Protein Complexes and Functional Modules in PPI Network | MCODE | LE | MTGO | DIAMOnD |

Protein-protein interaction (PPI) networks are commonly used to study the interactions and functions of proteins in a cell. Clustering methods can be used to identify groups or modules of proteins that interact with each other more closely than with other proteins in the network and perform some specific functions. Here are some common clustering methods for PPI networks: • MCODE (Molecular Complex Detection): MCODE (Molecular Complex Detection) is a plugin for the Cytoscape network visualization and analysis software that is used to identify densely connected regions, or clusters, in protein-protein interaction (PPI) networks. It is based on the idea that proteins interacting with each other are more likely to be part of the same complex or pathway and, thus more likely to form densely connected regions in the PPI network. • Leading Eigenvector(LE): The Leading Eigenvector (LE) community finding method is a graph-based clustering algorithm commonly used to identify network communities or modules. It is based on the idea that nodes within the same community tend to have a high degree of connectivity with each other and a low degree of connectivity with nodes in other communities. • MTGO (Module detection via Topological information and GO knowledge): Module detection via Topological information and GO knowledge (MTGO) is a clustering algorithm used to identify functional modules in protein-protein interaction (PPI) networks. The MTGO algorithm combines both topological information and gene ontology (GO) knowledge to identify functionally related genes. The MTGO algorithm begins by constructing a PPI network and annotating it with GO terms. The topological information of the network is then used to identify densely connected subgraphs, or modules, in the network. The GO knowledge is then used to assess the functional coherence of each module by comparing the enrichment of GO terms in the module to the background distribution of GO terms in the network. • DIseAse MOdule Detection (DIAMOnD): a method for identifying disease-associated subnetworks in protein-protein interaction (PPI) networks. It is based on the idea that disease-associated genes are more likely to be functionally related and, thus, more likely to form densely connected subnetworks in the PPI network.