Clicking on a protein in the networks displays the list of interactions for that protein.
The list of interactions involving ARV drugs is extensive and constantly expanding.
The subsets of overtargeted genes enriched in the select functional clusters were then used to filter the list of interactions between GbA miRNAs and overtargeted mRNAs.
If the greatest p value, over all possible eQTL, did not meet the FDR cut-off the SNP was removed from the list of interactions.
We therefore set an additional screening thresholds on the list of interactions, keeping only those that occur in at least four (out of 100) iterations.
We looked for evidence of interactions between genes in the master list and these 46 core clock genes (the list of interactions of the core clock genes was provided in Table S1 in [ 28]).
It is important to note that (i) the list of interactions reported in the database is far from being exhaustive, (ii) the interactions documented are either physical or genetic, which implies that they may not be direct interactions.
We built a protein interaction network by combining yeast two-hybrid (Y2H) data, reported protein co-complexes, and the list of interactions in the BioGRID (Biological General Repository for Interaction Datasets) database [ 30– 30].
To clarify the distinctive cellular networks and accuracy of interactions, bZIPDB provides the list of regulatory interactions conducted in a particular cell type.
Among the list of significant interaction metabolomics networks found by IPA (complete list in Additional file 11: Table S7), the most significant one is canonically referred to as " Increased Levels of Albumin, Cellular Growth and Proliferation, Organismal Development".
By probing these predicted interactions with independent knowledge from phylogenetic and sequence data we were able to narrow down the list of potential interactions to a smaller list of 109 validated interactions, which could be surveyed by manual inspection.
