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Title: Super paramagnetic clustering of DNA sequences
Keywords: data clustering, super paramagnetic clustering, promoter, DNA sequence, data mining, transcription factor
Issue Date: 2-Dec-2005
Citation: SUGIARTO RADJIMAN (2005-12-02). Super paramagnetic clustering of DNA sequences. ScholarBank@NUS Repository.
Abstract: An unsupervised clustering on a set of DNA sequences with active promoter regions was performed. We employed Super Paramagnetic Clustering method which is inspired by statistical physics model of a disordered ferromagnet. With this method, we were able to mine some important clusters and capture correlations contained within the clusters. Besides successfully separating arthropod and vertebrate class, we found two human viral genome clusters: EBV and HSV-1. Their members were gene sequences which expressed proteins in lytic and latent cycles of infection. Another important result is the separation of the vertebrate class into two big clusters. We deduced that these two clusters correspond to housekeeping and tissue-specific genes by conducting a rigorous analysis of consensus octa-nucleotides of transcription factor binding sites. The biological significance of these clusters are discussed.
Appears in Collections:Master's Theses (Open)

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