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Please use this identifier to cite or link to this item: http://ntour.ntou.edu.tw:8080/ir/handle/987654321/46766

Title: The Impact of Normalization and Phylogenetic Information on Estimating the Distance for Metagenomes
Authors: Chien-Hao Su
Tse-Yi Wang
Ming-Tsung Hsu
Francis Cheng-Hsuan Weng
Cheng-Yan Kao
Daryi Wang
Huai-Kuang Tsai
Contributors: 國立臺灣海洋大學:資訊工程學系
NTOU:Department of Computer Science and Engineering
Keywords: Metagenomics;normalization;phylogenetic information;distance functions;clustering
Date: 2012-04
Issue Date: 2018-06-04T08:20:41Z
Publisher: IEEE Transactions on Computational Biology and Bioinformatics
Abstract: Abstract:
Metagenomics enables the study of unculturable microorganisms in different environments directly. Discriminating between the compositional differences of metagenomes is an important and challenging problem. Several distance functions have been proposed to estimate the differences based on functional profiles or taxonomic distributions; however, the strengths and limitations of such functions are still unclear. Initially, we analyzed three well-known distance functions and found very little difference between them in the clustering of samples. This motivated us to incorporate suitable normalizations and phylogenetic information into the functions so that we could cluster samples from both real and synthetic data sets. The results indicate significant improvement in sample clustering over that derived by rank-based normalization with phylogenetic information, regardless of whether the samples are from real or synthetic microbiomes. Furthermore, our findings suggest that considering suitable normalizations and phylogenetic information is essential when designing distance functions for estimating the differences between metagenomes. We conclude that incorporating rank-based normalization with phylogenetic information into the distance functions helps achieve reliable clustering results.
Relation: 9(2), pp.619-628
URI: http://ntour.ntou.edu.tw:8080/ir/handle/987654321/46766
Appears in Collections:[資訊工程學系] 期刊論文

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