The ovary-specific proteome

The main function of the ovary, a paired organ forming a major component of the female genital system, is to produce and release mature oocytes and produce hormones needed for female reproduction. There are approximately 40,000 primary oocytes (germ cells) arrested in prophase at female puberty and from these, only some 400 undergo complete meiosis and develop into secondary oocytes. The main constituents of adult ovaries are hormone producing ovarian stromal cells. Transcriptome analysis shows that 67% (n=13461) of all human proteins (n=20162) are expressed in the ovary and 178 of these genes show an elevated expression in the ovary compared to other tissue types.

  • 178 elevated genes
  • 5 enriched genes
  • 28 group enriched genes
  • Ovary has most group enriched gene expression in common with brain and testis

The ovary transcriptome

Transcriptome analysis of the ovary can be visualized with regard to the specificity and distribution of transcribed mRNA molecules (Figure 1). Specificity illustrates the number of genes with elevated or non-elevated expression in the ovary compared to other tissues. Elevated expression includes three subcategory types of elevated expression:

  • Tissue enriched: At least four-fold higher mRNA level in ovary compared to any other tissues.
  • Group enriched: At least four-fold higher average mRNA level in a group of 2-5 tissues compared to any other tissue.
  • Tissue enhanced: At least four-fold higher mRNA level in ovary compared to the average level in all other tissues.

Distribution, on the other hand, visualizes how many genes have, or do not have, detectable levels (nTPM≥1) of transcribed mRNA molecules in the ovary compared to other tissues. As evident in Table 1, all genes elevated in ovary are categorized as:

  • 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 a third but not all tissues
  • Detected in all: Detected in all tissues

A. Specificity

B. Distribution

Figure 1. (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 (nTPM≥1) in ovary as well as in all other tissues.

As shown in Figure 1, 178 genes show some level of elevated expression in the ovary compared to other tissues. The three categories of genes with elevated expression in ovary compared to other organs are shown in Table 1. In Table 2, the 5 enriched genes are defined.

Table 1. The number of genes in the subdivided categories of elevated expression in ovary.

Distribution in the 36 tissues
Detected in singleDetected in someDetected in manyDetected in all Total
Tissue enriched 2120 5
Group enriched 01693 28
Tissue enhanced 4319119 145
Total 64810222 178

Table 2. The 5 genes with enriched expression in ovary. "Tissue distribution" describes the transcript detection (nTPM≥1) in ovary as well as in all other tissues. "mRNA (tissue)" shows the transcript level in ovary as nTPM values. "Tissue specificity score (TS)" corresponds to the fold-change between the expression level in ovary and the tissue with second highest expression level.

Gene Description Tissue distribution mRNA (tissue) Tissue specificity score
PADI6 peptidyl arginine deiminase 6 Detected in single 5.6 56
ZP4 zona pellucida glycoprotein 4 Detected in single 3.6 18
KLHDC8A kelch domain containing 8A Detected in many 275.0 9
LHX9 LIM homeobox 9 Detected in some 18.3 5
GREB1 growth regulating estrogen receptor binding 1 Detected in many 269.4 4

Protein expression of genes elevated in ovary

In-depth analysis of the elevated genes in ovary using antibody-based protein profiling allowed us to visualize where these proteins are expressed within the ovary including follicular cells and stromal cells.

Examples of proteins with elevated expression in the ovary include PWWP3B, a protein of unknown function expressed in both ovarian stroma cells and follicle cells, RBP1, a carrier protein involved in intracellular transport of vitamin A and CDH11, a type II classical cadherin that mediates calcium-dependent cell-cell adhesion, expressed in stromal cells.




Gene expression shared between ovary and other tissues

There are 28 group enriched genes expressed in ovary. Group enriched genes are defined as genes showing a 4-fold higher average level of mRNA expression in a group of 2-5 tissues, including ovary, compared to all other tissues.

To illustrate the relation of ovary tissue to other tissue types, a network plot was generated, displaying the number of genes with a shared expression between different tissue types.

