For a given functional category, protein folds and their respective phylogenetic ancestries were identified through a combination of data from the Gene Ontology database (GO) [ 27], the ASTRAL database [ 28], and the Molecular Ancestry Network database (MANET) [ 29].
ARS: Aminoacyl tRNA Synthetase; CDD: Conserved Domains Database; GO: Gene Ontology; LUCA: Last Universal Common Ancestor; MANET: Molecular Ancestry NETworks database; PDB Protein Data Bankk.
To gain insight into biological functions affected by these changes, we overlaid the top 80 genes (∼20% FDR) under both conditions (gain or loss of synchrony) onto the global molecular network of the Ingenuity knowledge database.
The m/ z 511, 495, and 477 ions clustered together in the molecular network, and inspection of the AntiMarin database for their exact masses (m/ z 511.2794, 495.2830, and 477.2732) suggested the polycyclic tetramic macrolactams alteramide A or maltophilin as possible matches for the m/ z 511.2794 compound.
APID2NET retrieves all the possible information on protein-protein interaction from five interaction databases namely, Database of Interacting Proteins [44], Biomolecular Interaction Network Database [45], IntAct [46], Molecular Interactions Database [47] and Human Protein Reference Database [48].
Data sets containing the Affymetrix probe set identifiers and fold changes of genes were overlaid onto a global molecular network developed from information contained in the database.
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.
The analysis of evolution of molecular networks advocated in this paper requires a large (preferably genome-wide) and unbiased (i.e. no anthropogenic selection present in databases) dataset describing a molecular network in a given species.
One is therefore allowed to use this Artificial Neural Network database as a guideline to design ultra-thin-film molecular magnet application in the future.
Genes present in this database, called Focus Genes, were overlaid onto a global molecular network developed from information contained in the Ingenuity Pathways Knowledge Base.
