Classification of oligonucleotide fingerprints: application for microbial community and gene expression analyses

Oligonucleotide fingerprinting is an array-based approach used for analysis of microbial community composition and gene expression profiling. Oligonucleotide fingerprinting of ribosomal RNA genes (OFRG) is an approach that sorts rDNA clones into taxonomic groups through a series of hybridization experiments. For every hybridization experiment, the signal intensities are transformed into three discrete values 0, 1, and N, where 0 and 1 respectively specify negative and positive hybridization events and N designates an uncertain assignment. Various approaches have been performed to resolve the uncertainty. These include Bayesian classification with the normal distribution, Bayesian classification with the exponential distribution and gamma distribution, along with tree-based classification. All 0-1 data produced from each classification approach, including the original 0-1-N data, were afterwards clustered using the Unweighted Pair Group Method with Arithmetic Mean. The performance of e...

• Type: Journal
• Year: 2005
• Where: BIOINFORMATICS
• Authors: Katechan Jampachaisri, Lea Valinsky, James Borneman, S. James Press
• Keywords: Array-based Approach, Bayesian Classification, BIOINFORMATICS 2005, Gene Expression