Evaluating homophily in networks via HONTO (HOmophily Network TOol): a case study of chromosomal interactions in human PPI networks

Abstract

Summary: It has been observed in different kinds of networks, such as social or biological ones, a typical behavior inspired by the general principle 'similarity breeds connections'. These networks are defined as homophilic as nodes belonging to the same class preferentially interact with each other. In this work, we present HONTO (HOmophily Network TOol), a user-friendly open-source Python3 package designed to evaluate and analyze homophily in complex networks. The tool takes in input from the network along with a partition of its nodes into classes and yields a matrix whose entries are the homophily/heterophily z-score values. To complement the analysis, the tool also provides z-score values of nodes that do not interact with any other node of the same class. Homophily/heterophily z-scores values are presented as a heatmap allowing a visual at-a-glance interpretation of results.

Availability and implementation: Tool's source code is available at https://github.com/cumbof/honto under the MIT license, installable as a package from PyPI (pip install honto) and conda-forge (conda install -c conda-forge honto), and has a wrapper for the Galaxy platform available on the official Galaxy ToolShed (Blankenberg et al., 2014) at https://toolshed.g2.bx.psu.edu/view/fabio/honto.

Fig. 1.

(A) a three-colors sample network; the blue, red-edges appear in (B), while the subgraph induced by red nodes is shown in (C); (D) heatmap with the edge z-scores computed by HONTO on the three-colors sample network reported in (A); (E) edge z-scores related to Homo sapiens PPI network, where proteins are partitioned into chromosomes, are reported along the diagonal for homophily and out of the diagonal for heterophily of heatmap; (F) z-scores of color-i isolated nodes for the H.sapiens PPI network (A color version of this figure appears in the online version of this article)