title: Proteogenomics Dashboard for the Human Proteome Project.
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.
authors.affiliation: ProteoRed-ISCIII, National Center for Biotechnology-CSIC (CNB) , C/Darwin 3, Madrid 28049, Spain.
authors.forename: Daniel
authors.initials: D
authors.lastname: Tabas-Madrid
authors.affiliation: ProteoRed-ISCIII, National Center for Biotechnology-CSIC (CNB) , C/Darwin 3, Madrid 28049, Spain.
authors.forename: Joao
authors.initials: J
authors.lastname: Alves-Cruzeiro
authors.affiliation: ProteoRed-ISCIII, Center for Applied Medical Research (CIMA), University of Navarra , Avda. Pío XII, 55, Pamplona E-31008, Spain.
authors.forename: Victor
authors.initials: V
authors.lastname: Segura
authors.affiliation: ProteoRed-ISCIII, Center for Applied Medical Research (CIMA), University of Navarra , Avda. Pío XII, 55, Pamplona E-31008, Spain.
authors.forename: Elizabeth
authors.initials: E
authors.lastname: Guruceaga
authors.affiliation: ProteoRed-ISCIII, National Center for Biotechnology-CSIC (CNB) , C/Darwin 3, Madrid 28049, Spain.
authors.forename: Vital
authors.initials: V
authors.lastname: Vialas
authors.affiliation: Department of Communication Engineering E.T.S. Ingenierı́a de Bilbao, University of the Basque Country (UPV/EHU) , Alda. Urquijo, s/n, Bilbao 48013, Spain.
authors.forename: Gorka
authors.initials: G
authors.lastname: Prieto
authors.affiliation: Computer Science Faculty, Complutense University of Madrid (UCM) , C/ Jose Garcı́á Santesmases 9, Madrid 28040, Spain.
authors.forename: Carlos
authors.initials: C
authors.lastname: García
authors.affiliation: ProteoRed-ISCIII, Center for Applied Medical Research (CIMA), University of Navarra , Avda. Pío XII, 55, Pamplona E-31008, Spain.
authors.forename: Fernando J
authors.initials: FJ
authors.lastname: Corrales
authors.affiliation: ProteoRed-ISCIII, National Center for Biotechnology-CSIC (CNB) , C/Darwin 3, Madrid 28049, Spain.
authors.forename: Juan Pablo
authors.initials: JP
authors.lastname: Albar
authors.affiliation: ProteoRed-ISCIII, National Center for Biotechnology-CSIC (CNB) , C/Darwin 3, Madrid 28049, Spain.
authors.forename: Alberto
authors.initials: A
authors.lastname: Pascual-Montano
mesh_terms: D023281:Genomics; D006801:Humans; D011499:Protein Processing, Post-Translational; D020543:Proteome; D059467:Transcriptome
chemical_list: D020543:Proteome
keywords: ENCODE; Human Proteome Project; RNA-Seq; bioinformatics; chromosome 16; proteogenomics; proteomics; spHPP; transcriptomics