We performed pathway enrichment tests using gene ontology (GO) terms, KEGG pathways and OMIM (Online Mend-elian Inheritance in Man) database.
To explore and analyze functional relevance of our identified GS BC modules, we performed pathway enrichment analysis from three aspects including GO terms, functional pathways and diseases using Gene Ontology (GO, KEGGG pathways, and OMIM diseases databases, respectively.
In addition, we also performed pathway mapping using Pathway Miner (http://www.biorag.org).
We performed pathway analysis on the predicted Ste20p substrates using the Gene Ontology (GO) [45].
In order to test this hypothesis, we performed pathway enrichment analyses on each disease interactome independently.
Finally, we performed pathway enrichment analysis of the two subnetworks, followed by examination of crosstalk between enriched pathways.
To investigate if these disease specific proteins have common annotated functional properties, we performed pathway analysis (Tables S5 and S6).
For comparison we have also performed pathway enrichment analysis of the original sets of up-regulated genes and proteins.
For further insight into genes regulated by UCH L1, we performed pathway analysis using the Ingenuity Pathway Analysis (IPA) [40], (www.ingenuity.com).com
To identify global differences between the phosphoproteomes, we performed pathway analysis on the phosphoproteins up-regulated in these proteomes using Ingenuity Pathways Analysis (Ingenuity® Systems, www.ingenuity.com).com
To examine the biological processes and pathways that might be impacted by the SNP-associated genes, we performed pathway analyses on the genes using Pathway Studio 7 software.
