Finding New Order in Biological Functions from the Network Structure of Gene Annotations

TL;DR

This paper introduces a novel network-based approach to group biological functions by gene annotations, revealing an alternative organization different from the traditional Gene Ontology hierarchy, aiding in gene function prediction.

Contribution

The study presents a new method to organize GO terms based on shared gene annotations, offering a different perspective from the established hierarchical structure.

Findings

Network-based grouping differs from GO hierarchy

Provides a new framework for gene function prediction

Enhances understanding of biological function organization

Abstract

The Gene Ontology (GO) provides biologists with a controlled terminology that describes how genes are associated with functions and how functional terms are related to each other. These term-term relationships encode how scientists conceive the organization of biological functions, and they take the form of a directed acyclic graph (DAG). Here, we propose that the network structure of gene-term annotations made using GO can be employed to establish an alternate natural way to group the functional terms which is different from the hierarchical structure established in the GO DAG. Instead of relying on an externally defined organization for biological functions, our method connects biological functions together if they are performed by the same genes, as indicated in a compendium of gene annotation data from numerous different experiments. We show that grouping terms by this alternate scheme is distinct from term relationships defined in the ontological structure and provides a new framework with which to describe and predict the functions of experimentally identified sets of genes.