A new algorithm for cluster analysis of genomic methylation: the Helicobacter pylori case

Filipa F. Vale; P. Encarnação; J. M.B. Vítor

doi:10.1093/bioinformatics/btm621

A new algorithm for cluster analysis of genomic methylation: the Helicobacter pylori case

Filipa F. Vale^*, P. Encarnação, J. M.B. Vítor

^*Corresponding author for this work

Research output: Contribution to journal › Article › peer-review

8 Citations (Scopus)

Abstract

Motivation: The genomic methylation analysis is useful to type bacteria that have a high number of expressed type II methyltransferases. Methyltransferases are usually committed to Restriction and Modification (R-M) systems, in which the restriction endonuclease imposes high pressure on the expression of the cognate methyltransferase that hinder R-M system loss. Conventional cluster methods do not reflect this tendency. An algorithm was developed for dendrogram construction reflecting the propensity for conservation of R-M Type II systems. Results: The new algorithm was applied to 52 Helicobacter pylori strains from different geographical regions and compared with conventional clustering methods. The algorithm works by first grouping strains that share a common minimum set of R-M systems and gradually adds strains according to the number of the R-M systems acquired. Dendrograms revealed a cluster of African strains, which suggest that R-M systems are present in H.pylori genome since its human host migrates from Africa.

Original language	English
Pages (from-to)	383-388
Number of pages	6
Journal	Bioinformatics
Volume	24
Issue number	3
DOIs	https://doi.org/10.1093/bioinformatics/btm621
Publication status	Published - Feb 2008

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title = "A new algorithm for cluster analysis of genomic methylation: the Helicobacter pylori case",

abstract = "Motivation: The genomic methylation analysis is useful to type bacteria that have a high number of expressed type II methyltransferases. Methyltransferases are usually committed to Restriction and Modification (R-M) systems, in which the restriction endonuclease imposes high pressure on the expression of the cognate methyltransferase that hinder R-M system loss. Conventional cluster methods do not reflect this tendency. An algorithm was developed for dendrogram construction reflecting the propensity for conservation of R-M Type II systems. Results: The new algorithm was applied to 52 Helicobacter pylori strains from different geographical regions and compared with conventional clustering methods. The algorithm works by first grouping strains that share a common minimum set of R-M systems and gradually adds strains according to the number of the R-M systems acquired. Dendrograms revealed a cluster of African strains, which suggest that R-M systems are present in H.pylori genome since its human host migrates from Africa.",

author = "Vale, {Filipa F.} and P. Encarna{\c c}{\~a}o and V{\'i}tor, {J. M.B.}",

note = "Funding Information: We thank Francis M{\'e}graud, Lurdes Monteiro, and Sebastian Suerbaum for the H.pylori strains; Nuno Taveira for critical reviewing of the manuscript; and three anonymous reviewers for their valuable comments and suggestions. This work was partially funded by New England Biolabs, Inc. (USA). Copyright: Copyright 2008 Elsevier B.V., All rights reserved.",

year = "2008",

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doi = "10.1093/bioinformatics/btm621",

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AU - Vale, Filipa F.

AU - Encarnação, P.

AU - Vítor, J. M.B.

N1 - Funding Information: We thank Francis Mégraud, Lurdes Monteiro, and Sebastian Suerbaum for the H.pylori strains; Nuno Taveira for critical reviewing of the manuscript; and three anonymous reviewers for their valuable comments and suggestions. This work was partially funded by New England Biolabs, Inc. (USA). Copyright: Copyright 2008 Elsevier B.V., All rights reserved.

PY - 2008/2

Y1 - 2008/2

N2 - Motivation: The genomic methylation analysis is useful to type bacteria that have a high number of expressed type II methyltransferases. Methyltransferases are usually committed to Restriction and Modification (R-M) systems, in which the restriction endonuclease imposes high pressure on the expression of the cognate methyltransferase that hinder R-M system loss. Conventional cluster methods do not reflect this tendency. An algorithm was developed for dendrogram construction reflecting the propensity for conservation of R-M Type II systems. Results: The new algorithm was applied to 52 Helicobacter pylori strains from different geographical regions and compared with conventional clustering methods. The algorithm works by first grouping strains that share a common minimum set of R-M systems and gradually adds strains according to the number of the R-M systems acquired. Dendrograms revealed a cluster of African strains, which suggest that R-M systems are present in H.pylori genome since its human host migrates from Africa.

AB - Motivation: The genomic methylation analysis is useful to type bacteria that have a high number of expressed type II methyltransferases. Methyltransferases are usually committed to Restriction and Modification (R-M) systems, in which the restriction endonuclease imposes high pressure on the expression of the cognate methyltransferase that hinder R-M system loss. Conventional cluster methods do not reflect this tendency. An algorithm was developed for dendrogram construction reflecting the propensity for conservation of R-M Type II systems. Results: The new algorithm was applied to 52 Helicobacter pylori strains from different geographical regions and compared with conventional clustering methods. The algorithm works by first grouping strains that share a common minimum set of R-M systems and gradually adds strains according to the number of the R-M systems acquired. Dendrograms revealed a cluster of African strains, which suggest that R-M systems are present in H.pylori genome since its human host migrates from Africa.

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A new algorithm for cluster analysis of genomic methylation: the Helicobacter pylori case

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