NDLI: A clustering method for comparative analysis between genomes and pathways

Content Provider	IEEE Xplore Digital Library
Author	Miyake, S. Tohsato, Y. Takenaka, Y. Matsuda, H.
Copyright Year	2003
Description	Author affiliation: Graduate Sch. of Inf. Sci. & Technol., Osaka Univ., Japan (Miyake, S.; Tohsato, Y.; Takenaka, Y.; Matsuda, H.)
Abstract	This paper presents a clustering method for the comparative analysis of genomes and metabolic pathways. Our method consists of several steps: (1) extract linear sequences of metabolic reactions (non-branching pathways) from a network of metabolic pathways, (2) perform pairwise alignments of every pair of non-branching pathways, and (3) explore a set of genes for each aligned non-branching pathways such that those genes encode enzymes of the pathway and the genes are closely located on a genome (such as operons or gene clusters). To measure the similarity between pathways, we formalized a scoring system by using the functional hierarchy of the EC numbers of enzymes. By applying our method to the metabolic pathways in Escherichia coli, we have obtained several pairs of pathways with similar reactions having enzymes encoded by neighbor genes on the E. coli genome. The resulting pathway pairs were mainly found in metabolisms between similar amino acids (tryptophan and histidine) and between similar sugars (fucose and rhamnose).
Sponsorship	Commun. Res. Lab. Hitachi Kyoto Univ
Starting Page	327
Ending Page	334
File Size	556783
Page Count	8
File Format	PDF
ISBN	0769518958
DOI	10.1109/DASFAA.2003.1192398
Language	English
Publisher	Institute of Electrical and Electronics Engineers, Inc. (IEEE)
Publisher Date	2003-03-26
Publisher Place	Japan
Access Restriction	Subscribed
Rights Holder	Institute of Electrical and Electronics Engineers, Inc. (IEEE)
Subject Keyword	Clustering methods Genomics Bioinformatics Database systems
Content Type	Text
Resource Type	Article

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