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J Proteome Res. 2015 Sep 4;14(9):3738-49. doi: 10.1021/acs.jproteome.5b00466. Epub 2015 Jul 16.

Proteogenomics Dashboard for the Human Proteome Project.

Author information

1
ProteoRed-ISCIII, National Center for Biotechnology-CSIC (CNB) , C/Darwin 3, Madrid 28049, Spain.
2
ProteoRed-ISCIII, Center for Applied Medical Research (CIMA), University of Navarra , Avda. Pío XII, 55, Pamplona E-31008, Spain.
3
Department of Communication Engineering E.T.S. Ingenierı́a de Bilbao, University of the Basque Country (UPV/EHU) , Alda. Urquijo, s/n, Bilbao 48013, Spain.
4
Computer Science Faculty, Complutense University of Madrid (UCM) , C/ Jose Garcı́á Santesmases 9, Madrid 28040, Spain.

Abstract

dasHPPboard is a novel proteomics-based dashboard that collects and reports the experiments produced by the Spanish Human Proteome Project consortium (SpHPP) and aims to help HPP to map the entire human proteome. We have followed the strategy of analog genomics projects like the Encyclopedia of DNA Elements (ENCODE), which provides a vast amount of data on human cell lines experiments. The dashboard includes results of shotgun and selected reaction monitoring proteomics experiments, post-translational modifications information, as well as proteogenomics studies. We have also processed the transcriptomics data from the ENCODE and Human Body Map (HBM) projects for the identification of specific gene expression patterns in different cell lines and tissues, taking special interest in those genes having little proteomic evidence available (missing proteins). Peptide databases have been built using single nucleotide variants and novel junctions derived from RNA-Seq data that can be used in search engines for sample-specific protein identifications on the same cell lines or tissues. The dasHPPboard has been designed as a tool that can be used to share and visualize a combination of proteomic and transcriptomic data, providing at the same time easy access to resources for proteogenomics analyses. The dasHPPboard can be freely accessed at: http://sphppdashboard.cnb.csic.es.

KEYWORDS:

ENCODE; Human Proteome Project; RNA-Seq; bioinformatics; chromosome 16; proteogenomics; proteomics; spHPP; transcriptomics

PMID:
26144527
DOI:
10.1021/acs.jproteome.5b00466
[Indexed for MEDLINE]

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