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As expected, classification of genes into functional categories using Pathway Express indicated that most of the significantly affected biological processes were associated with cancer (Fig. 3b).
Other prominent biological processes were associated with apoptosis and cell death.
Although only two biological processes were associated with overall survival, these processes correspond to levels 4 and 6.
To identify which biological processes were associated with the visceral adipose tissue genes altered by HFD at one or more time-points over 24 weeks, enriched functional features were identified using DAVID [ 19].
To determine what biological processes were associated with the identified Peromycsus ESTs, we analyzed the mouse and rat homologous gene lists using an online gene ontology analysis tool, FatiGO [ 34].
The following Gene Ontology biological processes were associated with maximum number of genes in all networks: GO: 0007165 (signal transduction), GO: 0006468 (protein phosphorylation), GO: 0006955 (immune response), and GO: 0055114 (oxidation-reduction process).
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For example, we might want to infer which biological processes are associated with the dysregulation of a gene in a disease, as well as detect whether a subject has the disease and predict the best therapy.
Both these biological processes are associated with nutritional costs [10], [12].
The results show that the number of PPIs between biological processes was associated with differential gene expression pattern (Figure 3a).
To investigate what biological processes are associated with the 153 miRNA-target set, we used DAVID (http://david.abcc.ncifcrf.gov/) [24], [25] to look for enrichment of functions within the Biological Process section of the Gene Ontology (GO) [26].
Since no unified pathway nomenclature exists, similar biological processes are associated with different pathway labels in different databases.
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