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Molecular relation of strains was determined by using pulsed-field gel electrophoresis (PFGE) after digestion of genomic DNA with restriction endonuclease Sma1 (Gibco BRL, Promega, Madison, WI) (13 ).
The Venn diagram was constructed by using the freely available software system R (http://www.r-project.org) in order to visualize the grade of molecular relation (common genes/proteins) between the generated subnetworks.
Nutrigenetics and nutrigenomics, which seek to identify genetic variation relevant to food's absorption, processing and effect in the body, is also absorbed with the molecular relation between food and DNA.
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Within cells, interactions between metabolites, proteins, or genes define a web of molecular relations which have well-defined organization.
Molecular relations (protein-protein and protein/DNA interactions) were connected based on SysBiomics platform (http://biomine.cigb.edu.cu/sysbiomics/).cigb.edu.cu/sysbiomics/
The Supplementary Materials provide additional tables with detailed molecular relations for further pathway/disease combinations across different databases.
The user must first generate visualization data with a preferred data mining algorithm and then upload the resulting data into the visualization package for graphic visualization of molecular relations.
The algorithm that counts the number of overlapping molecules and/or molecular relations between the extracted network and the canonical network identifies the canonical network showing the most statistically significant contribution to the extracted network.
The algorithm counting the number of overlapping molecular relations between the extracted network and the canonical pathway makes it possible to identify the canonical pathway showing the most significant contribution to the extracted network [ 12, 17].
By importing 932 genes into KeyMolnet, the neighboring network-search algorithm identified a highly complex network composed of 3,904 molecules and 8,423 molecular relations, showing a significant relationship with canonical pathways of transcriptional regulation by p53 (p = 9.898E-266), Rb/E2F (p = 1.032E-247), CREB (p = 5.084E-203), and SMAD (p = 7.510E-179).
In short, students have an eye for molecular detail (relation of structure and function), and they appreciate the colors, but at the same time, they are attracted by the clearness of the schematic representation.
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CEO of Professional Science Editing for Scientists @ prosciediting.com