. Table 3 shows the overlap for the fallopian tube elevated genes and tissue distribution category.

Figure 4, (A) The distribution of all genes across the five categories based on transcript specificity in fallopian tube as well as in all other tissues. (B) The distribution of all genes across the six categories, based on transcript detection (NX≥1) in fallopian tube as well as in all other tissues. The combination of the two categories is shown in table 3.

Table 3, Number of genes in the subdivided categories of elevated expression and tissue distribution in fallopian tube

Fallopian tube enriched expression

The large portion of ciliated cells in the fallopian tube is evident when examining the genes classified as fallopian tube elevated. However, since several other tissue types also include ciliated cells, cilia associated genes are often shared and classified as group enriched or enhanced. The fallopian tube only resulted in 4 genes classified as tissue enriched, where the gene with highest tissue specificity is oviduct-specific glycoprotein precursor OVGP1. OVGP1 codes for a large glycoprotein and suggested to be secreted from non-ciliated cells in the fallopian tube.

Table 4, The 4 genes classified as enriched in fallopian tube. "mRNA (tissue)" shows the transcript level in fallopian tube as NX values. "Tissue specificity score (TS)" corresponds to the fold-change between the expression level in fallopian tube and the tissue with second highest expression level.

Endometrium

The endometrium refers to the inner epithelial layer and mucosal layer of the uterus. In pig the uterus body is rather small in comparison to human. The uterine body acts more lika a part of the birth canal in pig rather than location for the development of fetuses, which instead mainly takes place in the uterine horn. The samples used in this study was taken from the upper part of the uterine body. Gene expression in endometrium is categorized based on two gene classification strategies, tissue detection and tissue specificity. Figure 5 summarizes the number of genes in respective category. In total, 15439 genes are detected above cut of (1NX) in pig endometrium. The tissue distribution category highlights 2 genes only detected in adrenal gland while 140 genes are classified as endometrium elevated compared to other tissues. Table 5 shows the overlap for the endometrium elevated genes and tissue distribution category.

Figure 5, (A) The distribution of all genes across the five categories based on transcript specificity in endometrium as well as in all other tissues. (B) The distribution of all genes across the six categories, based on transcript detection (NX≥1) in endometrium as well as in all other tissues. The combination of the two categories is shown in table 5.

Table 5, Number of genes in the subdivided categories of elevated expression and tissue distribution in endometrium

Endometrium enriched expression

The endometrium tissue resulted only in 4 genes classified as tissue enriched. All without gene name, except SLC39A2, coding for a zink transporter, which in human is mainly expressed by male tissues.

Table 6, The 10 genes with the highest level of enriched expression in endometrium. "mRNA (tissue)" shows the transcript level in endometrium as NX values. "Tissue specificity score (TS)" corresponds to the fold-change between the expression level in endometrium and the tissue with second highest expression level.

Examples of interesting findings among the genes classified as elevated in endometrium includes ADD2 shared between female tissues, brain and endocrine tissues. Both ACTA2 and AGTR2 are shared between male and female tissues.

Cervix

Gene expression in cervix is categorized based on two gene classification strategies, tissue detection and tissue specificity. Figure 6 summarizes the number of genes in respective category. In total, 14558 genes are detected above cut of (1NX) in pig cervix. The tissue distribution category highlights 2 genes only detected in cervix while 169 genes are classified as adrenal gland elevated compared to other tissues. Table 7 shows the overlap for the cervix elevated genes and tissue distribution category.

Figure 6, (A) The distribution of all genes across the five categories based on transcript specificity in cervix as well as in all other tissues. (B) The distribution of all genes across the six categories, based on transcript detection (NX≥1) in cervix as well as in all other tissues. The combination of the two categories is shown in table 7.

Table 7, Number of genes in the subdivided categories of elevated expression and tissue distribution in cervix

Cervix enriched expression

Table 8, The 4 genes with the highest level of enriched expression in cervix. "mRNA (tissue)" shows the transcript level in cervix as NX values. "Tissue specificity score (TS)" corresponds to the fold-change between the expression level in cervix and the tissue with second highest expression level.

Cervix includes a large proportion smooth muscle and a layer of epithelium, viewable in the tissue dictionary. Based on the tissue specificity classification cervix expression resulted in only 4 genes classified as enriched. HPSE2 overlaps with human expression profile, with highest expression in cervix, while HRK and ABL1 shows differences to human tissue expression. Cervix share several proteins with other female tissues, such as the estrogen receptor alpha (ESR1) and progesterone receptor (PGR), classified as group enriched and shared with endometrium and fallopian tube.

Surprisingly, there is a number of genes among the cervix elevated shared with the brain, for example GALNT9, NXPH3 and TRIM9.

Breast

In the sampling of the breast tissue, the fatty tissue close to the nipple was removed from the skin and half of each tissue sample was fixed and morphologically examined while the other half was used for RNA sequencing. Gene expression in breast is categorized based on two gene classification strategies, tissue detection and tissue specificity. Figure 7 summarizes the number of genes in respective category. In total, 15368 genes are detected above cut of (1NX) in pig breast. The tissue distribution category highlights 13 genes only detected in breast while 153 genes are classified as breast elevated compared to other tissues. Table 9 shows the overlap for the breast elevated genes and tissue distribution category.

Figure 7, (A) The distribution of all genes across the five categories based on transcript specificity in breast as well as in all other tissues. (B) The distribution of all genes across the six categories, based on transcript detection (NX≥1) in breast as well as in all other tissues. The combination of the two categories is shown in table 9.

Table 9, Number of genes in the subdivided categories of elevated expression and tissue distribution in breast

Breast enriched expression

Table 10, The 10 genes with the highest level of enriched expression in breast. "mRNA (tissue)" shows the transcript level in breast as NX values. "Tissue specificity score (TS)" corresponds to the fold-change between the expression level in breast and the tissue with second highest expression level.

Beta-lactoglobulin- 1A/1C Beta-lactoglobulin-1A/1C PAEP is highly enriched in pig breast tissue compared to other tissues, however, the human orthologue is not enriched in breast tissue. Compared to ABCC11, CSN1S1 and CSN2, which all show breast enriched expression in both pig and human.

An other example of breast enriched protein that differ between pig and human is SCGN, a calcium binding protein with important neuroendocrine functions. In human SCGN is highly expressed in pituitary gland and very low expression in breast, whereas in pig highest expression levels is observed in breast and much lower in pitutiary gland.

Immunohistochemically labeled SCGN in pig tissues (from left, breast, olfactory bulb, esophagus, retina) using HPA006641.

Gene expression in female tissues compared to other tissues

In order to illustrate the relation of female tissue to other tissue types, a network plot was generated, displaying the number of genes shared between different tissue types. Group enriched genes are defined as genes showing a 4-fold higher average level of mRNA expression in a group of 2-5 tissues, compared to all other tissues.

Figure 8. An interactive network plot of the female enriched and group enriched genes connected to their respective enriched tissues (grey circles). Black circles shows tissues representing the female reproductive tissues. Red nodes represent the number of tissue enriched genes and orange nodes represent the number of genes that are group enriched. The sizes of the red and orange nodes are related to the number of genes displayed within the node. Each node is clickable and results in a list of all enriched genes connected to the highlighted edges. The network is limited to group enriched genes in combinations of up to 3 tissues, but the resulting lists show the complete set of group enriched genes in the particular tissue.