Universidad Complutense de Madrid
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Surfing transcriptomic landscapes. A step beyond the annotation of chromosome 16 proteome.

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Segura, Víctor y Medina-Aunon, J. A. y Mora, Maria I. y Martínez-Bartolomé, S. y Abian, Joaquín y Aloria, Kerman y Antúnez, Oreto y Arizmendi, J. M. y Azkargorta, Mikel y Barceló Batllori, Silvia y Beaskoetxea, Jabier y Bech Serra, Joan J y Blanco, F. y Monteiro, Mariana B. y Cáceres, David y Canals, F. y Carrascal, Monserrat y Casal, J. Ignacio y Clemente, Felipe y Colomé, Nuria y Dasilva, Noelia y Díaz, Paula y Elortza, F. y Fernández Puente, Patricia y Fuentes, M. y Gallardo, Oscar y Gharbi, S. I. y Gil, Concha y González-Tejedo, C. y Hernáez, María Luisa y Lombardía, Manuel y Lopez Lucendo, Maria y Marcilla, Miguel y Mato, J. M. y Mendes, Marta y Oliveira, Eliandre y Orera, Irene y Pascual Montano, Alberto y Prieto, Gorka y Ruiz Romero, Cristina y Sánchez del Pino, M. M. y Tabas Madrid, Daniel y Valero, Maria L. y Vialás, Vital y Villanueva, Joan y Albar, J. P. y Corrales, F. J. (2013) Surfing transcriptomic landscapes. A step beyond the annotation of chromosome 16 proteome. Journal of proteome research, 13 . pp. 158-172. ISSN 1535-3907

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URL Oficial: http://dx.doi.org/10.1021/pr400721r




Resumen

The Spanish team of the Human Proteome Project (SpHPP) marked the annotation of Chr16 and data analysis as one of its priorities. Precise annotation of Chromosome 16 proteins according to C-HPP criteria is presented. Moreover, Human Body Map 2.0 RNA-Seq and Encyclopedia of DNA Elements (ENCODE) data sets were used to obtain further information relative to cell/tissue specific chromosome 16 coding gene expression patterns and to infer the presence of missing proteins. Twenty-four shotgun 2D-LC-MS/MS and gel/LC-MS/MS MIAPE compliant experiments, representing 41% coverage of chromosome 16 proteins, were performed. Furthermore, mapping of large-scale multicenter mass spectrometry data sets from CCD18, MCF7, Jurkat, and Ramos cell lines into RNA-Seq data allowed further insights relative to correlation of chromosome 16 transcripts and proteins. Detection and quantification of chromosome 16 proteins in biological matrices by SRM procedures are also primary goals of the SpHPP. Two strategies were undertaken: one focused on known proteins, taking advantage of MS data already available, and the second, aimed at the detection of the missing proteins, is based on the expression of recombinant proteins to gather MS information and optimize SRM methods that will be used in real biological samples. SRM methods for 49 known proteins and for recombinant forms of 24 missing proteins are reported in this study.


Tipo de documento:Artículo
Palabras clave:Human Proteome Project, Chromosome 16, proteomics, transcriptomics, RNA-Seq. ENCODE, bioinformatics
Materias:Ciencias Biomédicas > Farmacia > Microbiología
Código ID:33600
Depositado:17 Nov 2015 10:56
Última Modificación:01 Dic 2015 09:57

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