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  • Gremel, GabrielaUppsala universitet,Institutionen för immunologi, genetik och patologi,Science for Life Laboratory, SciLifeLab (author)

The human gastrointestinal tract-specific transcriptome and proteome as defined by RNA sequencing and antibody-based profiling

  • Article/chapterEnglish2015

Publisher, publication year, extent ...

  • 2014-05-01
  • Springer,2015
  • printrdacarrier

Numbers

  • LIBRIS-ID:oai:DiVA.org:umu-110913
  • https://urn.kb.se/resolve?urn=urn:nbn:se:umu:diva-110913URI
  • https://doi.org/10.1007/s00535-014-0958-7DOI
  • https://urn.kb.se/resolve?urn=urn:nbn:se:kth:diva-161632URI
  • https://urn.kb.se/resolve?urn=urn:nbn:se:uu:diva-239503URI

Supplementary language notes

  • Language:English
  • Summary in:English

Part of subdatabase

Classification

  • Subject category:ref swepub-contenttype
  • Subject category:art swepub-publicationtype

Notes

  • First online: 01 May 2014
  • QC 20150324
  • BACKGROUND: The 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. METHODS: RNA 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. RESULTS: Approximately 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. CONCLUSIONS: We 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.

Subject headings and genre

Added entries (persons, corporate bodies, meetings, titles ...)

  • Wanders, AlkwinUppsala universitet,Molekylär och morfologisk patologi(Swepub:uu)alkwwand (author)
  • Cedernaes, JonathanUppsala universitet,Funktionell farmakologi(Swepub:uu)jonce840 (author)
  • Fagerberg, LinnKTH,Proteomik och nanobioteknologi,Science for Life Laboratory, SciLifeLab(Swepub:kth)u1dglfid (author)
  • Hallström, BjörnKTH,Proteomik och nanobioteknologi,Science for Life Laboratory, SciLifeLab(Swepub:kth)u1ih19oh (author)
  • Edlund, KarolinaUppsala universitet,Institutionen för immunologi, genetik och patologi,Science for Life Laboratory, SciLifeLab(Swepub:uu)kaedl086 (author)
  • Sjöstedt, EvelinaUppsala universitet,Molekylär och morfologisk patologi,Science for Life Laboratory, SciLifeLab(Swepub:uu)evesj711 (author)
  • Uhlén, MathiasKTH,Proteomik och nanobioteknologi,Science for Life Laboratory, SciLifeLab(Swepub:kth)u1dulvmw (author)
  • Pontén, FredrikUppsala universitet,Molekylär och morfologisk patologi,Science for Life Laboratory, SciLifeLab(Swepub:uu)fredpont (author)
  • Uppsala universitetInstitutionen för immunologi, genetik och patologi (creator_code:org_t)

Related titles

  • In:Journal of gastroenterology: Springer50:1, s. 46-570944-11741435-5922

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