Pathways of highly interconnected genes were identified using the equation in [22].
First, using the Cytoscape plugin jActiveModules [40], we identified network regions (sub-portions of the full network referred to as "modules") enriched in differentially expressed, interconnected genes (nodes).
Thus, by targeting highly interconnected genes, HPVs reprogrammed the gene network of KCs in favor of immune escape and cell proliferation of HPV-positive cells.
In order to uncover changes in groups of functionally interconnected genes we utilised two online analysis tools the Database for Innovation, Visualization and Integrated Discovery (DAVID; [61] and Ingenuity Pathway Analysis (IPA).
Pathways of highly interconnected genes
In this way, it is possible to search the database for groups of potentially interconnected genes as a starting point to decipher regulatory networks of transcription factors, signaling molecules and membrane receptors, or for indications of genes that might be co-regulated by the same genetic pathways.
The online analysis tools The Database for Annotation, Visualization and Integrated Discovery (DAVID; [61] and Ingenuity Pathway Analysis (IPA; from Ingenuity Systems Inc., Redwood City, USA; http://www.ingenuity.com) were used to uncover changes in functionally interconnected genes from a list of the most differentially expressed genes (Further description in Text S1).
One important end product of GCENA is the construction of gene modules comprised of highly interconnected genes, and a number of studies have demonstrated that co-expression network modules are generally enriched for known biological pathways, for genes that are linked to common genetic loci, and for genes associated with disease [24] [32].
Pathways of highly interconnected genes
Modules are clusters of highly interconnected genes.
These included 953 highly interconnected genes.
