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STRING v10: protein-protein interaction networks, integrated over the tree of life.

Szklarczyk D, Franceschini A, Wyder S, Forslund K, Heller D, Huerta-Cepas J, Simonovic M, Roth A, Santos A, Tsafou KP, Kuhn M, Bork P, Jensen LJ, von Mering C - Nucleic Acids Res. (2014)

Bottom Line: However, known and predicted interactions are scattered over multiple resources, and the available data exhibit notable differences in terms of quality and completeness.For this purpose, we have introduced hierarchical and self-consistent orthology annotations for all interacting proteins, grouping the proteins into families at various levels of phylogenetic resolution.Further improvements in version 10.0 include a completely redesigned prediction pipeline for inferring protein-protein associations from co-expression data, an API interface for the R computing environment and improved statistical analysis for enrichment tests in user-provided networks.

View Article: PubMed Central - PubMed

Affiliation: Institute of Molecular Life Sciences and Swiss Institute of Bioinformatics, University of Zurich, 8057 Zurich, Switzerland.

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Related in: MedlinePlus

The STRING network view. Combined screenshots from the STRING website, which has been queried with a subset of proteins belonging to two different protein complexes in yeast (the COP9 signalosome, as well as the proteasome). Colored lines between the proteins indicate the various types of interaction evidence. Protein nodes which are enlarged indicate the availability of 3D protein structure information. Inset top right: for each protein, accessory information is available which includes annotations, cross-links and domain structures. Inset bottom right: the same network is shown after the addition of a user-configurable ‘payload’-dataset (26). In this case, the payload corresponds to color-coded protein abundance information, and reveals systematic differences in the expression strength of both complexes.
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Figure 1: The STRING network view. Combined screenshots from the STRING website, which has been queried with a subset of proteins belonging to two different protein complexes in yeast (the COP9 signalosome, as well as the proteasome). Colored lines between the proteins indicate the various types of interaction evidence. Protein nodes which are enlarged indicate the availability of 3D protein structure information. Inset top right: for each protein, accessory information is available which includes annotations, cross-links and domain structures. Inset bottom right: the same network is shown after the addition of a user-configurable ‘payload’-dataset (26). In this case, the payload corresponds to color-coded protein abundance information, and reveals systematic differences in the expression strength of both complexes.

Mentions: Once a protein or set of proteins is identified, users proceed to the network view (Figure 1). From there, it is possible to inspect the interaction evidence, to re-adjust the score-cutoffs and network size limits and to view detailed information about the interacting proteins. Upon switching to the ‘advanced’ mode (via the tool panel below the network), users can also cluster and rearrange the network and test for statistical enrichments in the network. The latter feature has been enhanced for the current version 10.0 of STRING: enrichment detection now also covers human disease associations and tissue annotations, which might be statistically enriched in a given network. For this feature, STRING connects with the partner databases TISSUES (http://tissues.jensenlab.org) and DISEASES (http://diseases.jensenlab.org), which also share sequence and name spaces with STRING, and which annotate proteins to tissues or to disease entities based on a combination of automated text-mining and knowledge imports.


STRING v10: protein-protein interaction networks, integrated over the tree of life.

Szklarczyk D, Franceschini A, Wyder S, Forslund K, Heller D, Huerta-Cepas J, Simonovic M, Roth A, Santos A, Tsafou KP, Kuhn M, Bork P, Jensen LJ, von Mering C - Nucleic Acids Res. (2014)

The STRING network view. Combined screenshots from the STRING website, which has been queried with a subset of proteins belonging to two different protein complexes in yeast (the COP9 signalosome, as well as the proteasome). Colored lines between the proteins indicate the various types of interaction evidence. Protein nodes which are enlarged indicate the availability of 3D protein structure information. Inset top right: for each protein, accessory information is available which includes annotations, cross-links and domain structures. Inset bottom right: the same network is shown after the addition of a user-configurable ‘payload’-dataset (26). In this case, the payload corresponds to color-coded protein abundance information, and reveals systematic differences in the expression strength of both complexes.
© Copyright Policy - creative-commons
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC4383874&req=5

Figure 1: The STRING network view. Combined screenshots from the STRING website, which has been queried with a subset of proteins belonging to two different protein complexes in yeast (the COP9 signalosome, as well as the proteasome). Colored lines between the proteins indicate the various types of interaction evidence. Protein nodes which are enlarged indicate the availability of 3D protein structure information. Inset top right: for each protein, accessory information is available which includes annotations, cross-links and domain structures. Inset bottom right: the same network is shown after the addition of a user-configurable ‘payload’-dataset (26). In this case, the payload corresponds to color-coded protein abundance information, and reveals systematic differences in the expression strength of both complexes.
Mentions: Once a protein or set of proteins is identified, users proceed to the network view (Figure 1). From there, it is possible to inspect the interaction evidence, to re-adjust the score-cutoffs and network size limits and to view detailed information about the interacting proteins. Upon switching to the ‘advanced’ mode (via the tool panel below the network), users can also cluster and rearrange the network and test for statistical enrichments in the network. The latter feature has been enhanced for the current version 10.0 of STRING: enrichment detection now also covers human disease associations and tissue annotations, which might be statistically enriched in a given network. For this feature, STRING connects with the partner databases TISSUES (http://tissues.jensenlab.org) and DISEASES (http://diseases.jensenlab.org), which also share sequence and name spaces with STRING, and which annotate proteins to tissues or to disease entities based on a combination of automated text-mining and knowledge imports.

Bottom Line: However, known and predicted interactions are scattered over multiple resources, and the available data exhibit notable differences in terms of quality and completeness.For this purpose, we have introduced hierarchical and self-consistent orthology annotations for all interacting proteins, grouping the proteins into families at various levels of phylogenetic resolution.Further improvements in version 10.0 include a completely redesigned prediction pipeline for inferring protein-protein associations from co-expression data, an API interface for the R computing environment and improved statistical analysis for enrichment tests in user-provided networks.

View Article: PubMed Central - PubMed

Affiliation: Institute of Molecular Life Sciences and Swiss Institute of Bioinformatics, University of Zurich, 8057 Zurich, Switzerland.

Show MeSH
Related in: MedlinePlus