Figure 2. An interactive network plot of the ovary enriched and group enriched genes connected to their respective enriched tissues (grey circles). Red nodes represent the number of ovary 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 4 tissues, but the resulting lists show the complete set of group enriched genes in the particular tissue.

The ovary shares most group enriched gene expression with the brain and testis, but also to a lesser degree with several other tissues, including heart muscle and fallopian tube. Inhibin alpha subunit, INHA, is a subunit of the inhibin A and B protein complexes. These complexes are involved in the male and female reproductive processes as negative regulators of sex hormone release, inhibiting follicle stimulating hormone (FSH) secretion from the pituitary gland. INHA is group enriched in both ovary and testis, and IHC show staining located to the ovarian follicles as well as to the testicular sex hormone producing leydig cells and the cells of the seminiferous ducts.

INHA - ovary

INHA - ovary (primary follicle)

INHA - testis

Ovary function

The function of the ovary is to develop female germinal cells, oocytes, and to produce the hormones estrogen, testosterone and progesterone which are necessary for reproduction. Estrogen is responsible for the appearance of secondary sex characteristics for females at puberty and the maturation and maintenance of the reproductive organs in their mature functional state. Progesterone prepares the uterus for pregnancy and the mammary glands for lactation. Together with estrogen, progesterone functions by promoting menstrual cycle changes in the endometrium.

The ovarian follicle is an anatomical structure in which the primary oocyte develops. The cell types of the ovarian follicle include the oocyte and the granulosa cells which surround the follicle. The granulosa cells, in turn, are enclosed in a thin layer of extracellular matrix - the follicular basement membrane or basal lamina. Outside the basal lamina, the layers theca interna and theca externa are found.

In the reproductive period the primordial follicles are scattered irregularly in clusters throughout the superficial cortex of the ovary. The primordial follicles eventually develop into primary, secondary and tertiary vesicular follicles. Each month, typically only one developing primary follicle becomes dominant and achieves complete maturation to release the oocyte. Other developing follicles undergo atresia.

Follicular phase

The follicular phase lasts from the beginning of menstruation to the start of ovulation and is the phase of the menstrual cycle during which the ovarian follicles mature.

Follicle-stimulating hormone (FSH), produced by the anterior pituitary gland, begins to rise in the last few days of the previous menstrual cycle and is highest during the first week of the follicular phase. The rise in FSH levels recruits tertiary-stage ovarian follicles for entry into the menstrual cycle.

The anterior pituitary gland also produces luteinizing hormone (LH), which induces androgen synthesis and secretion by theca cells. Under the influence of FSH, granulosa cells begin to convert androgens coming from the theca cells to estrogen. Elevated estrogen levels induce the proliferation of granulosa cells and thereby maturation of the follicle. The increase of estrogen also stimulates the production of gonadotropin-releasing hormone (GnRH) by the hypothalamus, which in turn increases the production of LH by the anterior pituitary gland.

Two or three days before LH levels begin to increase normally one of the follicles has emerged as dominant. In addition to effects on follicle maturation and hormone production by the CNS, the increase in estrogen levels also leads to the formation of a new layer of endometrium in the uterus, histologically identified as the proliferative endometrium.


The surge in levels of LH and FSH lasts from 24 to 36 hours, and results in the rupture of the ovarian follicles, causing the oocyte to be released from the ovary via the fallopian tube. The oocyte, or ovum, will travel down one of the fallopian tubes, pushed along by peristaltic contractions and ciliary movement, beginning its journey toward the uterus. If no fertilization occurs, the ovum will degenerate between 12 and 24 hours after ovulation and eventually be discharged through menstruation.

Figure 3. The ovaries, fallopian tubes and uterus. The menstrual cycle can be described both by the uterine cycle and the ovarian cycle which consists of the follicular phase, ovulation, and the luteal phase. During the follicular phase follicles in the ovary start to mature and during ovulation the dominant follicle releases an ovum (egg) via the fallopian tube. After ovulation, during the luteal phase, the remaining parts of the follicle transform into the corpus luteum which produces hormones that support the early pregnancy or if the ovum is not fertilized will undergo atrophy leading to falling levels of hormones and the beginning of the next menstrual cycle. If fertilized the ovum develops into a blastocyst and implantation in the uterus is made possible through changes in both the blastocyst and endometrial wall. Implantation enables the next step in embryogenesis which includes formation of the placenta.

