The flowchart of our pipeline to identify genes and protein complexes associated with recombination hotspots. Figure 1 shows the flowchart of our pipeline to identify genes and protein complexes associated with recombination hotspots. In particular, the inputs are the binding motifs of DNA-binding proteins, hotspots, as well as coldspots generated by ourselves. Individual genes will be identified (1) by various prioritizing methods, i.e., OR, HB and KM, using the binding information between genes and hotspots, (2) by the Random Walk with Restart (RWR) algorithm on the PPI networks. Protein complexes and conserved protein complexes are detected from the PPI subgraphs induced by the individual genes that are ranked top by the RWR algorithm.