Novel function discovery with GeneMANIA: a new integrated resource for gene function prediction in Escherichia coli

Research output: Contribution to journalArticlepeer-review


  • James Vlasblom
  • Khalid Zuberi
  • Harold Rodriguez
  • Alla Gagarinova
  • Viktor Deineko
  • Ashwani Kumar
  • Elisa Leung
  • Kamran Rizzolo
  • Bahram Samanfar
  • Luke Chang
  • Sadhna Phanse
  • Ashkan Golshani
  • Jack F Greenblatt
  • Walid A Houry
  • Andrew Emili
  • Quaid Morris
  • Gary Bader
  • Mohan Babu

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.


SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.


Original languageEnglish
Pages (from-to)306-310
Number of pages5
Issue number3
Publication statusPublished - 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