The pathway interaction networks might be powerful tools for interactive exploratory analysis, by browsing and filtering the network visualizations in different ways to find interesting structures.
From this result, we constructed T2D risk gene pathway interaction network (in Figure 2), if and only if interacting pathways involve 3 or more risk genes.
In biochemical pathways PRK interacts with Rbcl to complete the cycle, but according to our predicted pathway interaction between PRK with Rbcl is mediated through 3PGK.
This approach relies on the strength of 913 manually curated pathways from the Pathway Interaction Database [22].
As a source of reliable human protein pathway information we utilized 913 annotated pathways from the Pathway Interaction Database [22].
We determined the list of genes used in each pathway in by query of the Pathway Interaction Database [49].
We downloaded gene annotations from Gene ontology database (http://www.geneontology.org/), and pathway information from two databases, the molecular signature database (MSigDB) and the pathway interaction database (PID).
To identify groups of genes that were characterized by significant expression changes we assembled 184 annotated signaling pathways from the Pathway Interaction Database (PID) [39].
STRING is a comprehensive database, collecting the interactions from well-known resources, such as MINT, HPRD, BIND, DIP, BioGRID, KEGG, NCI-Nature Pathway Interaction, among others [30].
For the evaluation of gene expression network construction, we evaluated the constructed network with pathways in the Pathway Interaction Database (PID).
PID also records some pathway interaction information.
