Cytoscape is a wonderful tool. There are other great tools I also used for your reference.
Chen, E.Y., Tan, C.M., Kou, Y., Duan, Q.N., Wang, Z.C., Meirelles, G.V., Clark, N.R. & Ma'ayan, A. (2013). Enrichr: interactive and collaborative HTML5 gene list enrichment analysis tool. BMC Bioinformatics 14.
Mi, H.Y., Muruganujan, A., Casagrande, J.T. & Thomas, P.D. (2013). Large-scale gene function analysis with the PANTHER classification system. Nat. Protoc. 8, 1551-1566.
- GSEA (GSAA)
Subramanian, A., Tamayo, P., Mootha, V.K., Mukherjee, S., Ebert, B.L., Gillette, M.A., Paulovich, A., Pomeroy, S.L., Golub, T.R., Lander, E.S. & Mesirov, J.P. (2005). Gene set enrichment analysis: A knowledge-based approach for interpreting genome-wide expression profiles. Proceedings of the National Academy of Sciences of the United States of America 102, 15545-15550.
Xiong, Q., Mukherjee, S. & Furey, T.S. (2014). GSAASeqSP: A Toolset for Gene Set Association Analysis of RNA-Seq Data. Sci Rep 4, 6347.
Huang, D.W., Sherman, B.T. & Lempicki, R.A. (2009). Systematic and integrative analysis of large gene lists using DAVID bioinformatics resources. Nat. Protoc. 4, 44-57.
If you want not just visualize but analyze I would go for these two tools:
From the same author as STRING:
SNOW, a web-based tool for the statistical analysis of protein–protein interaction networks
NETWORK MINER: Discovering the hidden sub-network component in a ranked list of genes or proteins derived from genomic experiments
These tools are under Babelomics 5.0: functional interpretation for new generations of genomic data. In the menu functional
You can also use http://cellmaps.babelomics.org/ to visualize your network interactively.
igraph in R can now do everything and has many common metrics integrated, such as hub score, vertex degree, BC, etc.: Network plot from expression data in R using igraph