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How Do I Perform Network Analysis and Modeling of Regulatory Networks?

Best done by (a) network reconstruction, (b) network analysis, and (c) temporal analysis

of a network (biological system).

(a) A network reconstruction can be performed using a transcriptome-interactome map­

ping. For this, significantly expressed genes from an experimental dataset (own exper­

iments or e.g. microarrays from the GEO database; please always check here what

exactly was investigated and how the experiment was performed [which cell and array

type etc.]) are mapped to the interactome (e.g. PPI from STRING database). This can

be done using, for example, a mySQL database, which is free database creation soft­

ware. To do this, simply upload the microarray dataset and the interactome as a table

and reconstruct the network using the command Select * From ‘TableMA’, ‘TableI’

Where (‘TableMA’.id = ‘TableI’.A OR ‘TableMA’.id = ‘TableI’.C) (MA = microar­

ray; I = interactome; OR, since protein ID can occur in column A or C). Then save the

result as .sif (simple interaction file) to be able to read it into Cytoscape later. For step

a), it is best to refer to our two papers (https://www.ncbi.nlm.nih.gov/pubmed/24558299;

https://www.ncbi.nlm.nih.gov/pubmed/28265997), which provide a methodological

overview and a tutorial.

(b) To visualize and functionally analyze the created network, you can use CellDesigner

and Cytoscape. CellDesigner is a classical software for the creation of gene regulatory

and biochemical networks, but also includes numerous tools and packages, e.g. for

dynamic simulations and analyses. Cytoscape also allows the visualisation of a net­

work, but also data integration (e.g. microarray) and also has numerous plugins for

19.4  Cellular Communication, Signalling Cascades, Metabolism, Shannon Entropy