You have obtained a ranked list of proteins or genes ordered from some particular experiment (e.g. they are the result of a differential expression analysis, from a GWAS or they have an interesting impact on phenotype like cell cycle, etc). From this list of proteins/genes, you want to use protein-protein interaction data to find out their possible role as a protein complex, as a signaling pathway, etc. Network Miner looks for significant subnetworks of protein-protein interactions within a list of ranked genes/proteins to find out their possible role as a protein complex, as a signalling pathway, etc.

The program also offers the option of defining seed genes. These seed genes are genes known to be associated with the phenotype of interest and therefore you want to analyse the network relationship between you ranked list and them.

Moreover, the result is presented in a network viewer box. Different layouts are possible that implement different algorithms for distributing the net components in different ways. Furthermore, different backgrounds, including different cell views over which the network can be represented.

Network Miner is located at Functional profiling > Set enrichment analysis section in Babelomics suite http://babelomics.bioinfo.cipf.es/. Network Miner works in modern web browsers such as Google Chrome 14+, Microsoft Internet Explorer 9, Mozilla Firefox 6+ or Apple Safari 5+.