SANA: cross-species prediction of Gene Ontology GO annotations via topological network alignment.

ABSTRACT: Topological network alignment aims to align two networks node-wise in order to maximize the observed common connection (edge) topology between them. The topological alignment of two protein-protein interaction (PPI) networks should thus expose protein pairs with similar interaction partners allowing, for example, the prediction of common Gene Ontology (GO) terms. Unfortunately, no network alignment algorithm based on topology alone has been able to achieve this aim, though those that include sequence similarity have seen some success. We argue that this failure of topology alone is due to the sparsity and incompleteness of the PPI network data of almost all species, which provides the network topology with a small signal-to-noise ratio that is effectively swamped when sequence information

SUBMITTER: Wang S 

PROVIDER: S-EPMC9300714 | biostudies-literature | 2022 Jul

REPOSITORIES: biostudies-literature