A degree-distribution based hierarchical agglomerative clustering algorithm for protein complexes identification

► Based on indegree and outdegree of subgraph, we present a protein module definition. ► A measure is introduced for evaluating the partition of a PPI network. ► Using the measure, a hierarchical agglomerative clustering algorithm is developed. ► The new algorithm finds more protein complexes with high biological significance. ► Our complexes, dense or sparse, match well with known biological characteristics.