Applications of DNA tiling arrays for whole-genome analysis.
DNA microarrays are a well-established technology for measuring gene expression levels. Microarrays designed for this purpose use relatively few probes for each gene and are biased toward known and predicted gene structures. Recently, high-density oligonucleotide-based whole-genome microarrays have emerged as a preferred platform for genomic analysis beyond simple gene expression profiling. Potential uses for such whole-genome arrays include empirical annotation of the transcriptome, chromatin-immunoprecipitation-chip studies, analysis of alternative splicing, characterization of the methylome (the methylation state of the genome), polymorphism discovery and genotyping, comparative genome hybridization, and genome resequencing. Here we review different whole-genome microarray designs and applications of this technology to obtain a wide variety of genomic scale information.
Mockler
Todd C
TC
Plant Biology Laboratory, The Salk Institute for Biological Studies, La Jolla, CA 92037, USA.
Chan
Simon
S
Sundaresan
Ambika
A
Chen
Huaming
H
Jacobsen
Steven E
SE
Ecker
Joseph R
JR
D000818:Animals; D047369:Chromatin Immunoprecipitation / Q000379:methods / Q000639:trends; D019175:DNA Methylation; D020869:Gene Expression Profiling / Q000379:methods / Q000639:trends; D016678:Genome; D005838:Genotype; D006801:Humans; D020411:Oligonucleotide Array Sequence Analysis / Q000379:methods* / Q000639:trends; D011110:Polymorphism, Genetic / Q000235:genetics