STITCH 5: augmenting protein–chemical interaction networks with tissue and affinity data
Damian Szklarczyk,Alberto Santos,Christian von Mering,Lars Juhl Jensen,Peer Bork,Peer Bork,Michael Kuhn +6 more
TLDR
In the new, fifth release of STITCH, functionality to filter out the proteins and chemicals not associated with a given tissue is implemented and a new network view is implemented that gives the user the ability to view binding affinities of chemicals in the interaction network.Abstract:
Interactions between proteins and small molecules are an integral part of biological processes in living organisms. Information on these interactions is dispersed over many databases, texts and prediction methods, which makes it difficult to get a comprehensive overview of the available evidence. To address this, we have developed STITCH ('Search Tool for Interacting Chemicals') that integrates these disparate data sources for 430 000 chemicals into a single, easy-to-use resource. In addition to the increased scope of the database, we have implemented a new network view that gives the user the ability to view binding affinities of chemicals in the interaction network. This enables the user to get a quick overview of the potential effects of the chemical on its interaction partners. For each organism, STITCH provides a global network; however, not all proteins have the same pattern of spatial expression. Therefore, only a certain subset of interactions can occur simultaneously. In the new, fifth release of STITCH, we have implemented functionality to filter out the proteins and chemicals not associated with a given tissue. The STITCH database can be downloaded in full, accessed programmatically via an extensive API, or searched via a redesigned web interface at http://stitch.embl.de.read more
Citations
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Journal ArticleDOI
STRING v11: protein-protein association networks with increased coverage, supporting functional discovery in genome-wide experimental datasets.
Damian Szklarczyk,Annika L. Gable,David Lyon,Alexander Junge,Stefan Wyder,Jaime Huerta-Cepas,Milan Simonovic,Nadezhda Tsankova Doncheva,John H. Morris,Peer Bork,Lars Juhl Jensen,Christian von Mering +11 more
TL;DR: The latest version of STRING more than doubles the number of organisms it covers, and offers an option to upload entire, genome-wide datasets as input, allowing users to visualize subsets as interaction networks and to perform gene-set enrichment analysis on the entire input.
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References
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Journal ArticleDOI
STRING v10: protein–protein interaction networks, integrated over the tree of life
Damian Szklarczyk,Andrea Franceschini,Stefan Wyder,Kristoffer Forslund,Davide Heller,Jaime Huerta-Cepas,Milan Simonovic,Alexander Roth,Alberto Santos,Kalliopi Tsafou,Michael Kuhn,Peer Bork,Lars Juhl Jensen,Christian von Mering +13 more
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STRING v9.1: protein-protein interaction networks, with increased coverage and integration
Andrea Franceschini,Damian Szklarczyk,Sune Frankild,Michael Kuhn,Milan Simonovic,Alexander Roth,Jianyi Lin,Pablo Minguez,Peer Bork,Christian von Mering,Lars Juhl Jensen +10 more
TL;DR: The update to version 9.1 of STRING is described, introducing several improvements, including extending the automated mining of scientific texts for interaction information, to now also include full-text articles, and providing users with statistical information on any functional enrichment observed in their networks.
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The druggable genome
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