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Integration of Proteomics and Transcriptomics Data Sets for the Analysis of a Lymphoma B-Cell Line in the Context of the Chromosome-Centric Human Proteome Project

Diez, Paula; Droste, Conrad; Degano, Rosa M.; Gonzalez-Munoz, Maria; Ibarrola, Nieves; Perez-Andres, Martin; Garin-Muga, Alba; Segura, Victor; Marko-Varga, György LU and LaBaer, Joshua, et al. (2015) In Journal of Proteome Research 14(9). p.3530-3540
Abstract
A comprehensive study of the molecular active landscape of human cells can be undertaken to integrate two different but complementary perspectives: transcriptomics, and proteomics. After the genome era, proteomics has emerged as a powerful tool to simultaneously identify and characterize the compendium of thousands of different proteins active in a cell. Thus, the Chromosome-centric Human Proteome Project (C-HPP) is promoting a full characterization of the human proteome combining high-throughput proteomics with the data derived from genome-wide expression profiling of protein-coding genes. Here we present a full proteomic profiling of a human lymphoma B-cell line (Ramos) performed using a nanoUPLC-LTQ-Orbitrap Velos proteomic platform,... (More)
A comprehensive study of the molecular active landscape of human cells can be undertaken to integrate two different but complementary perspectives: transcriptomics, and proteomics. After the genome era, proteomics has emerged as a powerful tool to simultaneously identify and characterize the compendium of thousands of different proteins active in a cell. Thus, the Chromosome-centric Human Proteome Project (C-HPP) is promoting a full characterization of the human proteome combining high-throughput proteomics with the data derived from genome-wide expression profiling of protein-coding genes. Here we present a full proteomic profiling of a human lymphoma B-cell line (Ramos) performed using a nanoUPLC-LTQ-Orbitrap Velos proteomic platform, combined to an in-depth transcriptomic profiling of the same cell type. Data are available via ProteomeXchange with identifier PXD001933. Integration of the proteomic and transcriptomic data sets revealed a 94% overlap in the proteins identified by both -omics approaches. Moreover, functional enrichment analysis of the proteomic profiles showed an enrichment of several functions directly related to the biological and morphological characteristics of B-cells. In turn, about 30% of all protein-coding genes present in the whole human genome were identified as being expressed by the Ramos cells (stable average of 30% genes along all the chromosomes), revealing the size of the protein expression-set present in one specific human cell type. Additionally, the identification of missing proteins in our data sets has been reported, highlighting the power of the approach. Also, a comparison between neXtProt and UniProt database searches has been performed. In summary, our transcriptomic and proteomic experimental profiling provided a high coverage report of the expressed proteome from a human lymphoma B-cell type with a clear insight into the biological processes that characterized these cells. In this way, we demonstrated the usefulness of combining -omics for a comprehensive characterization of specific biological systems. (Less)
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subject
keywords
C-HPP, lymphoma B-cell line, protein expression profile, transcriptomics, subcellular fractionation
in
Journal of Proteome Research
volume
14
issue
9
pages
3530 - 3540
publisher
The American Chemical Society
external identifiers
  • wos:000361087100012
  • scopus:84941089325
ISSN
1535-3893
DOI
10.1021/acs.jproteome.5b00474
language
English
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yes
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7226cc8b-4816-453f-a616-f729fdbff3f3 (old id 8071213)
date added to LUP
2015-11-17 11:29:12
date last changed
2017-02-05 03:06:54
@article{7226cc8b-4816-453f-a616-f729fdbff3f3,
  abstract     = {A comprehensive study of the molecular active landscape of human cells can be undertaken to integrate two different but complementary perspectives: transcriptomics, and proteomics. After the genome era, proteomics has emerged as a powerful tool to simultaneously identify and characterize the compendium of thousands of different proteins active in a cell. Thus, the Chromosome-centric Human Proteome Project (C-HPP) is promoting a full characterization of the human proteome combining high-throughput proteomics with the data derived from genome-wide expression profiling of protein-coding genes. Here we present a full proteomic profiling of a human lymphoma B-cell line (Ramos) performed using a nanoUPLC-LTQ-Orbitrap Velos proteomic platform, combined to an in-depth transcriptomic profiling of the same cell type. Data are available via ProteomeXchange with identifier PXD001933. Integration of the proteomic and transcriptomic data sets revealed a 94% overlap in the proteins identified by both -omics approaches. Moreover, functional enrichment analysis of the proteomic profiles showed an enrichment of several functions directly related to the biological and morphological characteristics of B-cells. In turn, about 30% of all protein-coding genes present in the whole human genome were identified as being expressed by the Ramos cells (stable average of 30% genes along all the chromosomes), revealing the size of the protein expression-set present in one specific human cell type. Additionally, the identification of missing proteins in our data sets has been reported, highlighting the power of the approach. Also, a comparison between neXtProt and UniProt database searches has been performed. In summary, our transcriptomic and proteomic experimental profiling provided a high coverage report of the expressed proteome from a human lymphoma B-cell type with a clear insight into the biological processes that characterized these cells. In this way, we demonstrated the usefulness of combining -omics for a comprehensive characterization of specific biological systems.},
  author       = {Diez, Paula and Droste, Conrad and Degano, Rosa M. and Gonzalez-Munoz, Maria and Ibarrola, Nieves and Perez-Andres, Martin and Garin-Muga, Alba and Segura, Victor and Marko-Varga, György and LaBaer, Joshua and Orfao, Alberto and Corrales, Fernando J. and De Las Rivas, Javier and Fuentes, Manuel},
  issn         = {1535-3893},
  keyword      = {C-HPP,lymphoma B-cell line,protein expression profile,transcriptomics,subcellular fractionation},
  language     = {eng},
  number       = {9},
  pages        = {3530--3540},
  publisher    = {The American Chemical Society},
  series       = {Journal of Proteome Research},
  title        = {Integration of Proteomics and Transcriptomics Data Sets for the Analysis of a Lymphoma B-Cell Line in the Context of the Chromosome-Centric Human Proteome Project},
  url          = {http://dx.doi.org/10.1021/acs.jproteome.5b00474},
  volume       = {14},
  year         = {2015},
}