The stomach-specific proteome

The stomach is the first reservoir for food intake and is limited by the cardia at the esophageal-stomach junction and pylorus at the stomach-duodenal junction. The main function of the stomach is to digest food by providing an acidic milieu and secretion of digestive enzymes. The acidic environment ensures enzyme activity and provides a barrier against ingested microorganisms. Food is mechanically processed into chyme via muscular contortions and slowly released to the duodenum for further breakdown and nutrient uptake. The stomach mucosa consists of a number of specialized cell types including chief cells, parietal cells, mucous producing cells and endocrine cells. Transcriptome analysis shows that 75% (n=14707) of all human proteins (n=19670) are expressed in the stomach and 159 of these genes show an elevated expression in the stomach compared to other tissue types.

  • 159 elevated genes
  • 17 enriched genes
  • 52 group enriched genes
  • Stomach has most group enriched gene expression in common with intestine and gallbladder

The stomach transcriptome

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

  • Tissue enriched: At least four-fold higher mRNA level in stomach 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 stomach compared to the average level in all other tissues.

Distribution, on the other hand, visualizes how many genes that have, or do not have, detectable levels (NX≥1) of transcribed mRNA molecules in the stomach compared to other tissues. As evident in Table 1, all genes elevated in stomach 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 stomach as well as in all other tissues. (B) The distribution of all genes across the six categories, based on transcript detection (NX≥1) in stomach as well as in all other tissues.

As shown in Figure 1, 159 genes show some level of elevated expression in the stomach compared to other tissues. The three categories of genes with elevated expression in stomach compared to other organs are shown in Table 1. In Table 2, the 12 genes with the highest enrichment in stomach are defined.

Table 1. Number of genes in the subdivided categories of elevated expression in stomach.

Distribution in the 37 tissues
Detected in singleDetected in someDetected in manyDetected in all Total
Tissue enriched 01610 17
Group enriched 040120 52
Tissue enhanced 135495 90
Total 191625 159

Table 2. The 12 genes with the highest level of enriched expression in stomach. "Tissue distribution" describes the transcript detection (NX≥1) in stomach as well as in all other tissues. "mRNA (tissue)" shows the transcript level in stomach as NX values. "Tissue specificity score (TS)" corresponds to the fold-change between the expression level in stomach and the tissue with second highest expression level.

Gene Description Tissue distribution mRNA (tissue) Tissue specificity score
PGA4 pepsinogen 4, group I (pepsinogen A) Detected in some 924.0 120
GAST gastrin Detected in some 529.2 61
GKN1 gastrokine 1 Detected in some 918.9 41
PGA5 pepsinogen 5, group I (pepsinogen A) Detected in some 296.9 38
PGA3 pepsinogen 3, group I (pepsinogen A) Detected in some 1048.8 28
GIF gastric intrinsic factor Detected in some 185.6 25
LIPF lipase F, gastric type Detected in some 762.9 24
ATP4B ATPase H+/K+ transporting beta subunit Detected in some 156.3 24
ATP4A ATPase H+/K+ transporting alpha subunit Detected in some 120.1 24
GKN2 gastrokine 2 Detected in some 311.1 8
AP003071.5 Detected in some 19.5 7
RFLNA refilin A Detected in many 118.3 6

Protein expression of genes elevated in stomach

In-depth analysis of the elevated genes in the stomach using antibody-based protein profiling allowed us to visualize the protein expression patterns in the stomach with respect to cellular compartments. In the list of stomach elevated genes multiple protein locations are found; GKN1 is localized to the superficial layer of the gastric mucosa, GIF show clear relation to parietal cells and PGC is predominant in chief cells.

GKN1 - gastric mucosa

GIF - parietal cells

PGC - chief cells

Gene expression shared between stomach and other tissues

There are 52 group enriched genes expressed in stomach. 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 stomach, compared to all other tissues.

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

Figure 2. An interactive network plot of the stomach enriched and group enriched genes connected to their respective enriched tissues (grey circles). Red nodes represent the number of stomach 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.

