Evaluating homophily of human PPI with respect to chromosomes

DOI10.5281/zenodo.6941315Zenodo6941315MaRDI QIDQ6694969FDOQ6694969

Dataset published at Zenodo repository.

Daniele Santoni, Nicola Apollonio, Daniel Blankenberg, Fabio Cumbo, Paolo G. Franciosa

Publication date: 29 July 2022

Copyright license: Creative Commons Attribution 4.0 International

Description

Homophily/heterophily evaluation, expressed in terms of z-score values, is related to thehuman Protein-Protein Interaction Network (PPI),obtainedfrom 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) wereconsidered(excludingtheclasscorrespondingtochromosomeY because of the small number of genes occurring in the network). The homophily/heterophily nature of thenetwork, 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 investigatedand evaluated in terms of z-scores. Valuesrelated to intra (along the diagonal) and inter chromosomal interactions (other than the diagonal) arealsoreported as a heatmap. As one can observe, valuesoccurringin 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.

This page was built for dataset: Evaluating homophily of human PPI with respect to chromosomes