Novel function discovery with GeneMANIA: a new integrated resource for gene function prediction in Escherichia coli
Research output: Contribution to journal › Article › peer-review
Colleges, School and Institutes
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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SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.
|Number of pages||5|
|Publication status||Published - 13 Oct 2014|
- Algorithms, Escherichia coli, Escherichia coli Proteins, Gene Regulatory Networks, Phenotype, Software, Journal Article, Research Support, N.I.H., Extramural, Research Support, Non-U.S. Gov't