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Initial characterization of the human central proteome

BACKGROUND: On the basis of large proteomics datasets measured from seven human cell lines we consider their intersection as an approximation of the human central proteome, which is the set of proteins ubiquitously expressed in all human cells. Composition and properties of the central proteome are...

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Autores principales: Burkard, Thomas R, Planyavsky, Melanie, Kaupe, Ines, Breitwieser, Florian P, Bürckstümmer, Tilmann, Bennett, Keiryn L, Superti-Furga, Giulio, Colinge, Jacques
Formato: Texto
Lenguaje:English
Publicado: BioMed Central 2011
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3039570/
https://www.ncbi.nlm.nih.gov/pubmed/21269460
http://dx.doi.org/10.1186/1752-0509-5-17
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author Burkard, Thomas R
Planyavsky, Melanie
Kaupe, Ines
Breitwieser, Florian P
Bürckstümmer, Tilmann
Bennett, Keiryn L
Superti-Furga, Giulio
Colinge, Jacques
author_facet Burkard, Thomas R
Planyavsky, Melanie
Kaupe, Ines
Breitwieser, Florian P
Bürckstümmer, Tilmann
Bennett, Keiryn L
Superti-Furga, Giulio
Colinge, Jacques
author_sort Burkard, Thomas R
collection PubMed
description BACKGROUND: On the basis of large proteomics datasets measured from seven human cell lines we consider their intersection as an approximation of the human central proteome, which is the set of proteins ubiquitously expressed in all human cells. Composition and properties of the central proteome are investigated through bioinformatics analyses. RESULTS: We experimentally identify a central proteome comprising 1,124 proteins that are ubiquitously and abundantly expressed in human cells using state of the art mass spectrometry and protein identification bioinformatics. The main represented functions are proteostasis, primary metabolism and proliferation. We further characterize the central proteome considering gene structures, conservation, interaction networks, pathways, drug targets, and coordination of biological processes. Among other new findings, we show that the central proteome is encoded by exon-rich genes, indicating an increased regulatory flexibility through alternative splicing to adapt to multiple environments, and that the protein interaction network linking the central proteome is very efficient for synchronizing translation with other biological processes. Surprisingly, at least 10% of the central proteome has no or very limited functional annotation. CONCLUSIONS: Our data and analysis provide a new and deeper description of the human central proteome compared to previous results thereby extending and complementing our knowledge of commonly expressed human proteins. All the data are made publicly available to help other researchers who, for instance, need to compare or link focused datasets to a common background.
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spelling pubmed-30395702011-02-16 Initial characterization of the human central proteome Burkard, Thomas R Planyavsky, Melanie Kaupe, Ines Breitwieser, Florian P Bürckstümmer, Tilmann Bennett, Keiryn L Superti-Furga, Giulio Colinge, Jacques BMC Syst Biol Research Article BACKGROUND: On the basis of large proteomics datasets measured from seven human cell lines we consider their intersection as an approximation of the human central proteome, which is the set of proteins ubiquitously expressed in all human cells. Composition and properties of the central proteome are investigated through bioinformatics analyses. RESULTS: We experimentally identify a central proteome comprising 1,124 proteins that are ubiquitously and abundantly expressed in human cells using state of the art mass spectrometry and protein identification bioinformatics. The main represented functions are proteostasis, primary metabolism and proliferation. We further characterize the central proteome considering gene structures, conservation, interaction networks, pathways, drug targets, and coordination of biological processes. Among other new findings, we show that the central proteome is encoded by exon-rich genes, indicating an increased regulatory flexibility through alternative splicing to adapt to multiple environments, and that the protein interaction network linking the central proteome is very efficient for synchronizing translation with other biological processes. Surprisingly, at least 10% of the central proteome has no or very limited functional annotation. CONCLUSIONS: Our data and analysis provide a new and deeper description of the human central proteome compared to previous results thereby extending and complementing our knowledge of commonly expressed human proteins. All the data are made publicly available to help other researchers who, for instance, need to compare or link focused datasets to a common background. BioMed Central 2011-01-26 /pmc/articles/PMC3039570/ /pubmed/21269460 http://dx.doi.org/10.1186/1752-0509-5-17 Text en Copyright ©2011 Burkard et al; licensee BioMed Central Ltd. http://creativecommons.org/licenses/by/2.0 This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/2.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.
spellingShingle Research Article
Burkard, Thomas R
Planyavsky, Melanie
Kaupe, Ines
Breitwieser, Florian P
Bürckstümmer, Tilmann
Bennett, Keiryn L
Superti-Furga, Giulio
Colinge, Jacques
Initial characterization of the human central proteome
title Initial characterization of the human central proteome
title_full Initial characterization of the human central proteome
title_fullStr Initial characterization of the human central proteome
title_full_unstemmed Initial characterization of the human central proteome
title_short Initial characterization of the human central proteome
title_sort initial characterization of the human central proteome
topic Research Article
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3039570/
https://www.ncbi.nlm.nih.gov/pubmed/21269460
http://dx.doi.org/10.1186/1752-0509-5-17
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