reference_network: Reference gene family network

In olgakamneva/genomics2ecology: Methods of genomic analysis for microbial ecology

Description

Global network of functionally linked gene families extracted from STRING 10.0 database. Only gene neighbor scores are used as evidence of functional association. Edges with original score less than 275 were removed, then weights (w) were unit normalized as follows: (w-275)/1000.

Usage

reference_network

Format

A data frame with 3 variables: node1 gene family one, node2 gene family two, weight unit normalized gene neighbor score.

Source

STRING 10.0 database http://string-db.org/.

References

1. Szklarczyk D, Franceschini A, Wyder S, Forslund K, Heller D, Huerta-Cepas J, Simonovic M, Roth A, Santos A, Tsafou KP, Kuhn M, Bork P, Jensen LJ, von Mering C. STRING v10: protein-protein interaction networks, integrated over the tree of life. Nucleic Acids Res. 2015 Jan; 43:D447-52.4.

2. Kamneva OK. Genome composition of microbes predicts their co-occurrence in the environment. In review.

Examples

data(reference_network)

olgakamneva/genomics2ecology documentation built on May 24, 2019, 12:51 p.m.