An integrated landscape of protein expression in human cancer

Abstract Using 11 proteomics datasets, mostly available through the PRIDE database, we assembled a reference expression map for 191 cancer cell lines and 246 clinical tumour samples, across 13 lineages. We found unique peptides identified only in tumour samples despite a much higher coverage in cell...

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Autores principales:	Andrew F. Jarnuczak, Hanna Najgebauer, Mitra Barzine, Deepti J. Kundu, Fatemeh Ghavidel, Yasset Perez-Riverol, Irene Papatheodorou, Alvis Brazma, Juan Antonio Vizcaíno
Formato:	article
Lenguaje:	EN
Publicado:	Nature Portfolio 2021
Materias:	Science Q
Acceso en línea:	https://doaj.org/article/b91373af618f49f2b3ea1c128209c620
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spelling	oai:doaj.org-article:b91373af618f49f2b3ea1c128209c6202021-12-02T13:39:29ZAn integrated landscape of protein expression in human cancer10.1038/s41597-021-00890-22052-4463https://doaj.org/article/b91373af618f49f2b3ea1c128209c6202021-04-01T00:00:00Zhttps://doi.org/10.1038/s41597-021-00890-2https://doaj.org/toc/2052-4463Abstract Using 11 proteomics datasets, mostly available through the PRIDE database, we assembled a reference expression map for 191 cancer cell lines and 246 clinical tumour samples, across 13 lineages. We found unique peptides identified only in tumour samples despite a much higher coverage in cell lines. These were mainly mapped to proteins related to regulation of signalling receptor activity. Correlations between baseline expression in cell lines and tumours were calculated. We found these to be highly similar across all samples with most similarity found within a given sample type. Integration of proteomics and transcriptomics data showed median correlation across cell lines to be 0.58 (range between 0.43 and 0.66). Additionally, in agreement with previous studies, variation in mRNA levels was often a poor predictor of changes in protein abundance. To our knowledge, this work constitutes the first meta-analysis focusing on cancer-related public proteomics datasets. We therefore also highlight shortcomings and limitations of such studies. All data is available through PRIDE dataset identifier PXD013455 and in Expression Atlas.Andrew F. JarnuczakHanna NajgebauerMitra BarzineDeepti J. KunduFatemeh GhavidelYasset Perez-RiverolIrene PapatheodorouAlvis BrazmaJuan Antonio VizcaínoNature PortfolioarticleScienceQENScientific Data, Vol 8, Iss 1, Pp 1-14 (2021)
institution	DOAJ
collection	DOAJ
language	EN
topic	Science Q
spellingShingle	Science Q Andrew F. Jarnuczak Hanna Najgebauer Mitra Barzine Deepti J. Kundu Fatemeh Ghavidel Yasset Perez-Riverol Irene Papatheodorou Alvis Brazma Juan Antonio Vizcaíno An integrated landscape of protein expression in human cancer
description	Abstract Using 11 proteomics datasets, mostly available through the PRIDE database, we assembled a reference expression map for 191 cancer cell lines and 246 clinical tumour samples, across 13 lineages. We found unique peptides identified only in tumour samples despite a much higher coverage in cell lines. These were mainly mapped to proteins related to regulation of signalling receptor activity. Correlations between baseline expression in cell lines and tumours were calculated. We found these to be highly similar across all samples with most similarity found within a given sample type. Integration of proteomics and transcriptomics data showed median correlation across cell lines to be 0.58 (range between 0.43 and 0.66). Additionally, in agreement with previous studies, variation in mRNA levels was often a poor predictor of changes in protein abundance. To our knowledge, this work constitutes the first meta-analysis focusing on cancer-related public proteomics datasets. We therefore also highlight shortcomings and limitations of such studies. All data is available through PRIDE dataset identifier PXD013455 and in Expression Atlas.
format	article
author	Andrew F. Jarnuczak Hanna Najgebauer Mitra Barzine Deepti J. Kundu Fatemeh Ghavidel Yasset Perez-Riverol Irene Papatheodorou Alvis Brazma Juan Antonio Vizcaíno
author_facet	Andrew F. Jarnuczak Hanna Najgebauer Mitra Barzine Deepti J. Kundu Fatemeh Ghavidel Yasset Perez-Riverol Irene Papatheodorou Alvis Brazma Juan Antonio Vizcaíno
author_sort	Andrew F. Jarnuczak
title	An integrated landscape of protein expression in human cancer
title_short	An integrated landscape of protein expression in human cancer
title_full	An integrated landscape of protein expression in human cancer
title_fullStr	An integrated landscape of protein expression in human cancer
title_full_unstemmed	An integrated landscape of protein expression in human cancer
title_sort	integrated landscape of protein expression in human cancer
publisher	Nature Portfolio
publishDate	2021
url	https://doaj.org/article/b91373af618f49f2b3ea1c128209c620
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An integrated landscape of protein expression in human cancer

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