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United States Department of Agriculture

Agricultural Research Service

Research Project: THE MAIZE GENETICS AND GENOMICS DATABASE

Location: Corn Insects and Crop Genetics Research

Title: Metabolic pathway resources at MaizeGDB)

Author
item Sen, Taner
item Monaco, Marcela
item Chae, Lee
item Dharmawardhana, Palitha
item Schaeffer, Mary
item Dreher, Kate
item Zhang, Peifen
item Naithani, Sushma
item Thomason, Jim
item Harper, Elisabeth
item Gardiner, Jack
item Cannon, Ethalinda
item Andorf, Carson
item Campbell, Darwin
item Rhee, Seung
item Ware, Doreen
item Jaiswal, Pankaj
item Lawrence, Carolyn

Submitted to: Meeting Abstract
Publication Type: Abstract only
Publication Acceptance Date: 2/1/2013
Publication Date: 3/14/2013
Citation: Sen, T.Z., Monaco, M., Chae, L., Dharmawardhana, P., Schaeffer, M.L., Dreher, K., Zhang, P., Naithani, S., Thomason, J., Harper, E.C., Gardiner, J., Cannon, E., Andorf, C.M., Campbell, D.A., Rhee, S.Y., Ware, D., Jaiswal, P., Lawrence, C.J. 2013. Metabolic pathway resources at MaizeGDB [abstract]. In: Proceedings of Maize Genetics Conference, March 14-17, St. Charles, Illinois. p. 3.

Interpretive Summary:

Technical Abstract: Two maize metabolic networks are available at MaizeGDB: MaizeCyc (http://maizecyc.maizegdb.org, also at Gramene) and CornCyc (http://corncyc.maizegdb.org, also at the Plant Metabolic Network). MaizeCyc was developed by Gramene, and CornCyc by the Plant Metabolic Network, both in collaboration with MaizeGDB. MaizeCyc and CornCyc are both based on B73 RefGen_v2 filtered gene set models, and offer visualization and analysis capabilities of Pathway Tools developed by SRI. Their pipelines for enzymatic function assignment indicate some differences: MaizeCyc is mainly based on the exonerate scores generated via the Ensembl XRef pipeline, whereas CornCyc employs a scoring matrix based on performances obtained using BLAST, CatFam, and Priam. As a result of these different assignment criteria, the metabolic networks differ in coverage and confidence levels. Here we present some statistics from both metabolic networks, provide snapshots of various views and analysis tools available in Pathway Tools, and show examples of how these tools and resources can be used to derive biologically-meaningful hypotheses.

Last Modified: 8/24/2016
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