SPINNER is an automated software tool, which can rank and compare genes or proteins from constructed phenotype-specific biomolecular interaction networks. Given the user input of a list of phenotype-specific genes, our tool can query the STRING protein-protein interaction database automatically to retrieve protein-protein interactions among the input genes with user-specified network expansion levels to construct a phenotype-specific network. All the sub-networks are ranked and evaluated statistically to obtain a P-value for its index of aggregation before subsequent analysis. To compare the significant contribution of each protein, we consider its node degree of connectivity, protein interaction quality for its surrounding interacting partners (including both direct and indirect connected partners through iterations), the protein’ significance in both unfiltered global network and phenotype-specific network, and other network characteristics. Our tool also provides the genes/proteins PubMed reference citation count for the specific phenotype to help users evaluate the ranked proteins. A family-wise adjusted P-value of all significant ranks against randomized topology-preserving networks are also provided to help assess the rank.