I need to finds out same functions of the interacting nodes in the gene network analysis.
One option is querying any database for the function of your genes and score the overlap between them using a Jaccard Index: http://en.wikipedia.org/wiki/Jaccard_index
If you don't have any trustable source of function annotation, what about trying a GO term enrichment analysis?
Among others, you can use AmiGO (http://amigo.geneontology.org/cgi-bin/amigo/term_enrichment?session_id=) or FuncAssociate (http://llama.mshri.on.ca/cgi/func/funcassociate). You decide a p-value threshold (maximum 0.05) and annotate your genes with those annotations scoring equal or below your threshold.
When you build-up a network, functional data should be also considered so that network analysis (tools) could make more sense. A recent example - Signaling Network Assessment of Mutations and Copy Number Variations Predict Breast Cancer Subtype-Specific Drug Targets - http://www.cell.com/cell-reports/fulltext/S2211-1247%2813%2900469-5
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