Affymetrix provides a broad range of expression, whole genome, and custom arrays. Please visit http://www.affymetrix.com/products/arrays/index.affx for a complete, up-to-date listing of arrays available.

 

 

The GeneChip® Human Exon 1.0 ST (sense target) Array combines a novel array design strategy with the highest density array manufacturing capability, offering, for the first time, exon-level expression profiling at the whole-genome scale on a single array. The Exon Array system solution presents new dimensions for researchers to explore the human genome so they can investigate global expression of individual exons to uncover and document novel alternative splicing events. The Exon 1.0 ST Array has the highest resolution analysis yet, with over 1 million exon clusters being interrogated. The Exon 1.0 ST Array also possesses flexible data analysis solutions and comprehensive annotation providing users the opportunity to explore and dissect the data, bringing the focus to the more relevant data.

 

In addition to the Human Exon 1.0 ST Array, Affymetrix has also produced a Mouse Exon and a Rat Exon Array.

 

 

Large-scale sequencing of the human genome has revealed the unforeseeable fact that the vast degree of observed proteomic complexity is achieved through less than 30,000 coding transcripts. Therefore, the diversity of the proteome is, to a large extent, created by alternative splicing of pre-mRNAs expressed from individual genes. Reports suggest that 40% to 60% of the mRNAs transcribed from human and mouse genes undergo alternative splicing using in silico alignment of expressed sequence tags aligned to genomic sequences. (Modrek et al, 2001, Kan et al, 2001, Zavolan et al 2006).

 

More recently, the frequencies of alternative splicing of human genes were estimated in experiments to be 74% in a genome-wide survey of mRNA from multiple tissues using hybridization microarrays with more than 10,000 exon-junction probes (Johnson et al, 2003). Using Affymetrix GeneChip® Tiling microarrays, arrayed with closely spaced genomic probes, Kampa et al (2004) found that more than 80% of the genes on chromosomes 21 and 22 appeared to undergo alternative splicing. The use of splice sites imparts an adaptable mechanism for controlling gene expression and for generating multiplicity of the proteome.

 

The splice sites are recognized by the splicing machinery, a ribonuclear protein complex termed the spliceosome. Alternative splicing of mRNAs can occur in a number of different scenarios including; the exclusion or inclusion of a complete exon, the use of alternative 5’ or 3’ splice site or mutually exclusive splicing by selection (Relogio et al, 2005). At the protein level, differentially spliced mRNAs can result in the use of alternative translation initiation sites, altered translation termination that are attributable to frame shifts, or the creation or removal of a stop codon, thus causing truncation or extension of the protein product (Modrek et al, 2003).

 

The ability to reduce the detectable feature size of individual probes on the glass surface has allowed the arraying of over 5 million features and resulted in the recent release of the highest density exon array, the GeneChip® Human Exon 1.0 ST. The array interrogates 1 million exon clusters (predicted genes) of overlapping exons allowing interrogation of every known exon with one probe set over the entire genome. However in the interest of probe lengths, only exons that are longer than 25bp are included on the array. Approximately ¼ of the array content is based on EST and another ¼ is based GENSCAN. The remaining half of the array consists of probes that were derived from a combination of annotation sources. Approximately 1/6 of the probe sets derived solely from ESTs are supported by more than one EST annotation. The array is capable of capturing moderate to large variations in diversity thus events less than 25 bp are not represented on the array. There are no exon junction probe sets on the array. This first generation, whole genome exon array permits detection of exon skipping, exon retention, mutually exclusive exon usage, alternative promoter usage, alternative polyadenlyation, and alternative splicing donor/acceptor sites with changes over 25bp. It is difficult to evaluate the usefulness of the array since at the time of this writing; there were no available publications that had used the technology. Some useful databases of alternatively spliced genes include: EASED http://eased.bioinf.mdc-berlin.de/, Alternative Splicing Database Project http://www.ebi.ac.uk/asd/, PALS http://palsdb.ym.edu.tw.