neXtProt: a knowledge platform for human proteins

Abstract

neXtProt (http://www.nextprot.org/) is a new human protein-centric knowledge platform. Developed at the Swiss Institute of Bioinformatics (SIB), it aims to help researchers answer questions relevant to human proteins. To achieve this goal, neXtProt is built on a corpus containing both curated knowledge originating from the UniProtKB/Swiss-Prot knowledgebase and carefully selected and filtered high-throughput data pertinent to human proteins. This article presents an overview of the database and the data integration process. We also lay out the key future directions of neXtProt that we consider the necessary steps to make neXtProt the one-stop-shop for all research projects focusing on human proteins.

Identification of PCAG1 as a novel prostate cancer-associated gene

“…Using Uniprot (13) and Nextprot (14), PCAG1 was predicted to be a transmembrane protein with a transmembrane domain of 22 amino acids. The present study showed that the PCAG1 protein was mainly localized within the cytoplasm and mitochondria.…”

Functional Genomics, Proteomics, Metabolomics and Bioinformatics for Systems Biology

“…DNA and associated proteins, which play an important role in gene regulation, gene- [44], IMS [144,147] Metabolomics tools MetabolomeExpress [150], metaP [151], KEGG [145], human metabolome project [142] Lipidomics methods MS [44,161], orbitraps [160], IMS [144,147] Lipidomics tools LIPID MAPS [165], XCMS [162], MZmine2 [163] environment interactions, development and in diseases such as inflammation and cancer [60,61]. Such modifications involve the DNA itself but not its sequence, i.e.…”

“…Protein-protein interactions and cell signalling cascades are mainly studied with the following approaches: yeast two-hybrid complementation, protein microarray, immunoaffinity chromatography and MS [137], and with a lower throughput by immunoprecipitation and mass spectrometry in Mammals [138,139]. Attempts to integrate proteomics with other omics data are hindered by current drawbacks of proteomics analysis: proteome not completely sampled, uncertain identification of protein, difficulties in mapping identifiers across the different omics sources, hence the need for protein-centric knowledge bases such as TransProteomic Pipeline [140], Protein Atlas [141] and neXProt [142].…”

Exploring the potential of public proteomics data

“…An example of the direct use of proteomics data is by looking up information about a given protein as indexed in an online protein knowledge‐base, such as UniProt 31 or neXtProt 32. This does not result in knowledge beyond what has already been published, but does provide the means to understand the current context of the protein(s) in question.…”