NeXO is a gene ontology
inferred directly from large-scale molecular networks. A gene ontology
provides structured knowledge about the cellular components, processes,
and functions encoded by genes. While most ontologies – including the highly
successful Gene Ontology Database (GO) – are constructed through manual expert
curation, NeXO is a data-driven gene ontology inferred directly from ‘omics
data. NeXO (The Network Extracted Ontology) uses a principled computational
approach which integrates evidence from hundreds of thousands of individual
gene and protein interactions to construct a complete hierarchy of cellular
components and processes. This data-derived ontology aligns with known
biological machinery in the GO Database and also uncovers many new structures.
How to Cite
A gene ontology inferred from molecular networks.
Dutkowski J, Kramer M, Surma MA, Balakrishnan R, Cherry JM, Krogan NJ, Ideker T.,
Nature Biotechnology 2013 Jan;31(1):38-45.
NeXO Web: the NeXO ontology database and visualization platform.
Dutkowski J, Ono K, Kramer M, Yu M, Pratt D, Demchak B, Ideker T.,
Nucleic Acids Res. 2014 Jan;42(Database issue).
NeXO Web overview. Users can browse NeXO DAG and raw
interactions from web browsers.
Raw interaction view. Source interaction data for each NeXO term is visualized
NeXO terms can be searched by keywords, term ID, or gene names.
NeXO term enrichment analysis is a built-in feature in NeXO Web
Gene Ontology Viewer. Tree-version of Gene Ontology can be visualized by NeXO Web.