Our current analysis suggests that each pathway, particularly the one encoded by a large number of operons, tends to consist of a few operon clusters along the genome, as illustrated in Figure 1 (taking the four largest pathways in EcoCyc as examples).
The largest pathway in the final data set was 'Protein processing in endoplasmic reticulum' with a more comparable 78 genes.
The largest pathway in the original data set was 'Metabolism' containing 310 genes, which would have dominated much of the network.
With the ever increasing amounts of interaction data it becomes more evident that an extra dimension will be valuable for the visualisation of large pathways and eventually an in silico cell.
Biosynthetic pathways can reach 100 kb in size; however, because cosmid and fosmid library inserts are restricted to around 40 kb, large pathways cannot be captured in their entirety as a single clone and further manipulations are frequently necessary to assemble a complete gene cluster from multiple cosmids.
On the other hand, the standard graphical notations provided by SBGN are successfully implemented by REACTOME and PANTHER database to show the complex and large pathway diagram in the database web interface.
However, in transferring large pathways to alternate hosts and manipulating expression levels, the native regulation of carbon flux through the pathway may be lost leading to imbalances in the pathways.
Whilst all of these objectives are valid, fulfilling them in practice is far from trivial and there are few worked examples of large pathway diagrams depicted in standard notations, available in the public domain.
Furthermore, neither of these methods consider the situation where some identified pathways contain both dense physical and dense GIs, resulting in large pathway sizes that need to be further clustered.
Such steps are uncovered through painstaking study of genes (genomics), the proteins that they encode (proteomics), and the larger biological pathways in which they act.
