Title
Combination of dendrograms with plots of latent-variables - application to g-protein coupled receptor sequences Combination of dendrograms with plots of latent-variables - application to g-protein coupled receptor sequences
Author
Publication type
article
Publication
Amsterdam ,
Subject
Mathematics
Physics
Chemistry
Computer. Automation
Source (journal)
Chemometrics and intelligent laboratory systems. - Amsterdam
Volume/pages
16() :2 , p. 145-154
ISSN
0169-7439
ISI
A1992JY54200004
Carrier
E
Target language
English (eng)
Full text (Publishers DOI)
Abstract
Dendrograms provide the logical connectedness of the elements of a set, such as proteins that have evolved from common ancestors. The arrangement of the branches of a dendrogram is not unique and many equivalent dendrograms may represent the same logical structure. Plots of latent variables (LV) reproduce the geometrical structure of the elements in low-dimensional space. The reliability of such a low-dimensional plot is determined by how well spatial structure is preserved by the first two or three latent variables. In cases where the number of relevant latent variables is larger, the reliability of an LV plot may be low. We show that LV plots can be used for the display of logical structure even when the spatial structure is poorly represented. Applications are found in the comparison of amino acid sequences of proteins that have evolved through random mutations and natural selection. More generally, the approach is feasible when elements have evolved from one another or from unknown common ancestors. In that case, dendrograms and low-dimensional LV plots can be combined into a single display which preserves as much as possible of the logical and of the spatial structure.
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