Glossary

Edgelist

An edge-list file (.edg) is a representation of the network. It contains either two columns (unweighted) or three columns (weighted). The first two columns are gene pairs representing edges in the network. Since the network is assumed to be undirected, reversed direction is unnecessary. When the network is weigthed, the edge weights should be encoded in the third column.

gene1  gene2   <weight>

Embedding

Network embeddings generated using [node2vec].

GSC

A gene set collection (GSC) is a set of gene sets, each of which defines a set of positive genes for a specific term (i.e., a label). Currently supported GSCs are [GO], [Monarch] and [Mondo].

SixSpeciesN2V

Features where made by first constucting a six species network, connecting genes from the single species networks together using the [EggNOG] orthology database and then embedding this network using [node2vec].