īruckner A, Polge C, Lentze N et al (2009) Yeast two-hybrid, a powerful tool for systems biology. Mishra B, Kumar N, Mukhtar MS (2021) Network biology to uncover functional and structural properties of the plant immune system. Mishra B, Kumar N, Shahid Mukhtar M (2022) A rice protein interaction network reveals high centrality nodes and candidate pathogen effector targets. Mishra B, Sun Y, Ahmed H et al (2017) Global temporal dynamic landscape of pathogen-mediated subversion of Arabidopsis innate immunity. Mishra B, Sun Y, Howton TC et al (2018) Dynamic modeling of transcriptional gene regulatory network uncovers distinct pathways during the onset of Arabidopsis leaf senescence. Mott GA, Smakowska-Luzan E, Pasha A et al (2019) Map of physical interactions between extracellular domains of Arabidopsis leucine-rich repeat receptor kinases. Mukhtar MS, Carvunis AR, Dreze M et al (2011) Independently evolved virulence effectors converge onto hubs in a plant immune system network. Smakowska-Luzan E, Mott GA, Parys K et al (2018) An extracellular network of Arabidopsis leucine-rich repeat receptor kinases. Wessling R, Epple P, Altmann S et al (2014) Convergent targeting of a common host protein-network by pathogen effectors from three kingdoms of life. Mishra B, Kumar N, Mukhtar MS (2019) Systems biology and machine learning in plant-pathogen interactions. McCormack ME, Lopez JA, Crocker TH et al (2016) Making the right connections: network biology and plant immune system dynamics. Lopez J, Mukhtar MS (2017) Mapping protein-protein interaction using high-throughput yeast 2-hybrid. Kumar N, Mishra B, Mukhtar MS (2022) A pipeline of integrating transcriptome and interactome to elucidate central nodes in host-pathogens interactions. Kumar N, Mishra B, Mehmood A et al (2020) Integrative network biology framework elucidates molecular mechanisms of SARS-CoV-2 pathogenesis. Klopffleisch K, Phan N, Augustin K et al (2011) Arabidopsis G-protein interactome reveals connections to cell wall carbohydrates and morphogenesis. Gonzalez-Fuente M, Carrere S, Monachello D et al (2020) EffectorK, a comprehensive resource to mine for Ralstonia, Xanthomonas, and other published effector interactors in the Arabidopsis proteome. Īrabidopsis Interactome Mapping C (2011) Evidence for network evolution in an Arabidopsis interactome map. Īhmed H, Howton TC, Sun Y et al (2018) Network biology discovers pathogen contact points in host protein-protein interactomes. Garbutt CC, Bangalore PV, Kannar P et al (2014) Getting to the edge: protein dynamical networks as a new frontier in plant-microbe interactions. This chapter aims to illustrate the Cytoscape application to visualize and analyze the PPI network using Arabidopsis interactome-1 main (AI-1 MAIN) PPI network dataset from Plant Interactome Database. It comes with hundreds of in-built Apps in App Manager to resolve research questions related to network visualization and integration. It provides an interactive visualization interface along with other core features to import, navigate, filter, cluster, search, and export networks. Cytoscape, an open-source software tool, is one of them. Currently, a variety of tools are available for network graph visualization and analysis. The PPI network analysis and visualization can help identify functional modules of the network, pathway genes involved in common cellular functions, and functional annotations of novel genes. As the protein–protein interaction (PPI) data increase exponentially, the development and usage of computational methods to analyze these datasets have become a new research horizon in systems biology.

Cytoscape network visualization