Algorithm for the Construction of a Global Enzymatic Network to be used for Gene Network Reconstruction

Title:Algorithm for the Construction of a Global Enzymatic Network to be used for Gene Network Reconstruction

Volume: 15 Issue: 5

Author(s): Andres Quintero, Jorge Ramírez, Luis Guillermo Leal and Liliana Lopez-Kleine

Affiliation:

Keywords: EC number, Gene network reconstruction, Global enzymatic network, KEGG, Perl.

Abstract: Relationships between genes are best represented using networks constructed from information of different types, with metabolic information being the most valuable and widely used for genetic network reconstruction. Other types of information are usually also available, and it would be desirable to systematically include them in algorithms for network reconstruction. Here, we present an algorithm to construct a global metabolic network that uses all available enzymatic and metabolic information about the organism. We construct a global enzymatic network (GEN) with a total of 4226 nodes (EC numbers) and 42723 edges representing all known metabolic reactions. As an example we use microarray data for Arabidopsis thaliana and combine it with the metabolic network constructing a final gene interaction network for this organism with 8212 nodes (genes) and 4606,901 edges. All scripts are available to be used for any organism for which genomic data is available.

Cite this article as:

Quintero Andres, Ramírez Jorge, Leal Guillermo Luis and Lopez-Kleine Liliana, Algorithm for the Construction of a Global Enzymatic Network to be used for Gene Network Reconstruction, Current Genomics 2014; 15 (5) . https://dx.doi.org/10.2174/1389202915666140807004909