One of the essential requirements of the proteomics community is a high quality annotated nonredundant protein sequence database with an archival service and stable identifiers to enable protein identification and characterization.
Offers a seamless integration of and navigation through protein-related data. NeXtProt contains proteomics data for over 85% of human proteins. Moreover, this tool includes over 8000 phenotypic observations for over 4000 variations in a number of genes involved in hereditary cancers and channelopathies. All of the data are available via a user interface and FTP site. An API access and a SPARQL endpoint are also provided for more technical applications.
Stores protein sequence and annotation data. UniProt provides complete coverage of sequence space at several resolutions while hiding redundant sequences. It can be used as ‘gold standard’ reference proteome dataset for orthologue benchmarking. This database regroups several entities: the UniProt Knowledgebase (UniProtKB), the UniProt Reference Clusters (UniRef), the UniProt Archive (UniParc) and the UniProt Metagenomic and Environmental Sequences (UniMES) database.
Provides access to experimentally derived information about the human proteome including protein–protein interactions (PPIs), post-translational modifications (PTMs) and tissue expression. HPRD is an integrated knowledgebase for genomic and proteomic investigators. The database also includes (i) PhosphoMotif Finder that contains known kinase/phosphatase substrate and binding motifs, (ii) links to a signaling pathway resource called NetPath, (iii) a distributed annotation system, called Human Proteinpedia for enhanced community participation and allows the use of BLAST for querying mRNA/protein data.
Gathers information about Tetrahymena thermophila genome sequence. TGD Wiki provides a curation interface that allows users to update information about each gene: gene names, descriptions, Gene Ontology (GO) annotations and Pubmed references. The database includes all 24 725 protein-coding genes in Tetrahymena, each with its own dedicated Gene Page. Moreover, the base also contains a genome browser and a BLAST server.
Supports functional Listeria genome analyses by combining information obtained by applying bioinformatics methods and from public databases to improve the original annotations. LEGER offers three unique key features: (i) it is the first comprehensive information system focusing on the functional assignment of genes and proteins; (ii) integrated visualization tools, KEGG pathway and Genome Viewer, alleviate the functional exploration of complex data; and (iii) LEGER presents results of systematic post-genome studies, thus facilitating analyses combining computational and experimental results.
Provides a comprehensive overview and thus a valuable resource for finding relevant data. CHOmine is an InterMine based data warehouse for Chinese Hamster Ovary (CHO) data that connects gene information to each other and provides links to outside websites. It integrates a recently published consensus genome-scale metabolic reconstruction of different CHO cell lines. This resource can become an important point where to search information when working with CHO cells.
Reflects alterations between normal versus diseased conditions. CliPro contains proteins, diseases, biomarker, biofluid, protein type and plasma catalogues. Enables comparison between protein concentration levels of disease oriented studies and normal/control studies. The knowledgebase also contains information on post-translational modifications, genetic variations associated with disease.