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Mapping Bacterial Functional Networks and Pathways in Escherichia Coli using Synthetic Genetic Arrays
Published on: November 12, 2012
Uncovering the co-evolutionary network among prokaryotic genes
Ofir Cohen1, Haim Ashkenazy, David Burstein
1Department of Cell Research and Immunology, George S. Wise Faculty of Life Sciences, Tel Aviv University, Tel Aviv 69978, Israel.
Bioinformatics (Oxford, England)
|September 11, 2012
Summary
We developed a new method to map gene co-evolution in prokaryotes. This reveals functional gene relationships not found through other network analyses, offering novel insights into cellular functions.
Area of Science:
- Genomics
- Systems Biology
- Bioinformatics
Background:
- Gene co-evolutionary relationships can be inferred from correlated events of gains and losses.
- Reconstructing these networks in prokaryotes can uncover functional gene associations.
Purpose of the Study:
- To develop a novel probabilistic method for detecting gene co-evolutionary interactions.
- To infer and analyze the co-evolutionary network in prokaryotes.
Main Methods:
- Developed a probabilistic methodology for detecting co-evolutionary interactions between gene pairs.
- Inferred the co-evolutionary network across 4593 Clusters of Orthologous Genes (COGs).
- Partitioned the network into clusters to identify modular gene assemblies.
Main Results:
- Over 40% of COGs exhibited co-evolutionary interactions with at least one partner.
- Identified modular assemblies of genes with distinct functions within the co-evolutionary network.
- Co-evolutionary relations showed only partial overlap with genomic proximity, gene fusion, co-expression, protein-protein interactions, and metabolic networks.
Conclusions:
- The inferred co-evolutionary network in prokaryotes is highly informative for revealing functional gene relationships.
- This network provides insights into functional associations that are not detectable through other network types.
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