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Integration of Prot...
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
- Artikel/kapitelEngelska2015
Förlag, utgivningsår, omfång ...
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2015-08-05
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American Chemical Society (ACS),2015
Nummerbeteckningar
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LIBRIS-ID:oai:lup.lub.lu.se:7226cc8b-4816-453f-a616-f729fdbff3f3
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https://lup.lub.lu.se/record/8071213URI
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https://doi.org/10.1021/acs.jproteome.5b00474DOI
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Språk:engelska
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Sammanfattning på:engelska
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Ämneskategori:art swepub-publicationtype
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Ämneskategori:ref swepub-contenttype
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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.
Ämnesord och genrebeteckningar
Biuppslag (personer, institutioner, konferenser, titlar ...)
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Droste, Conrad
(författare)
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Degano, Rosa M.
(författare)
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Gonzalez-Munoz, Maria
(författare)
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Ibarrola, Nieves
(författare)
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Perez-Andres, Martin
(författare)
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Garin-Muga, Alba
(författare)
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Segura, Victor
(författare)
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Marko-Varga, GyörgyLund University,Lunds universitet,Avdelningen för Biomedicinsk teknik,Institutionen för biomedicinsk teknik,Institutioner vid LTH,Lunds Tekniska Högskola,Institutionen för kliniska vetenskaper, Lund,Medicinska fakulteten,Department of Biomedical Engineering,Departments at LTH,Faculty of Engineering, LTH,Department of Clinical Sciences, Lund,Faculty of Medicine(Swepub:lu)akem-gmv
(författare)
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LaBaer, Joshua
(författare)
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Orfao, Alberto
(författare)
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Corrales, Fernando J.
(författare)
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De Las Rivas, Javier
(författare)
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Fuentes, Manuel
(författare)
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Avdelningen för Biomedicinsk teknikInstitutionen för biomedicinsk teknik
(creator_code:org_t)
Sammanhörande titlar
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Ingår i:Journal of Proteome Research: American Chemical Society (ACS)14:9, s. 3530-35401535-38931535-3907
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Till lärosätets databas
- Av författaren/redakt...
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Diez, Paula
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Droste, Conrad
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Degano, Rosa M.
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Gonzalez-Munoz, ...
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Ibarrola, Nieves
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Perez-Andres, Ma ...
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visa fler...
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Garin-Muga, Alba
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Segura, Victor
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Marko-Varga, Gyö ...
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LaBaer, Joshua
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Orfao, Alberto
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Corrales, Fernan ...
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De Las Rivas, Ja ...
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Fuentes, Manuel
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visa färre...
- Om ämnet
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- MEDICIN OCH HÄLSOVETENSKAP
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MEDICIN OCH HÄLS ...
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och Medicinsk biotek ...
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och Medicinsk biotek ...
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- MEDICIN OCH HÄLSOVETENSKAP
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MEDICIN OCH HÄLS ...
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och Medicinska och f ...
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och Cell och molekyl ...
- Artiklar i publikationen
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Journal of Prote ...
- Av lärosätet
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Lunds universitet