BioPAX is a community standard ontology for describing pathway and protein interaction data, suitable for qualitatively representing the current knowledge of biological systems.
The biological pathway information describing pathway types, regulations for genes, and/or experiments was retrieved from HPRD, KEGG [ 26] and CGAP [ 27].
Directly modeling pathway dynamics is complicated by the need for high-quality temporal data describing pathway activity and high-confidence parameter values, which can be directly obtained only from highly structured experimental data.
We next evaluated similarities and differences in over-represented biological pathways using the c2 gene set matrix, describing pathways.
Consequently, considerable information is needed for describing pathways and characterizing the function and structure of the pathways.
In the following we present a theory describing pathways that may depend on OPP and contribute to glaucomatous damage.
In silico, this can be achieved by coupling the software tools developed for describing pathways to tools developed for study of protein dynamics.
The Beacon Pathway Editor consists of a tool designed to draw pathways encoded in the Systems Biology Graphical Notation Activity Flow language that is a standard for describing pathways in terms of perturbations, influences, activities, logical operators, and phenotypes [ 41].
To analyze modulator-antibody combinations, hereafter defined as signaling nodes, several metrics were developed to describe pathway activity: Basal (basal, modulator-independent activity), Fold Change (modulator-induced), and Total (overall pathway activity) (Figure 1 and Methods).
One of these alpha subunits, the stimulatory alpha subunit of G-proteins (Gs-alpha), activates the cAMP pathway, a well described pathway which is important in multiple complex processes, including cell proliferation and differentiation.
We propose that Rxyl_2849, adjacent to Rxyl_2847 and Rxyl_2848, also plays a crucial role in this newly described pathway.
