Applying Automatically Derived Gene-Groups to Automatically Predict and Refine Metabolic Pathways

Arvind K. Bansal; Christopher J. Woolverton

doi:10.1109/TKDE.2003.1209006

Publication
2003
Issue No. 4 - July/August
Abstract - Applying Automatically Derived Gene-Groups to Automatically Predict and Refine Metabolic Pathways

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	Similar Articles Articles by Arvind K. Bansal Articles by Christopher J. Woolverton

Applying Automatically Derived Gene-Groups to Automatically Predict and Refine Metabolic Pathways

July/August 2003 (vol. 15 no. 4)

pp. 883-894

	ASCII Text	x
	Arvind K. Bansal, Christopher J. Woolverton, "Applying Automatically Derived Gene-Groups to Automatically Predict and Refine Metabolic Pathways," IEEE Transactions on Knowledge and Data Engineering, vol. 15, no. 4, pp. 883-894, July/August, 2003.

	BibTex	x
	@article{ 10.1109/TKDE.2003.1209006, author = {Arvind K. Bansal and Christopher J. Woolverton}, title = {Applying Automatically Derived Gene-Groups to Automatically Predict and Refine Metabolic Pathways}, journal ={IEEE Transactions on Knowledge and Data Engineering}, volume = {15}, number = {4}, issn = {1041-4347}, year = {2003}, pages = {883-894}, doi = {http://doi.ieeecomputersociety.org/10.1109/TKDE.2003.1209006}, publisher = {IEEE Computer Society}, address = {Los Alamitos, CA, USA}, }

	RefWorks Procite/RefMan/Endnote	x
	TY - JOUR JO - IEEE Transactions on Knowledge and Data Engineering TI - Applying Automatically Derived Gene-Groups to Automatically Predict and Refine Metabolic Pathways IS - 4 SN - 1041-4347 SP883 EP894 EPD - 883-894 A1 - Arvind K. Bansal, A1 - Christopher J. Woolverton, PY - 2003 KW - Automation KW - bacteria KW - drug-discovery KW - enzymes KW - gene-groups KW - homologs KW - metabolic pathway KW - microbes KW - operons KW - orthologs KW - pathogenicity KW - pathway. VL - 15 JA - IEEE Transactions on Knowledge and Data Engineering ER -

Arvind K. Bansal, IEEE

Christopher J. Woolverton

DOI Bookmark: http://doi.ieeecomputersociety.org/10.1109/TKDE.2003.1209006

Abstract—This paper describes an automated technique to predict integrated pathways and refine existing metabolic pathways using the information of automatically derived, functionally similar gene-groups and orthologs (functionally equivalent genes) derived by the comparison of complete microbial genomes archived in GenBank. The described method integrates automatically derived orthologous and homologous gene-groups (http://www.mcs.kent.edu/~arvind/orthos.html) with the biochemical pathway template available at the KEGG database (http://www.genome.ad.jp), the enzyme information derived from the SwissProt enzyme database (http://expasys.hcuge.ch/), and the Ligand database (http://www.genome.ad.jp). The technique refines existing pathways (based upon the network of reactions of enzymes) by associating corresponding nonenzymatic and regulatory proteins to enzymes and operons and by identifying substituting homologs. The technique is suitable for building and refining integrated pathways using evolutionary diverse organisms. A methodology and the corresponding algorithm are presented. The technique is illustrated by comparing the genomes of E. coli and B. subtilis with M. tuberculosis. The findings about integrated pathways are briefly discussed.

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Index Terms:

Automation, bacteria, drug-discovery, enzymes, gene-groups, homologs, metabolic pathway, microbes, operons, orthologs, pathogenicity, pathway.

Citation:

Arvind K. Bansal, Christopher J. Woolverton, "Applying Automatically Derived Gene-Groups to Automatically Predict and Refine Metabolic Pathways," IEEE Transactions on Knowledge and Data Engineering, vol. 15, no. 4, pp. 883-894, July-Aug. 2003, doi:10.1109/TKDE.2003.1209006

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