I have a network of 201 genes with around 703 edges. I have to find high-scoring, functionally enriched subnetworks. I tried to use mcode plugin for this purpose. I got around 14 subnetworks with very low score. Moreover, the functional enrichment for these networks were not very significant. There are many other cytoscape plugins as well as many ways to find such subnetworks. I would like to know which other plugins I could use for this purpose..
In addition to MCODE and BINGO, MCL is quite popular to detect complexes, it is not a Cytoscape plugin though. If gene expression data is available JActiveModules could be a good choice. For using BINGO and JActiveModules see this tutorial.
Have you tried the cytoscape plug-in BiNGO ?
I think BiNGO will be an ideal choice for your problem as it performs functional enrichment analysis using GO annotations using genes in a network. See the BiNGO manuscript here.
EDIT: Added after Sanchari's question on 'modules':
AFAIK, Module is a conceptual framework to group a set of nodes in a network based on a prior biological knowledge. For example module in a network could be a group of physically interacting or proteins that share similar functional properties (as in protein complex, signaling, transcription). BiNGO will group your proteins based on GO annotations, where as MCODE perform clustering (highly interconnected regions). Even if you provide a random bunch of interconnected proteins, MCODE will give you a subnetwork, but that won't have a biological meaning (please try this yourself). But BINGO networks have the power of underlying biological annotations.
Once you finished BiNGO using your interaction data, you can find enriched modules, say for example a set of proteins annotated with GO term "protein binding" with a significant p-value. You can consider this as a biologically relevant module in your dataset.