STRING: Known and predicted protein-protein associations, integrated and transferred across organisms

Radboud University Nijmegen, Nymegen, Gelderland, Netherlands
Nucleic Acids Research (Impact Factor: 9.11). 02/2005; 33(Database issue):D433-7. DOI: 10.1093/nar/gki005
Source: PubMed


A full description of a protein's function requires knowledge of all partner proteins with which it specifically associates.
From a functional perspective, ‘association’ can mean direct physical binding, but can also mean indirect interaction such
as participation in the same metabolic pathway or cellular process. Currently, information about protein association is scattered
over a wide variety of resources and model organisms. STRING aims to simplify access to this information by providing a comprehensive,
yet quality-controlled collection of protein–protein associations for a large number of organisms. The associations are derived
from high-throughput experimental data, from the mining of databases and literature, and from predictions based on genomic
context analysis. STRING integrates and ranks these associations by benchmarking them against a common reference set, and
presents evidence in a consistent and intuitive web interface. Importantly, the associations are extended beyond the organism
in which they were originally described, by automatic transfer to orthologous protein pairs in other organisms, where applicable.
STRING currently holds 730 000 proteins in 180 fully sequenced organisms, and is available at

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Available from: Markus Krupp
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    • "Seven putative orthologous sequences were retrieved in R. irregularis; Uniprot accession numbers U9U1X0, U9UEK3, U9UFF5, U9TTI3, U9UF16, U9UI83 and U9UJR1, respectively. Furthermore, clusters of orthologous genes (COGs), gathering sequences from numerous organisms, were determined using STRING version 9.05[63]for each protein candidate. The resulting COGs were aligned using COBALT version 2.01[64]. "
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    ABSTRACT: Background: Arbuscular mycorrhizal fungi (AMF) are members of the phylum Glomeromycota, an early divergent fungal lineage that forms symbiotic associations with the large majority of land plants. These organisms are asexual obligate biotrophs, meaning that they cannot complete their life cycle in the absence of a suitable host. These fungi can exchange genetic information through hyphal fusions (i.e. anastomosis) with genetically compatible isolates belonging to the same species. The occurrence of transient mitochondrial length-heteroplasmy through anastomosis between geographically distant Rhizophagus irregularis isolates was previously demonstrated in single spores resulting from crossing experiments. However, (1) the persistence of this phenomenon in monosporal culture lines from crossed parental isolates, (2) its correlation with nuclear exchanges and (3) the potential mechanisms responsible for mitochondrial inheritance are still unknown. Using the AMF model organism R. irregularis, we tested whether the presence of a heteroplasmic state in progeny spores was linked to the occurrence of nuclear exchanges and whether the previously observed heteroplasmic state persisted in monosporal in vitro crossed-culture lines. We also investigated the presence of a putative mitochondrial segregation apparatus in Glomeromycota by identifying proteins similar to those found in other fungal groups. Results: We observed the occurrence of biparental inheritance both for mitochondrial and nuclear markers tested in single spores obtained from crossed-isolates. However, only one parental mitochondrial DNA and nuclear genotype were recovered in each monosporal crossed-cultures, with an overrepresentation of certain mitochondrial haplotypes. These results strongly support the presence of a nuclear-independent mitochondrial segregation mechanism in R. irregularis. Furthermore, a nearly complete set of genes was identified with putative orthology to those found in other fungi and known to be associated with the mitochondrial segregation in Saccharomyces cerevisiae and filamentous fungi. Conclusions: Our findings suggest that mitochondrial segregation might take place either during spore formation or colony development and that it might be independent of the nuclear segregation machinery. We present the basic building blocks for a better understanding of the mitochondrial inheritance process and segregation in these important symbiotic fungi. The comprehension of these processes is of great importance since it has been shown that different segregated lines of the same isolate can have variable effects on the host plant.
    Full-text · Article · Dec 2016 · BMC Microbiology
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    • "Thus we use the hadoop framework for the extraction of chemicals from the abstracts. Currently a top-to-bottom approach is used in most of the text mining applications, which means parsing important words from vast amounts of text, and then spread downwards through databases or software such as STRING[7], STITCH[8] [9], Biotextquest[10], Bioalma[11], Whatizit[12] [13] or iHop[14].Other tools, reviewed in[11], try to analyze literature using semantic concepts, clustering algorithms or ranking algorithms and most generic attempts go one step further by using semantic web concepts to further enrich and annotate terms found in literature[1]. In the proposed system the user will just need to provide the name of the disease of interest. "

    Preview · Article · Dec 2015
    • "The default cutoff for confident interactions is 0.4 [11] [17]. Chemical– protein interactions were transferred among species based on the sequence similarity of the proteins [17]. The chemical–protein interactions have also been successfully utilized to predict nongenotoxic hepatocarcinogenicity [18] [19]. "
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    ABSTRACT: Maleic acid is a multi-functional chemical widely applied in the manufacturing of polymer products including food packaging. However, the contamination of maleic acid in modified starch has raised the concerns about the effects of chronic exposure to maleic acid on human health. This study proposed a novel toxicogenomics approach for inferring functions, pathways and diseases potentially affected by maleic acid on humans by using known interactions between maleic acid and proteins. Neuronal signal transmission and cell metabolism were identified to be most influenced by maleic acid in this study. The top disease categories inferred to be associated with maleic acid were mental disorder, nervous system diseases, cardiovascular diseases, and cancers. The results from an in silico analysis showed that maleic acid could penetrate the blood-brain barrier to affect the nervous system. Several functions and pathways were further analyzed and identified to give insights into the mechanisms of maleic acid-associated diseases. The toxicogenomics approach may offer both a better understanding of the potential risks of maleic-acid exposure to humans and a direction for future toxicological investigation.
    No preview · Article · Sep 2014 · Chemico-Biological Interactions
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