Data files used for the molecular network have been uploaded to Global Natural Products Social Molecular Networking (http://gnps.ucsd.edu), accession number MSV000078621.
For example, a multi-level technology approach was used to unravel the molecular network that lead to cryptorchidism [ 37].
The entries are used to label the molecular network in Additional file 4 : Figure S2 and Additional file 5 : Figure S3.
The molecular equations, together with the definitions of coefficients and their values that were used to mathematically model the molecular network described above have been detailed in [ 3- 5] and have presented by the author in his dissertation thesis (see below legend of Figure 1).
We identified 16 genes encoding shared proteins in the molecular network, built using the literature- and database-mining (ANDSystem, Pathway Studio and STRING), that simultaneously connected with PE, DM, GD and Ob.
Such pairs of spectra connected by edges in the molecular network are revealed using the spectral alignment approach.
Desorption electrospray ionization (DESI) has verified already known metabolic interactions between competing Bacillus subtilis and Streptomyces coelicolor (Watrous et al., 2010), and nano-DESI has been used to examine the molecular networks of living colonies, including the possible identities of unknown metabolites through time (Watrous et al., 2012).
To investigate the molecular network around Oct4/Pou5f1, we used an epitope-tagging affinity purification strategy.
In order to perform this analysis in metabolic networks, we used the molecular signature descriptor, a 2D representation of molecular graphs that provides a characterization of compounds and reactions in the network.
For the molecular networks, we used a restart probability of 0.5, adopted from our previous work (Cho et al., 2015).