The stomach shares group enriched gene expression with several tissues, for example with the gallbladder, small intestine and duodenum. One example of a protein enriched in the stomach and duodenum is TFF2, encoding a secretory protein with undefined function. However, the protein may have protective characteristics for the mucus epithelium layer against various insults. TFF2 is expressed in gastric mucosa in the stomach and Brunner’s glands in the duodenum.

TFF2 - stomach

TFF2 - duodenum

Stomach histology

The stomach lies in the upper part of the abdomen between the esophagus and duodenum which forms the most proximal portion of the small intestine. It mixes food with gastric enzymes and fluids, converting the contents to a semi-fluid mass of partly digested food (chyme). The chyme is then slowly passed to the duodenum for further breakdown and absorption.

The stomach is a direct continuation of the esophagus and can be divided into different regions; the most proximal part is the cardia, followed by the fundus, corpus, antrum and pylorus. The fundus and corpus constitute about 80% of the stomach and differ from the antrum and pylorus both functionally and histologically. At the gastroesophageal junction the mucosa abruptly changes from a stratified squamous epithelium to simple cuboidal. The mucosa is thick and lined with simple columnar epithelium. The surface epithelium invaginates, creating gastric pits into which the fundus glands open. The fundus glands are straight glands that extend from the lowest portion of the mucosa to their opening at the bottom of the gastric pits. The fundic glands stain darker compared to the gastric pits. In the stomach, the lamina muscularis mucosae consist of two layers of smooth muscle and can easily be recognized. The submucosa is a thick layer of loose connective tissue with numerous blood and lymphatic vessels. Villous folds separate the gastric pits and display a connective tissue core, which is part of the lamina propria mucosae. The gastric pits are lined by pale stained simple columnar epithelium which secretes mucus into the stomach lumen. This mucus protects the stomach wall from the acidic gastric contents. A mucinous globule is typically present in the apical portion of the cells with an oval-shaped nucleus. The fundus glands have a narrow neck, a middle principal part and a lower base. In the neck portion, mucous neck cells are located. Their cytoplasm stain poorly with hematoxylin and eosin, but they can be recognized by their round nuclei. They secrete acidic mucus. In the principal part, parietal (oxyntic) cells are located. They have a strongly eosinophilic cytoplasm and a round, centrally located nucleus. They secrete hydrochloric acid and intrinsic factor. At the base of the glands, strongly basophilic cells are present. These are the chief cells that secrete large amounts of pepsinogen, a proteolytic enzyme.

The distal portion of the stomach, or the pylorus, connects the stomach to the duodenum. It has the same general structure as the fundus and body of the stomach with epithelial lined villous folds that invaginate into gastric pits. The cells lining the villous folds are surface mucous cells that produce alkaline mucus to protect the gastric mucosa from the acidic content of the stomach. At the bottom of the gastric pits the pyloric glands open. Instead of being simple tubular glands as the fundus glands, they are branched tubular glands. The cells of the pyloric glands are almost exclusively mucous secreting, resembling the mucous neck cells of the fundus glands. Within the pyloric glands gastrin producing enteroendocrine cells are also present.

The histology of human stomach 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 stomach are described and characterized, together with examples of immunohistochemically stained tissue sections that visualize corresponding protein expression patterns of genes with elevated expression in stomach.

Transcript profiling was based on a combination of three transcriptomics datasets (HPA, GTEx and FANTOM5), corresponding to a total of 9332 samples from 113 different human normal tissue types. The final consensus normalized expression (NX) value for each tissue type was used for 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

Yu NY et al., Complementing tissue characterization by integrating transcriptome profiling from the Human Protein Atlas and from the FANTOM5 consortium. Nucleic Acids Res. (2015)
PubMed: 26117540 DOI: 10.1093/nar/gkv608

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

Gremel G et al., The human gastrointestinal tract-specific transcriptome and proteome as defined by RNA sequencing and antibody-based profiling. J Gastroenterol. (2014)
PubMed: 24789573 DOI: 10.1007/s00535-014-0958-7

Histology dictionary - the stomach