NDLI: Grouping and visualizing human endogenous retroviruses by bootstrapping median self-organizing maps

Content Provider	IEEE Xplore Digital Library
Author	Oja, M. Sperber, G. Blomberg, J. Kaski, S.
Copyright Year	2004
Description	Author affiliation: Neural Networks Res. Centre, Helsinki Univ. of Technol., Espoo, Finland (Oja, M.)
Abstract	About eight percent of the human genome consists of human endogenous retrovirus sequences. Human endogenous retroviruses (HERV) are remains from ancient infections by retroviruses. The HERVs are mutated and deficient, but they still may give rise to transcripts or may affect the expression of human genes. The HERVs stem from several kinds of retroviruses., The possible current functioning of the HERV sequences may reflect the origin of the HERVs. Hence, the classification of the diverse HERV sequences is a natural starting point when investigating the effect of HERVs in humans. The current HERV taxonomy is incomplete: some sequences cannot be assigned to any class and the classification is ambiguous for others. A median self-organizing map (SOM), a SOM for data about pairwise distances between samples, can be used to group all the HERVs found in the human genome. It visualizes the collection of 3661 HERV sequences found by the RetroTector system, on a two-dimensional display that represents similarity relationships between individual sequences, as well as cluster structures and similarities of clusters. The SOM, as any dimensionality reduction method, necessarily has to make compromises when representing the data. In this work we extend the visualizations by bootstrap-based estimates on which parts of the visualization are reliable and which not, and use the SOM to find potentially new HERV groups.
Sponsorship	IEEE Comput. Intelligence Soc
Starting Page	95
Ending Page	101
File Size	670426
Page Count	7
File Format	PDF
ISBN	0780387287
DOI	10.1109/CIBCB.2004.1393939
Language	English
Publisher	Institute of Electrical and Electronics Engineers, Inc. (IEEE)
Publisher Date	2004-10-07
Publisher Place	USA
Access Restriction	Subscribed
Rights Holder	Institute of Electrical and Electronics Engineers, Inc. (IEEE)
Subject Keyword	Humans Self organizing feature maps Sequences Genomics Bioinformatics Data visualization Taxonomy DNA Phylogeny Two dimensional displays
Content Type	Text
Resource Type	Article

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