2.5 │ Generation of histone H1 subtypes and interacting proteins
networks
Histone H1-partner proteins interaction networks were created with
STRING (Search Tool for the Retrieval of Interacting Genes/Proteins)
platform (Version 11.0). 17 Protein-protein
interaction data were predicted based on the active interaction sources
including seven available parameters, i.e. co-expression, co-occurrence,
databases, experiments, gene fusion, neighborhood and text mining, with
medium (0.400) confidence interaction score. A STRING graph networks
were further analyzed with Cytoscape (version 3.8.0) plugin app Network
Analyzer 18 based on several topological parameters
such as average number of neighbors (the average connectivity of a node
in the network), network diameter (the largest distance between two
nodes), network radius (the minimum among the non-zero eccentricites of
the nodes in the network), network heterogeneity (the tendency of a
network to contain hub nodes), network clustering coefficient (the
average of the clustering coefficients for all nodes in the network) and
the number of connected components (the connectivity of a network). An
identification of hub objects in the networks was performed with the use
of cytoHubba Cytoscape plugin, adopting the maximal clique centrality
method (MCM) which was proposed as most effective in the exploration of
the hub nodes in the network. 19 To find subnetworks,
a Diffusion tool which is an integrated Cytoscape function for
performing a network propagation 20 was adopted.