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  • Sjöstedt, EvelinaUppsala universitet,KTH,Science for Life Laboratory, SciLifeLab,Systembiologi,Science for Life Laboratory, SciLifeLab,Klinisk och experimentell patologi,KTH Royal Inst Technol, Sch Engn Sci Chem Biotechnol & Hlth, Sci Life Lab, SE-17121 Stockholm, Sweden (author)

Integration of Transcriptomics and Antibody-Based Proteomics for Exploration of Proteins Expressed in Specialized Tissues

  • Article/chapterEnglish2018

Publisher, publication year, extent ...

  • 2018-10-01
  • American Chemical Society (ACS),2018
  • printrdacarrier

Numbers

  • LIBRIS-ID:oai:DiVA.org:kth-236474
  • https://urn.kb.se/resolve?urn=urn:nbn:se:kth:diva-236474URI
  • https://doi.org/10.1021/acs.jproteome.8b00406DOI
  • https://urn.kb.se/resolve?urn=urn:nbn:se:uu:diva-373020URI

Supplementary language notes

  • Language:English
  • Summary in:English

Part of subdatabase

Classification

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

Notes

  • QC 20181018
  • A large portion of human proteins are referred to as missing proteins, defined as protein-coding genes that lack experimental data on the protein level due to factors such as temporal expression, expression in tissues that are difficult to sample, or they actually do not encode functional proteins. In the present investigation, an integrated omics approach was used for identification and exploration of missing proteins. Transcriptomics data from three different sourcesthe Human Protein Atlas (HPA), the GTEx consortium, and the FANTOM5 consortiumwere used as a starting point to identify genes selectively expressed in specialized tissues. Complementing the analysis with profiling on more specific tissues based on immunohistochemistry allowed for further exploration of cell-type-specific expression patterns. More detailed tissue profiling was performed for >300 genes on complementing tissues. The analysis identified tissue-specific expression of nine proteins previously listed as missing proteins (POU4F1, FRMD1, ARHGEF33, GABRG1, KRTAP2-1, BHLHE22, SPRR4, AVPR1B, and DCLK3), as well as numerous proteins with evidence of existence on the protein level that previously lacked information on spatial resolution and cell-type- specific expression pattern. We here present a comprehensive strategy for identification of missing proteins by combining transcriptomics with antibody-based proteomics. The analyzed proteins provide interesting targets for organ-specific research in health and disease.

Subject headings and genre

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

  • Sivertsson, ÅsaKTH,Systembiologi,KTH Royal Inst Technol, Sch Engn Sci Chem Biotechnol & Hlth, Sci Life Lab, SE-17121 Stockholm, Sweden(Swepub:kth)u195d5b0 (author)
  • Noraddin, Feria HikmetUppsala universitet,Klinisk och experimentell patologi,Science for Life Laboratory, SciLifeLab(Swepub:uu)ferhi854 (author)
  • Katona, BorbalaUppsala universitet,Science for Life Laboratory, SciLifeLab,Klinisk och experimentell patologi(Swepub:uu)borka244 (author)
  • Näsström, ÅsaUppsala universitet,Institutionen för immunologi, genetik och patologi,Science for Life Laboratory, SciLifeLab (author)
  • Vuu, JimmyUppsala universitet,Klinisk och experimentell patologi,Science for Life Laboratory, SciLifeLab(Swepub:uu)jimvu995 (author)
  • Kesti, DennisUppsala universitet,Klinisk och experimentell patologi,Science for Life Laboratory, SciLifeLab(Swepub:uu)denke239 (author)
  • Oksvold, PerKTH,Science for Life Laboratory, SciLifeLab,KTH Royal Inst Technol, Sch Engn Sci Chem Biotechnol & Hlth, Sci Life Lab, SE-17121 Stockholm, Sweden(Swepub:kth)u1qey3lv (author)
  • Edqvist, Per-Henrik DUppsala universitet,Experimentell och klinisk onkologi,Science for Life Laboratory, SciLifeLab(Swepub:uu)peedq227 (author)
  • Olsson, IngmarieUppsala universitet,Science for Life Laboratory, SciLifeLab,Klinisk och experimentell patologi(Swepub:uu)iol00457 (author)
  • Uhlén, MathiasKTH,Science for Life Laboratory, SciLifeLab,Systembiologi,KTH Royal Inst Technol, Sch Engn Sci Chem Biotechnol & Hlth, Sci Life Lab, SE-17121 Stockholm, Sweden(Swepub:kth)u1dulvmw (author)
  • Lindskog, CeciliaUppsala universitet,Science for Life Laboratory, SciLifeLab,Klinisk och experimentell patologi(Swepub:uu)cecli129 (author)
  • KTHScience for Life Laboratory, SciLifeLab (creator_code:org_t)

Related titles

  • In:Journal of Proteome Research: American Chemical Society (ACS)17:12, s. 4127-41371535-38931535-3907

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