title: Nearest hyperplane distance neighbor clustering algorithm applied to gene co-expression analysis in Alzheimer's disease.
abstract: Microarray analysis can contribute considerably to the understanding of biologically significant cellular mechanisms that yield novel information regarding co-regulated sets of gene patterns. Clustering is one of the most popular tools for analyzing DNA microarray data. In this paper, we present an unsupervised clustering algorithm based on the K-local hyperplane distance nearest-neighbor classifier (HKNN). We adapted the well-known nearest neighbor clustering algorithm for use with hyperplane distance. The result is a simple and computationally inexpensive unsupervised clustering algorithm that can be applied to high-dimensional data. It has been reported that the NFkB1 gene is progressively over-expressed in moderate-to-severe Alzheimer's disease (AD) cases, and that the NF-kB complex plays a key role in neuroinflammatory responses in AD pathogenesis. In this study, we apply the proposed clustering algorithm to identify co-expression patterns with the NFkB1 in gene expression data from hippocampal tissue samples. Finally, we validate our experiments with biomedical literature search.
authors.affiliation: Department of Health Informatics and Information Management, Louisiana Tech university, Ruston, LA 71270, USA. cpasluos@latech.edu
authors.forename: Cristian F
authors.initials: CF
authors.lastname: Pasluosta
authors.forename: Prerna
authors.initials: P
authors.lastname: Dua
authors.forename: Walter J
authors.initials: WJ
authors.lastname: Lukiw
mesh_terms: D000465:Algorithms; D000544:Alzheimer Disease / Q000235:genetics / Q000378:metabolism*; D001921:Brain / Q000378:metabolism*; D016000:Cluster Analysis; D020869:Gene Expression Profiling / Q000379:methods*; D005786:Gene Expression Regulation; D006801:Humans; D005810:Multigene Family; D052002:NF-kappa B p50 Subunit / Q000378:metabolism*; D009419:Nerve Tissue Proteins / Q000235:genetics / Q000378:metabolism*; D020411:Oligonucleotide Array Sequence Analysis / Q000379:methods; D025941:Protein Interaction Mapping / Q000379:methods*
chemical_list: D052002:NF-kappa B p50 Subunit; C489548:NFKB1 protein, human; D009419:Nerve Tissue Proteins