TY - GEN
T1 - An approach for determining evolutionary distance in network-based phylogenetic analysis
AU - Zhou, Tingting
AU - Chan, Chun Chung
AU - Pan, Yi
AU - Wang, Zhenghua
PY - 2008/8/27
Y1 - 2008/8/27
N2 - Network-based phylogenetic analysis explores phylogenetic relationships among different organisms by comparing their biological networks, especially metabolic networks. The differences between networks, often expressed as evolutionary distances, are normally measured using the plain Jaccard distance. In this paper, we show enzymes are different in phylogenetic conservation and topological importance, which are correlated significantly. Inspired by this observation, we propose a new approach to determine evolutionary distances. Our approach considers not only the number of different enzymes in different organisms, but also the phylogenetic or topological difference of individual enzymes. The resulting evolutionary distance measures are compared with the plain Jaccard distance by use of 16s rRNA-based distance as reference. It shows that new distance measures make errors smaller in all test cases of comparison.
AB - Network-based phylogenetic analysis explores phylogenetic relationships among different organisms by comparing their biological networks, especially metabolic networks. The differences between networks, often expressed as evolutionary distances, are normally measured using the plain Jaccard distance. In this paper, we show enzymes are different in phylogenetic conservation and topological importance, which are correlated significantly. Inspired by this observation, we propose a new approach to determine evolutionary distances. Our approach considers not only the number of different enzymes in different organisms, but also the phylogenetic or topological difference of individual enzymes. The resulting evolutionary distance measures are compared with the plain Jaccard distance by use of 16s rRNA-based distance as reference. It shows that new distance measures make errors smaller in all test cases of comparison.
KW - Evolutionary distance
KW - Jaccard distance
KW - Metabolic network comparison
KW - Network-based phylogenetic analysis
KW - Phylogenetic conservation
KW - Topological importance
UR - http://www.scopus.com/inward/record.url?scp=49949095008&partnerID=8YFLogxK
U2 - 10.1007/978-3-540-79450-9_5
DO - 10.1007/978-3-540-79450-9_5
M3 - Conference article published in proceeding or book
SN - 3540794492
SN - 9783540794493
T3 - Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics)
SP - 38
EP - 49
BT - Bioinformatics Research and Applications - Fourth International Symposium, ISBRA 2008, Proceedings
T2 - 4th International Symposium on Bioinformatics Research and Applications, ISBRA 2008
Y2 - 6 May 2008 through 9 May 2008
ER -