For the signaling network, we compiled signaling interactions from KEGG, BioCarta (http://pid.nci.nih.gov/) and TRANSPATH [ 36], as well as through manual curation of some undirected protein-protein interactions.
Instead of using multiple individual databases of protein interactions, we used the iRefIndex database [ 20] http://irefindex.uio.no, since it comprehensively compiles protein interaction data from multiple public databases in a non-redundant manner.
To assess robustness, we also repeat the analysis on networks derived from two other sources and report the results in the Additional file 1 In particular, we also use the Bossi network [ 30], a comprehensive protein-protein interaction network compiled from several protein interaction databases (e.g., BIND [ 37], BioGRID [ 26] and HPRD [ 38]).
Using previously identified genetic and physical interactions compiled at SGD, we determined the interaction network for the 9 genes (BEM1, CTF4, CTK1, HFI1, MFT1, NUP133, THO2, THP1 and THP2) which demonstrated diploid-specific sensitivity to DOX.
For this purpose, we implement the same validation process based on the large compiled domain-domain interaction network that is composed of all interactions in the DOMINE database and high-confidence interactions in the InterDom database.
We notice that the two compiled domain-domain interaction networks have different properties.
The dataset was assembled and manually curated by Cui et al. by merging the interactions compiled in different databases, followed by validation of each interaction by accurate revision of the literature.
Taken together, optimal use of all the databases compiling the interactions obtained by different methods will reduce the time and expense of finding a specific PDZ-binding partner for further studies at a genome-wide level, and will also aid its functional characterization [ 24, 73, 111].
Examining this topic further, we validated the most distinctly deregulated over- and under expressed miRNAs by RT-qPCR, utilized traverse analysis of altered miRNAs between the sample groups, characterized the reorganized miRNAs by compiling their interactions in ingenuity pathway analysis, expression in multiple tumor systems, and their functional role in metastasis and tumor progression.
These interaction data have been compiled in public biomolecular interaction databases.
