Provides manually curated published data sets of large-scale subcellular proteomics, fluorescent protein visualization, protein-protein interaction (PPI) as well as subcellular targeting calls from 22 prediction programs. SUBA4 contains an additional 35 568 localizations totalling more than 60 000 experimental protein location claims as well as 37 new suborganellar localization categories. The SUBA4 user interface enables users to choose quickly from the filter categories: ‘subcellular location’, ‘protein properties’, ‘protein-protein interaction’ and ‘affiliations’ to build complex queries. Furthermore, a ‘BLAST’ tab contains a sequence alignment tool to enable a sequence fragment from any species to find the closest match in Arabidopsis and retrieve data on subcellular location. Finally, using the location consensus SUBAcon, the SUBA4 toolbox delivers three novel data services allowing interactive analysis of user data to provide relative compartmental protein abundances and proximity relationship analysis of PPI and coexpression partners from a submitted list of Arabidopsis gene identifiers.
A web-accessible database of protein subcellular localization (SCL) for bacteria that contains both information determined through laboratory experimentation and computational predictions. The dataset of experimentally verified information (approximately 2000 proteins) was manually curated by us and represents the largest dataset of its kind. PSORTdb will be of particular interest to researchers studying microbes outside those with the classical Gram-negative diderm and Gram-positive monoderm cell envelope structures, including medically relevant species such as Mycobacterium tuberculosis and Mycoplasma pneumoniae, agriculturally relevant species such as Spiroplasma citri and industrially relevant species such as Thermotoga maritima.
A database for proteins temporally and spatially localized in distinct subcellular positions including midbody, centrosome, kinetochore, telomere and mitotic spindle during cell division/mitosis. MiCroKiTS can serve as a useful resource for further analyzing the molecular mechanisms during cell division.
Provides integrated access to complementary DNA (cDNA)-data, experimental results and bioinformatics information. LIFEdb is a database enabling researchers to systematically select and characterize genes and proteins of interest. The database was developed to publish data on full-length cDNAs and the subcellular localization of the encoded proteins.
Offers a database that regards nuclear localization signals (NLSs) and proteins translocated into the nucleus by signal sequences. NLSdb is a comprehensive source of information that can be easily integrated with other public and proprietary databases. NLSdb can greatly help in better understanding signal dependent nuclear transport of proteins. It contains over 6000 predicted nuclear proteins and their targeting signals from the protein database (PDB) and SWISS-PROT/TrEMBL databases.
Holds information about the protein names, their organism and the cell-type. NMP-db provides a database with proteins associated to the nuclear matrix. This database can be accessed from a search-engine interface that allows the querying by different database fields and the linking of queries through ‘AND’, ‘OR’ and ‘AND-NOT’. It also links to the respective PubMed abstracts that are given in each entry.
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.
Maps validated gene and protein expression, phenotype and images related to cell types. The data allow characterization and comparison of cell types and can be browsed by using the body browser and by searching for cells or genes. All cells are related to more complex systems such as tissues, organs and organisms and arranged according to their position in development. CellFinder provides long-term data storage for validated and curated primary research data and provides additional expert-validation through relevant information extracted from text.
An online resource for Caulobacter studies. CauloBrowser provides a user-friendly interface for quickly searching genes of interest and downloading genome-wide results. Search results about individual genes are displayed as tables, graphs of time resolved expression profiles, and schematics of protein localization throughout the cell cycle. In addition, the site provides a genome viewer that enables customizable visualization of all published high-throughput genomic data. The depth and diversity of data sets collected by the Caulobacter community makes CauloBrowser a unique and valuable systems biology resource.
Provides gene ontology (GO) and subcellular localization annotations. PA-GOSUB offers search and browsing capabilities that add query functionality to the pre-computed model organisms. It contains more than 140 000 proteins, about 27 000 Gene Ontology Annotation (GOA) and more than 100 000 Proteome Analyst (PA) for Gene Ontology (GO) molecular function. The database can be used to assist users to understand why a classifier makes a particular classification thank to the implementation of an explanation mechanism.
A cellular compartment-specific database of proteins and their interactions enabling an extensive, compartmentalized protein-protein interaction network analysis. ComPPI enables the user to filter biologically unlikely interactions, where the two interacting proteins have no common subcellular localizations and to predict novel properties, such as compartment-specific biological functions. ComPPI is an integrated database covering four species (S. cerevisiae, C. elegans, D. melanogaster and H. sapiens).
Provides information about human cells. SHOGoiN Cell Database contains cell differentiation pathways compiled from biomedical textbooks and journal papers and includes its own cell classification scheme in which each human cell is classified according to physical locations. Several cell taxonomy keys exist to tidy human differentiated cells and stem cells.
An improved and updated version of the fungal secretome and subcellular proteome, i. e. protein subcellular location, knowledgebase. The fungal protein sequence data were retrieved from UniProtKB, consisting of nearly 2 million entries with 167 species having a complete proteome. The assignments of protein subcellular locations were based on curated information and prediction using seven computational tools. The tools used for subcellular location prediction include SignalP, WoLF PSORT, Phobius, TargetP, TMHMM, FragAnchor, and PS-Scan. Secreted proteins, i.e. secretomes, along with 15 other subcellular proteomes were predicted. FunSecKB can be searched by users using several different types of identifiers, gene name or keyword(s). A subcellular proteome from a species can be searched or downloaded. BLAST searching whole fungal protein data or secretomes is available.
Collates more than 550 data sets from previously published fluorescent tagging or mass spectrometry studies and eight pre-computed subcellular predictions for barley, wheat, rice and maize proteomes. The data collection including metadata for proteins and studies can be accessed through the search portal. The reciprocal blast and EnsemblPLants homology tree allows the search for location data across the four crop species as well as compares it to Arabidopsis data from SUBA. The subcellular localization information housed in cropPAL helps to depict plant cells as compartmentalized protein networks that can be investigated for improving crop yield and quality, and developing new biotechnological solutions to agricultural challenges.
Provides access to information on tagged lines for nuclear-encoded chloroplast proteins, including their phenotypes and genotypes. The Chloroplast Function Database is a publicly available web-based resource that offers significant improvements in usability. It also provides additional important information to the plant biology community, enabling searches for visible phenotypes of genes of interest.
A public database, developed to organize a large data set of confocal images generated from the maize marker lines, for studying native gene expression in specific cell types and subcellular compartments using fluorescent proteins. Maize Cell Genomics Database represents two types of data: (i) information which describes fluorescent-tagged gene constructs used for maize marker line generation; and (ii) confocal images representing spatial and temporal expression of the fluorescent markers in the maize marker lines.