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The Impact of Normalization and Phylogenetic Information on Estimating the Distance for Metagenomes
March/April 2012 (vol. 9 no. 2)
pp. 619-628
ASCII Text
x 
 
Chien-Hao Su, Tse-Yi Wang, Ming-Tsung Hsu, Francis Cheng-Hsuan Weng, Cheng-Yan Kao, Daryi Wang, Huai-Kuang Tsai, "The Impact of Normalization and Phylogenetic Information on Estimating the Distance for Metagenomes," IEEE/ACM Transactions on Computational Biology and Bioinformatics, vol. 9, no. 2, pp. 619-628, March/April, 2012.
 
 
BibTex
x
 
@article{ 10.1109/TCBB.2011.111,
author = {Chien-Hao Su and Tse-Yi Wang and Ming-Tsung Hsu and Francis Cheng-Hsuan Weng and Cheng-Yan Kao and Daryi Wang and Huai-Kuang Tsai},
title = {The Impact of Normalization and Phylogenetic Information on Estimating the Distance for Metagenomes},
journal ={IEEE/ACM Transactions on Computational Biology and Bioinformatics},
volume = {9},
number = {2},
issn = {1545-5963},
year = {2012},
pages = {619-628},
doi = {http://doi.ieeecomputersociety.org/10.1109/TCBB.2011.111},
publisher = {IEEE Computer Society},
address = {Los Alamitos, CA, USA},
}
 
 
RefWorks Procite/RefMan/Endnote
x 
 
TY - JOUR
JO - IEEE/ACM Transactions on Computational Biology and Bioinformatics
TI - The Impact of Normalization and Phylogenetic Information on Estimating the Distance for Metagenomes
IS - 2
SN - 1545-5963
SP619
EP628
EPD - 619-628
A1 - Chien-Hao Su,
A1 - Tse-Yi Wang,
A1 - Ming-Tsung Hsu,
A1 - Francis Cheng-Hsuan Weng,
A1 - Cheng-Yan Kao,
A1 - Daryi Wang,
A1 - Huai-Kuang Tsai,
PY - 2012
KW - Metagenomics
KW - normalization
KW - phylogenetic information
KW - distance functions
KW - clustering.
VL - 9
JA - IEEE/ACM Transactions on Computational Biology and Bioinformatics
ER -
 
Chien-Hao Su, Academia Sinica, Taipei
Tse-Yi Wang, Academia Sinica, Taipei
Ming-Tsung Hsu, Academia Sinica, Taipei
Francis Cheng-Hsuan Weng, Academia Sinica, Taipei
Cheng-Yan Kao, National Taiwan University, Taipei
Daryi Wang, Academia Sinica, Taipei
Huai-Kuang Tsai, Academia Sinica, Taipei
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.

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Index Terms:
Metagenomics, normalization, phylogenetic information, distance functions, clustering.
Citation:
Chien-Hao Su, Tse-Yi Wang, Ming-Tsung Hsu, Francis Cheng-Hsuan Weng, Cheng-Yan Kao, Daryi Wang, Huai-Kuang Tsai, "The Impact of Normalization and Phylogenetic Information on Estimating the Distance for Metagenomes," IEEE/ACM Transactions on Computational Biology and Bioinformatics, vol. 9, no. 2, pp. 619-628, March-April 2012, doi:10.1109/TCBB.2011.111
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