Motivation: The model bacterium Escherichia coli is among the best studied prokaryotes, yet nearly half of its proteins are still of unknown biological function. This is despite a wealth of available large-scale physical and genetic interaction data. To address this, we extended the GeneMANIA function prediction web application developed for model eukaryotes to support E.coli. Results: We integrated 48 distinct E.coli functional interaction datasets and used the GeneMANIA algorithm to produce thousands of novel functional predictions and prioritize genes for further functional assays. Our analysis achieved cross-validation performance comparable to that reported for eukaryotic model organisms, and revealed new functions for previously uncharacterized genes in specific bioprocesses, including components required for cell adhesion, iron-sulphur complex assembly and ribosome biogenesis. The GeneMANIA approach for network-based function prediction provides an innovative new tool for probing mechanisms underlying bacterial bioprocesses.

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Journal Bioinformatics
Vlasblom, J. (James), Zuberi, K. (Khalid), Rodriguez, H. (Harold), Arnold, R. (Roland), Gagarinova, A. (Alla), Deineko, V. (Viktor), … Babu, M. (Mohan). (2015). Novel function discovery with GeneMANIA: A new integrated resource for gene function prediction in Escherichia coli. Bioinformatics, 31(3), 306–310. doi:10.1093/bioinformatics/btu671