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Defining the human gallbladder proteome by transcriptomics and affinity proteomics
KTH, School of Biotechnology (BIO), Proteomics and Nanobiotechnology. KTH, Centres, Science for Life Laboratory, SciLifeLab.ORCID iD: 0000-0003-0198-7137
KTH, School of Biotechnology (BIO), Proteomics and Nanobiotechnology. KTH, Centres, Science for Life Laboratory, SciLifeLab.
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2014 (English)In: Proteomics, ISSN 1615-9853, E-ISSN 1615-9861, Vol. 14, no 21-22, 2498-2507 p.Article in journal (Refereed) Published
Abstract [en]

Global protein analysis of human gallbladder tissue is vital for identification of molecular regulators and effectors of its physiological activity. Here, we employed a genome-wide deep RNA sequencing analysis in 28 human tissues to identify the genes overrepresented in the gallbladder and complemented it with antibody-based immunohistochemistry in 48 human tissues. We characterized human gallbladder proteins and identified 140 gallbladder-specific proteins with an elevated expression in the gallbladder as compared to the other analyzed tissues. Five genes were categorized as enriched, with at least fivefold higher levels in gallbladder, 60 genes were categorized as group enriched with elevated transcript levels in gallbladder shared with at least one other tissue and 75 genes were categorized as enhanced with higher expression than the average expression in other tissues. We explored the localization of the genes within the gallbladder through cell-type specific antibody-based protein profiling and the subcellular localization of the genes through immunofluorescent-based profiling. Finally, we revealed the biological processes and metabolic functions carried out by these genes through the use of GO, KEGG Pathway, and HMR2.0 that is compilation of the human metabolic reactions. We demonstrated the results of the combined analysis of the transcriptomics and affinity proteomics.

Place, publisher, year, edition, pages
2014. Vol. 14, no 21-22, 2498-2507 p.
Keyword [en]
Gallbladder, Proteome, RNA-sequencing, Systems biology, Transcriptome
National Category
Biochemistry and Molecular Biology
Identifiers
URN: urn:nbn:se:kth:diva-157616DOI: 10.1002/pmic.201400201ISI: 000344807600014PubMedID: 25175928Scopus ID: 2-s2.0-84908886781OAI: oai:DiVA.org:kth-157616DiVA: diva2:770882
Funder
Knut and Alice Wallenberg FoundationEU, FP7, Seventh Framework Programme, HEALTH-F4-2008-201648/PROSPECTSScience for Life Laboratory - a national resource center for high-throughput molecular bioscience
Note

QC 20141211

Available from: 2014-12-11 Created: 2014-12-11 Last updated: 2017-12-05Bibliographically approved

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Fagerberg, LinnUhlén, Mathias

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