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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

AutorDíez, Paula; Dégano, Rosa M.; González-Nuñez, María; Ibarrola, Nieves ; Pérez-Andrés, Martin; Marko-Varga, György; LaBaer, Joshua; Orfao, Alberto ; Corrales, Fernando J.; De Las Rivas, Javier ; Fuentes, Manuel
Fecha de publicación2015
EditorAmerican Chemical Society
CitaciónJournal of Proteome Research 14(9): 3530-3540 (2015)
ResumenA 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.
Descripciónet al.
URIhttp://hdl.handle.net/10261/123258
DOI10.1021/acs.jproteome.5b00474
Identificadoresdoi: 10.1021/acs.jproteome.5b00474
issn: 1535-3893
e-issn: 1535-3907
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