Surfing transcriptomic landscapes. A step beyond the annotation of chromosome 16 proteome.



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Segura, Víctor and Medina-Aunon, J. A. and Mora, Maria I. and Martínez-Bartolomé, S. and Abian, Joaquín and Aloria, Kerman and Antúnez, Oreto and Arizmendi, J. M. and Azkargorta, Mikel and Barceló Batllori, Silvia and Beaskoetxea, Jabier and Bech Serra, Joan J and Blanco, F. and Monteiro, Mariana B. and Cáceres, David and Canals, F. and Carrascal, Monserrat and Casal, J. Ignacio and Clemente, Felipe and Colomé, Nuria and Dasilva, Noelia and Díaz, Paula and Elortza, F. and Fernández Puente, Patricia and Fuentes, M. and Gallardo, Oscar and Gharbi, S. I. and Gil, Concha and González-Tejedo, C. and Hernáez, María Luisa and Lombardía, Manuel and Lopez Lucendo, Maria and Marcilla, Miguel and Mato, J. M. and Mendes, Marta and Oliveira, Eliandre and Orera, Irene and Pascual Montano, Alberto and Prieto, Gorka and Ruiz Romero, Cristina and Sánchez del Pino, M. M. and Tabas Madrid, Daniel and Valero, Maria L. and Vialás, Vital and Villanueva, Joan and Albar, J. P. and 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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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.

Item Type:Article
Uncontrolled Keywords:Human Proteome Project, Chromosome 16, proteomics, transcriptomics, RNA-Seq. ENCODE, bioinformatics
Subjects:Medical sciences > Pharmacy > Microbiology
ID Code:33600
Deposited On:17 Nov 2015 10:56
Last Modified:01 Dec 2015 09:57

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