Analysis of Genomic Tiling Microarrays for Transcript Mapping and the Identification of Transcription Factor Binding Sites

The recently developed technology of genomic tiling microarrays, which can be used for genome annotation, has required the development of new methodologies [Royce et.al] for their design and analysis. Genomic tiling arrays use PCR amplicons or short oligonucleotide probes to tile the non-repetitive DNA sequence of a genome in an unbiased fashion for the purposes of detecting novel genomic features. Specifically, they can be used for the identification of novel transcripts, distinguishing between different splice isoforms and for finding transcription factor binding sites using Chromatin-Immunoprecipitation on chip experiments (ChIP-chip).