High-throughput transcriptomics with Affymetrix exon arrays

 

Micha&#322; Okoniewski, Paterson Institute for Cancer Research, Manchester, UK

 

Until recently, the majority of microarrays considered transcription at the level of individual genes. 
They were, for the majority of genes, unable to distinguish between different isoforms, and, depending on
 the location of their probes, there was also the potential to miss certain transcripts entirely. 
Some groups have designed arrays to investigate genes by using many probes placed along their length
 in order to interrogate each exon separately. However, the number of features required to do this 
systematically, for the entire human genome, was prohibitively large. Affymetrix Exon arrays [1, 2],
 which use over 5.5 million features, is the first microarray platform that enables comprehensive h
igh-throughput transcriptomic studies on a single chip.

X:MAP is a database of the Affymetrix exon array annotations built by performing an in silico search between 
its probes and the entire genome. These data are stored in a relational database and associated with a copy 
of Ensembl [3]. In this way, the potential places where probesets may hybridize to the (expressed) genome 
are recorded. The approach also mirrors the strategy used to design the arrays. X:MAP has a web-based genome
 browser (based on Google Maps) that allows the relationship between probesets, the genome and gene-structure
 to be explored [4]. 

Associated with X:MAP is a BioConductor [5] package, exonmap [6, 7]. X:MAP and exonmap provide mappings 
between potential probe hits, probesets, exons, transcripts and genes, functions to include or exclude
 probesets from an analysis based on the genomic features they target, or whether they are likely to 
hybridize to multiple locations, functions to systematically identify differentially expressed and 
alternatively spliced transcripts, and visualization tools that map expression data onto gene structure.
 By supporting mappings to ESTs and GenScan predictions, and through the ability to pursue intergenic 
and intronic probesets, X:MAP allows the systematic exploration of both well-characterized genes and regions 
of novel transcription.

 

1.         Clark T, Schweitzer A, Chen T, Staples M, Lu G, Wang H, Williams A, Blume J: Discovery of
 tissue-specific exons using comprehensive human exon microarrays. Genome Biol 2007, 8(4):R64.

2.         Okoniewski MJ, Hey Y, Pepper SD, Miller C: High correspondence between Affymetrix exon and
 standard expression arrays. Biotechniques 2007, 42(2):181-185.

3.         Hubbard TJ, Aken BL, Beal K, Ballester B, Caccamo M, Chen Y, Clarke L, Coates G, Cunningham 
F, Cutts T et al: Ensembl 2007. Nucleic Acids Res 2007, 35(Database issue):D610-617.

4.         X:MAP main page [http://xmap.picr.man.ac.uk]

5.         Gentleman RC, Carey VJ, Bates DM, Bolstad B, Dettling M, Dudoit S, Ellis B, Gautier L, 
Ge Y, Gentry J et al: Bioconductor: open software development for computational biology and bioinformatics. 
Genome Biol 2004, 5(10):R80.

6.         exonmap in BioConductor [http://www.bioconductor.org/packages/2.0/bioc/html/exonmap.html]

7.         Okoniewski MJ, Yates T, Dibben S, Miller CJ: An annotation infrastructure for the analysis and interpretation of Affymetrix exon array data. Genome Biol 2007, 8(5):R79.