To identify signaling and metabolic pathways enriched in specific data sets, Ingenuity Pathway Analysis software core analysis (Ingenuity systems) was utilized to determine the statistical significance of enrichment for the pathways within a given data set.
In addition, the interaction network generated using literature specific to skin through Ingenuity Pathway Analysis (IPA) identified interactions with genes that are key regulators of normal wound healing and are altered in non-healing skin.
Among these latter genes, 17 (43%) had no reference to a specific functional class according to Ingenuity pathway analysis results (Ingenuity Systems, Redwood City, CA, USA, http://www.ingenuity.com), whereas 11 (28%) were kinases and only 25(5%) were transcription regulators.
To assess whether the association of the identified biological modulators with the top networks was specific (p<0.01), we resampled the Ingenuity database 100 times of with random gene lists of equivalent sizes.
We further expanded our analysis by examining the overrepresentation of canonical genetic pathways specific to muscle tissue using ingenuity pathway analysis (www.ingenuity.com) (Table S6, Supporting Information).
Ingenuity Pathways Analysis identified specific biological pathways behind each given cluster on different ECMs.
Prioritized signaling pathways for each cluster exhibited specific functional enrichment upon analysis by Ingenuity Pathways Analysis (Fig. 1c).
The subgraph patterns were evaluated using experimentally determined cancer-specific protein-protein interaction data from the Ingenuity knowledgebase, to identify distinct functional modules that are specific to each cancer type.
To better understand how differentially expressed genes were integrated into specific regulatory and signaling pathway networks, we used Ingenuity Pathway Analysis (Ingenuity Systems, Redwood City, USA).
Functional and Canonical Pathway analyses of specific gene datasets were generated through the use of Ingenuity Pathway Analysis (Ingenuity Systems®, http://www.ingenuity.com).com
