Evaluating homophily of human PPI with respect to chromosomes

Homophily/heterophily evaluation, expressed in terms of z-score values, is related to the human Protein-Protein Interaction Network (PPI), obtained from the STRING v11.5 database (https://string-db.org) setting standard threshold on edge score (T=700). Each protein occurring in the PPI was assigned to a class corresponding to the chromosome the related gene belongs to.

A total of 23 classes (chr1, chr2, ..., chr22, chrX) were considered (excluding the class corresponding to chromosome Y because of the small number of genes occurring in the network).

The homophily/heterophily nature of the network, with respect to chromosome classes, was evaluated through HONTO tool (https://github.com/cumbof/honto).

In other words, the tendency of proteins to preferentially interact with proteins whose genes are physically located on the same chromosome (homophily) or on different chromosomes (heterophily) was investigated and evaluated in terms of z-scores.

Values related to intra (along the diagonal) and inter chromosomal interactions (other than the diagonal) are also reported as a heatmap.

As one can observe, values occurring in the diagonal are clearly higher than values out of the diagonal, leading to assess a homophilic nature of the network, confirming the link between shared chromosome and interaction in the PPI.