title: neXtProt: organizing protein knowledge in the context of human proteome projects.
abstract: About 5000 (25%) of the ~20400 human protein-coding genes currently lack any experimental evidence at the protein level. For many others, there is only little information relative to their abundance, distribution, subcellular localization, interactions, or cellular functions. The aim of the HUPO Human Proteome Project (HPP, www.thehpp.org ) is to collect this information for every human protein. HPP is based on three major pillars: mass spectrometry (MS), antibody/affinity capture reagents (Ab), and bioinformatics-driven knowledge base (KB). To meet this objective, the Chromosome-Centric Human Proteome Project (C-HPP) proposes to build this catalog chromosome-by-chromosome ( www.c-hpp.org ) by focusing primarily on proteins that currently lack MS evidence or Ab detection. These are termed "missing proteins" by the HPP consortium. The lack of observation of a protein can be due to various factors including incorrect and incomplete gene annotation, low or restricted expression, or instability. neXtProt ( www.nextprot.org ) is a new web-based knowledge platform specific for human proteins that aims to complement UniProtKB/Swiss-Prot ( www.uniprot.org ) with detailed information obtained from carefully selected high-throughput experiments on genomic variation, post-translational modifications, as well as protein expression in tissues and cells. This article describes how neXtProt contributes to prioritize C-HPP efforts and integrates C-HPP results with other research efforts to create a complete human proteome catalog.
authors.affiliation: CALIPHO Group, SIB-Swiss Institute of Bioinformatics, Faculty of Medicine, University of Geneva, CMU-1, rue Michel Servet 1211 Geneva 4, Switzerland.
authors.forename: Pascale
authors.initials: P
authors.lastname: Gaudet
authors.forename: Ghislaine
authors.initials: G
authors.lastname: Argoud-Puy
authors.forename: Isabelle
authors.initials: I
authors.lastname: Cusin
authors.forename: Paula
authors.initials: P
authors.lastname: Duek
authors.forename: Olivier
authors.initials: O
authors.lastname: Evalet
authors.forename: Alain
authors.initials: A
authors.lastname: Gateau
authors.forename: Anne
authors.initials: A
authors.lastname: Gleizes
authors.forename: Mario
authors.initials: M
authors.lastname: Pereira
authors.forename: Monique
authors.initials: M
authors.lastname: Zahn-Zabal
authors.forename: Catherine
authors.initials: C
authors.lastname: Zwahlen
authors.forename: Amos
authors.initials: A
authors.lastname: Bairoch
authors.forename: Lydie
authors.initials: L
authors.lastname: Lane
mesh_terms: D002877:Chromosomes, Human; D019295:Computational Biology; D030562:Databases, Protein; D015894:Genome, Human; D006801:Humans; D020407:Internet; D051188:Knowledge Bases; D013058:Mass Spectrometry; D011499:Protein Processing, Post-Translational; D011506:Proteins / Q000235:genetics / Q000378:metabolism; D020543:Proteome
chemical_list: D011506:Proteins; D020543:Proteome