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The MIntAct project has recently emerged as an international effort to standardize curation and retrieval of interactions from source databases (2).
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DECOBRA employs a rather relaxed definition of co-expression whose predictive power comes from combining it with the retrieval of interaction relationships.
The remaining 2,706 protein interfaces were used to build an M-Tree (see subsection Similarity-based retrieval of interaction interfaces under Methods).
An "interaction browser" lists DNA baits and TFs for which interactions are available and facilitates the retrieval of stored interactions.
We also presented the STRING network of some known/novel protein-protein interactions as an evidence view by using String 9.0 (Search Tool for the Retrieval of Interacting Genes/Proteins) database of physical and functional interactions (http://string-db.org/) [ 34].
The protein-protein interaction network of Mycobacterium tuberculosis H37Rv was retrieved from Search Tool for the Retrieval of Interacting Genes/Proteins (STRING) database [ 16].
The identification of the experimental methods (as described by PSI-MI) linked to protein interactions can be an important resource facilitating the retrieval of protein interactions, but this requires an extra effort to increase the aliases of the dictionary and/or to identify the critical textual passages.
The Search Tool for the Retrieval of Interacting Genes/Proteins (STRING) database of physical and functional interactions was used to analyze the protein-protein interaction (PPI) of all the proteins identified in the current study.
Subsequently weighted protein-protein interaction network of the pathogen was constructed by using a dataset retrieved from Search Tool for the Retrieval of Interacting Genes/Proteins (STRING) database.
More specifically, we used the Search Tool for the Retrieval of Interacting Genes/Proteins (STRING) to construct a protein interaction network.
Data were taken from STRING Search Tooll for the Retrieval of Interacting Genes/Proteins) version 9.05, which contains experimental, predicted and transferred protein protein interactions, together with interactions obtained through text mining (Franceschini et al., 2013).
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