The stomach-specific proteome

The stomach is a 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. The transcriptome analysis shows that 69% of all human proteins (n=19628) are expressed in the stomach and 161 of these genes show an elevated expression in stomach compared to other tissue types. An analysis of the corresponding proteins with regard to tissue distribution shows that a large fraction of these proteins are secreted and mainly expressed in various glandular cells of the stomach mucosa.

  • 23 stomach enriched genes
  • 161 genes defined as elevated in the stomach
  • Most of elevated genes encode proteins in the stomach that are secreted

Figure 1. The distribution of all genes across the five categories based on transcript abundance in stomach as well as in all other tissues.

161 genes show some level of elevated expression in the stomach compared to other tissues. The four categories of genes with elevated expression in stomach compared to other organs are shown in Table 1. The list of genes defined as tissue enriched in stomach (n=23), are mainly secreted and well in-line with the major functions of the stomach.

Table 1. The genes with elevated expression in stomach


Number of genes


Tissue enriched 23 At least five-fold higher mRNA levels in a particular tissue as compared to all other tissues
Group enriched 47 At least five-fold higher mRNA levels in a group of 2-7 tissues
Tissue enhanced 91 At least five-fold higher mRNA levels in a particular tissue as compared to average levels in all tissues
Total 161 Total number of elevated genes in stomach

Table 2. The 12 genes with the highest level of enriched expression in stomach. "Predicted localization" shows the classification of each gene into three main classes: Secreted, Membrane, and Intracellular, where the latter consists of genes without any predicted membrane and secreted features. "mRNA (tissue)" shows the transcript level asáTPM values,áTS-score (Tissue Specificity score) corresponds to the score calculated as the fold change to the second highest tissue.



Predicted localization

mRNA (tissue)


PGA4 pepsinogen 4, group I (pepsinogen A) Intracellular,Secreted 27159.5 4166
GIF gastric intrinsic factor (vitamin B synthesis) Secreted 1264.8 1634
GKN1 gastrokine 1 Secreted 31692.5 1194
PGA5 pepsinogen 5, group I (pepsinogen A) Intracellular,Secreted 2980.0 590
PGA3 pepsinogen 3, group I (pepsinogen A) Intracellular,Secreted 35557.1 480
ATP4A ATPase, H+/K+ exchanging, alpha polypeptide Membrane 537.7 250
GAST gastrin Secreted 11343.0 197
ATP4B ATPase, H+/K+ exchanging, beta polypeptide Membrane 919.0 85
LIPF lipase, gastric Secreted 21780.0 82
MUC5AC mucin 5AC, oligomeric mucus/gel-forming Secreted 365.1 63
GKN2 gastrokine 2 Secreted 3848.0 37
TFF1 trefoil factor 1 Secreted 6481.5 32

Some of the proteins predicted to be membrane-spanning are intracellular, e.g. in the Golgi or mitochondrial membranes, and some of the proteins predicted to be secreted can potentially be retained in a compartment belonging to the secretory pathway, such as the ER, or remain attached to the outer face of the cell membrane by a GPI anchor.

The stomach transcriptome

An analysis of the expression levels of each gene makes it possible to calculate the relative mRNA pool for each of the categories. The analysis shows that 66% of the mRNA molecules derived from stomach correspond to housekeeping genes and that 26% of the mRNA pool corresponds to genes categorized as stomach enriched, group enriched, or stomach enhanced. Thus, most of the transcriptional activity in the stomach relates to proteins with presumed housekeeping functions as they are found in all tissues and cells analyzed.

Protein expression of genes elevated in stomach

In-depth analysis of the elevated genes in 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 present in chief cells.

GKN1 - gastric mucosa
GIF - parietal cells
PGC - chief cells

Genes shared between stomach and other tissues

There are 47 group enriched genes expressed in the stomach. Group enriched genes are defined as genes showing a 5-fold higher average level of mRNA expression in a group of 2-7 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 commonly expressed genes between different tissue types.

Figure 2. An interactive network plot of theástomach 1áenriched and group enriched genes connected to their respective enriched tissues (grey circles).áRedánodes represent the number ofástomach 1 enriched genes andáorangeánodes 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 toá3átissues, but the resulting lists show the complete set of group enriched genes in the particular tissue.

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 into 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 in the bottom of the gastric pits. The fundus 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 that secrete mucous into the stomach lumen. This mucous protects the stomach wall from the acidic gastric contents. A mucinous globule is typically present in the apical portion of the cells. The nucleus is oval in shape. 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 mucous. In the principle part, parietal (oxyntic) cells are located. They have 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 amount 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 mucus 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 the stomach are described and characterized, together with examples of immunohistochemically stained tissue sections that visualize protein expression patterns of proteins that correspond to genes with elevated expression in the stomach.

Transcript profiling and RNA-data analyses based on normal human tissues have been described previously (Fagerberg et al., 2013). Analyses of mRNA expression including over 99% of all human protein-coding genes was performed using deep RNA sequencing of 172 individual samples corresponding to 37 different human normal tissue types. RNA sequencing results of 4 fresh frozen tissues representing normal stomach was compared to 168 other tissue samples corresponding to 36 tissue types, in order to determine genes with elevated expression in stomach. A tissue-specific score, defined as the ratio between mRNA levels in stomach compared to the mRNA levels in all other tissues, was used to divide the genes into different categories of expression. These categories include: genes with elevated expression in stomach, genes expressed in all tissues, genes with a mixed expression pattern, genes not expressed in stomach, and genes not expressed in any tissue. Genes with elevated expression in stomach were further sub-categorized as i) genes with enriched expression in stomach, ii) genes with group enriched expression including stomach and iii) genes with enhanced expression in stomach.

Human tissue samples used for protein and mRNA expression analyses were collected and handled in accordance with Swedish laws and regulation and obtained from the Department of Pathology, Uppsala University Hospital, Uppsala, Sweden as part of the sample collection governed by the Uppsala Biobank. All human tissue samples used in the present study were anonymized in accordance with approval and advisory report from the Uppsala Ethical Review Board.

Relevant links and publications

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

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

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

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

Histology dictionary - the stomach