Luteal phase

After ovulation FSH and LH cause the remaining parts of the dominant follicle to transform into the corpus luteum. It continues to grow for some time after ovulation and produces significant amounts of hormones, particularly progesterone and, to a lesser extent, estrogen. Progesterone plays a vital role in making the endometrium receptive to implantation of the blastocyst and supportive of the early phase of pregnancy.

The hormones produced by corpus luteum suppress the production of FSH and LH that the corpus luteum needs to maintain itself. With continued low levels of FSH and LH, the corpus luteum will undergo atrophy. The death of the corpus luteum results in falling levels of progesterone and estrogen. These falling levels of ovarian hormones cause increased levels of FSH, which begins recruiting follicles for the next cycle. Continued drops in levels of estrogen and progesterone trigger the end of the luteal phase: menstruation and the beginning of the next cycle.

The loss of the corpus luteum can be prevented by implantation of an embryo: after implantation, human embryos produce human chorionic gonadotropin (hCG), which is structurally similar to LH and can preserve the corpus luteum. If implantation occurs, the corpus luteum will continue to produce progesterone for eight to twelve weeks, after which the placenta takes over this function.

Ovary histology

The ovaries are paired organs that lie on either side of the uterus close to the lateral pelvic wall, behind the broad ligament and anterior to the rectum. Each ovary is attached to a broad ligament along by a double fold of peritoneum, the mesovarium.

Ovaries of adult women in the reproductive age-group are approximately 3 to 5 x 1.5 to 3 x 0.6-1.5 cm but their size varies considerably due to follicular derivatives. The external surface is usually convoluted. Three ill-defined zones may be discerned on the cut surface: an outer cortex, a central medulla and the hilus. Follicular structures (cystic follicles, corpora lutea and white corpora albicantia) are usually visible in the cortex.

The ovarian cortex consists of ovarian follicles with stroma in between them. Included in the follicles are the cumulus oophorus, membrana granulosa (and the granulosa cells inside it), corona radiata, zona pellucida, and primary oocyte. The zona pellucida, theca of follicle, antrum and liquor folliculi are also contained in the follicle. Also in the cortex is the corpus luteum derived from the follicles. The innermost layer is the ovarian medulla. It can be hard to distinguish between the cortex and medulla, but follicles are usually not found in the medulla.

The ovary also contains blood and lymphatic vessels.

The surface epithelium, or germinal epithelium, of the ovary forms a simple, focally pseudostratified layer. The cells vary from flat to cuboidal to columnar, and several types may be seen in different areas of the same ovary. The cells are separated from the underlying stroma by a basement membrane.

The primordial follicles are comprised of a primary oocyte, 40 to 70 µm in diameter, surrounded by a single layer of mitotically inactive squamous follicular cells, resting on thin basal lamina.

The histology of human ovary including detailed images and information about the different cell types can be viewed in the Protein Atlas Histology Dictionary.


Here, the protein-coding genes expressed in ovary are described and characterized, together with examples of immunohistochemically stained tissue sections that visualize corresponding protein expression patterns of genes with elevated expression in ovary.

Transcript profiling was based on a combination of two transcriptomics datasets (HPA and GTEx), corresponding to a total of 14590 samples from 50 different human normal tissue types. The final consensus normalized expression (nTPM) value for each tissue type was used for the classification of all genes according to the tissue-specific expression into two different categories, based on specificity or distribution.

Relevant links and publications

Uhlén M et al., Tissue-based map of the human proteome. Science (2015)
PubMed: 25613900 DOI: 10.1126/science.1260419

Fagerberg L et al., Analysis of the human tissue-specific expression by genome-wide integration of transcriptomics and antibody-based proteomics. Mol Cell Proteomics. (2014)
PubMed: 24309898 DOI: 10.1074/mcp.M113.035600

Histology dictionary - the ovary