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Several user-friendly and programmatic interfaces can be used for interaction (a list and their descriptions can be found in [23]).
RegulonDB reports, for each interaction, a list of evidence codes indicating which experimental techniques reported a particular interaction.
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MImerge provides three outputs: a list of interactions a list of interactors a list of interactor synonyms a list of interactions a list of interactors a list of interactor synonyms Each interaction is the result of merging all the experimental evidences indicating that a specific pair of molecules interacts.
To evaluate the ability of these tools to identify cancer-related genes and interactions, a list of cancer-related genes was extracted from OMIM, using text string matching and manual curation.
An overview on the experiments used and the time-points available is given in table 2. Data on known TF gene interactions, a list of known and predicted TFs, position within the chromosome and arrangement within operons were collected from RegulonDB release 6.1 [ 10].
According to the minimal information required to report a protein interaction (MIMIx) (24), each interaction requires a list of interactors and their database identifiers, a basic description of the experiment used to detect the interaction and an associated publication which reports the interaction.
In particular, we searched for protein interactions with a list of 46 core circadian genes gathered by Wallach et al. [ 28].
The online version gives access to medication monographs and allows checking for drug interactions among a list of drugs selected by the practitioner.
It is represented by a logical interaction hypergraph, and a list of logical functions describing the interactions (Additional file 1: Table S1).
Thus, for each predicted interaction we generate a list of GO annotations for both interacting partners.
The GeneMANIA Cytoscape app enables users to construct a weighted composite functional interaction network from a list of genes.
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