However, if the newly connected pathway map requires many kinds of initial substrates, the extended pathway-map network needs many additional pathway maps that will supply the initial substrates.
These maps include many of the 16 pathway maps uniquely identified by the integrated 'omics' analysis, e.g. "G-Proteins mediated regulation MARK-ERK signaling", "Beta-adrenergic receptors regulation of ERK", "G-Protein alpha-i signaling cascades", "Rap2A regulation pathway" and "PDGF signaling via MAPK cascades".
In the first part, the conserved pathway maps among many genomes are determined, based on the comparative genomics.
The biological KEGG pathways represent a collection of biological pathway maps that integrate many units, including genes, proteins, RNAs, chemical compounds, and chemical reactions, as well as disease genes and drug targets, which are stored as individual entries in other KEGG databases.
More mathematically complex definitions have been proposed but they are limited in that they assume a given node is assigned exclusively to one module [ 43, 44] a property that is inconsistent with inclusion of many genes in in multiple pathways (Pathway Maps > 1; e.g. AKT1, MAP2K1, STAT3, NFKB1).
Biological pathway maps are highly relevant tools for many tasks in molecular biology.
Many genes were included in multiple pathways and we therefore defined the metric Pathway Maps as the number of pathways onto which a given gene is assigned across all resources used in ensemble construction.
These results indicate that there are many possibilities to synthesize the biomass components from extracellular nutrients, i.e., many solutions to realize the autonomous pathway maps*, if the total number of the pathway maps is unlimited.
Moreover, many key regulators have hundreds of target genes and not nearly all of them are represented on pathway maps.
