MANET and the evolution, structure and function of biological networks
Mughal, Fizza
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https://hdl.handle.net/2142/50497
Description
Title
MANET and the evolution, structure and function of biological networks
Author(s)
Mughal, Fizza
Issue Date
2014-09-16
Director of Research (if dissertation) or Advisor (if thesis)
Caetano-Anolles, Gustavo
Department of Study
Crop Sciences
Discipline
Bioinformatics
Degree Granting Institution
University of Illinois at Urbana-Champaign
Degree Name
M.S.
Degree Level
Thesis
Keyword(s)
Metabolic Networks
Enzyme Evolution
Phylogenomics
Protein Domain
Abstract
The metabolic MANET is an online resource that incorporates data from KEGG, SCOP and structural phylogenomics. A revised version of MANET was here produced that not only uses recent data from KEGG and SCOP, but also evolutionary information of fold families derived from structural phylogenomic reconstructions. In addition, a fourth data source, PDBsum, has been added to this resource amalgamation, which serves to provide the link between enzyme and PDB information. With the introduction of fold family data, the updated version offers a 10-fold increase of data entries compared to the current version that is based on fold data. The global analysis of metabolism at mesonetwork as well as the subnetwork level puts forth interesting patterns of enzyme sharing that lend support to the patchwork model of metabolic evolution. The sharing patterns we identify are not just restricted to subnetworks. Instead, they transcend mesonetwork boundaries.
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