We also implemented the gene regulatory network as a continuous system using the Glass model of differential equations, that can be considered as a first approximation of kinetic-reaction equations, but which are not necessarily equivalent to the Boolean model.
This model [ 29, 30] implements the gene circuit approach [ 63, 64] used to reverse-engineer the regulatory interactions of the gap genes by fitting to quantitative spatio-temporal gene expression data, which can be mRNA [ 29] or protein [ 30].
Gene Set analysis (GSA) was undertaken using the GenGen package [49] which implements the Gene-Set Enrichment Analysis introduced by Subramanian, Tamayo et al [50].
Synthetic biology faces a dilemma: it will either implement the corresponding genes, and cells will evolve in an unpredictable manner, or omit them, and cells will age and have to be reconstructed periodically.
To provide consistency in gene predictions across all three assemblies, we implemented the bacterial gene prediction program fgenesb (Tyson et al. 2004), using the "generic BACTERIAL" model.
However, our complementation strategy might be more diffcult to implement when the gene studied is too similar to the T. brucei counterpart.
The drug sensitivity signatures implemented the Parametric Gene Set Enrichment Analysis method to align NCI-60 cell line sensitivity signatures that are predictive across at least two independent cell contexts with the patient's differentially expressed genes.
During development, homeostasis, and disease, cells integrate diverse environmental inputs and implement the appropriate changes in gene expression to survive stresses or execute developmental programs.
Figure 1 describes the procedure of how to implement the MAVTgsa package for gene set enrichment analysis.
Two signal enhancement techniques based on isothermal circular strand-displacement polymerization reaction, cyclical nucleic acid strand-displacement polymerization (CNDP) and cyclical common (nonnucleic acid) target-displacement polymerization (CCDP), were employed to implement the amplification assay for p53 gene and PDGF-BB, respectively.
