ArticleJournal of gastroenterology2015
The human gastrointestinal tract-specific transcriptome and proteome as defined by RNA sequencing and antibody-based profiling.
Article in Journal of gastroenterology, 2015. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 41 papers.
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Who cites it
41 citing papers in PubMed, 83 citations in OpenAlex.
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- Epigenetic modulation of the NLRP6 inflammasome sensor as a therapeutic modality to reduce necroptosis-driven gastrointestinal mucosal dysfunction in HIV/SIV infection.Cell communication and signaling : CCS · 2025Article
- Pattern Recognition by NOD-Like Receptors.Advances in experimental medicine and biology · 2025Review
- Gut metabolic changes during pregnancy reveal the importance of gastrointestinal region in sample collection.Metabolomics : Official journal of the Metabolomic Society · 2024Article
- A human stomach cell type transcriptome atlas.BMC biology · 2024Article
- Intelectin-1 binds and alters the localization of the mucus barrier-modifying bacterium Akkermansia muciniphila.The Journal of experimental medicine · 2023Article
- Lactobacillus rhamnosus and Staphylococcus epidermidis in gut microbiota: in vitro antimicrobial resistance.AMB Express · 2022Article
- The latest breakthrough on NLRP6 inflammasome.Precision clinical medicine · 2022Review
- CD10 and Das1: a biomarker study using immunohistochemistry to subtype gastric intestinal metaplasia.BMC gastroenterology · 2022Article
- Tissue extracellular matrix hydrogels as alternatives to Matrigel for culturing gastrointestinal organoids.Nature communications · 2022Article
- The role of goblet cells in viral pathogenesis.The FEBS journal · 2021Review
- Host-Viral Interactions in the Pathogenesis of Ulcerative Colitis.International journal of molecular sciences · 2021Review
- A short C-terminal peptide in Gγ regulates Gβγ signaling efficacy.Molecular biology of the cell · 2021Article
- ZNF37A promotes tumor metastasis through transcriptional control of THSD4/TGF-β axis in colorectal cancer.Oncogene · 2021Article
- NLRP6 in host defense and intestinal inflammation.Cell reports · 2021Review
- Tissue-selective alternate promoters guide NLRP6 expression.Life science alliance · 2021Article
- NLRP6-associated host microbiota composition impacts in the intestinal barrier to systemic dissemination of Brucella abortus.PLoS neglected tropical diseases · 2021Article
- The Human Protein Atlas-Spatial localization of the human proteome in health and disease.Protein science : a publication of the Protein Society · 2021Article
Corrections and comments
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Authors and funding
9 authors at 3 institutions in 1 country.
Funding
No grant is acknowledged in the PubMed record.
Abstract
backgroundThe gastrointestinal tract (GIT) is subdivided into different anatomical organs with many shared functions and characteristics, but also distinct differences. We have combined a genome-wide transcriptomics analysis with immunohistochemistry-based protein profiling to describe the gene and protein expression patterns that define the human GIT.
methodsRNA sequencing data derived from stomach, duodenum, jejunum/ileum and colon specimens were compared to gene expression levels in 23 other normal human tissues analysed with the same method. Protein profiling based on immunohistochemistry and tissue microarrays was used to sub-localize the corresponding proteins with GIT-specific expression into sub-cellular compartments and cell types.
resultsApproximately 75% of all human protein-coding genes were expressed in at least one of the GIT tissues. Only 51 genes showed enriched expression in either one of the GIT tissues and an additional 83 genes were enriched in two or more GIT tissues. The list of GIT-enriched genes with validated protein expression patterns included various well-known but also previously uncharacterised or poorly studied genes. For instance, the colon-enriched expression of NXPE family member 1 (NXPE1) was established, while NLR family, pyrin domain-containing 6 (NLRP6) expression was primarily found in the human small intestine.
conclusionsWe have applied a genome-wide analysis based on transcriptomics and antibody-based protein profiling to identify genes that are expressed in a specific manner within the human GIT. These genes and proteins constitute important starting points for an improved understanding of the normal function and the different states of disease associated with the GIT.
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Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.