Wikiomics:Exon microarrays

Technology overview

Overview of the GeneChip® Exon and Gene Array Systems: http://www.affymetrix.com/products/arrays/exon_application.affx

Affymetrix White Papers:

1. Alternative Transcript Analysis Methods for Exon Arrays v1.1 (pdf, 79 KB)]: [1]
2. Exon Array Background Correction v1.0 (pdf, 78 KB): [2]
3. Exon Probeset Annotations and Transcript Cluster Groupings v1.0 (pdf, 87 KB): [3]
4. Exon Related Changes FAQ (pdf, 268 KB):[4]
5. Gene Level Summarization on Exon Arrays (pdf, 747 KB):[5]
6. Gene Signal Estimates from Exon Arrays v1.0 (pdf, 428 KB): [6]
7. Quality Assessment of Exon and Gene Arrays (pdf, 180 KB):[7]

Web-based seminars, including several archived events specific for the Exon arrays can be found at:

1. http://www.affymetrix.com/corporate/events/archive.affx

Quality control

Affymetrix Whitepaper on exon array QA: http://www.affymetrix.com/support/technical/whitepapers/exon_gene_arrays_qa_whitepaper.pdf

A Core Lab Case Study: Exon Array Challenges and Opportunities: http://www.affymetrix.com/support/technical/appnotes/exonarray_challenge_appnote.pdf

Data analysis

Exonmap is a BioConductor package, currently under development, that uses the underlying data from X:MAP to support fine grained analysis of Exon array data. http://bioinf.picr.man.ac.uk/

Analysis tools

Affymetrix support pages for the human, mouse and rat Exon arrays provide library files, annotation files and demonstration data:

• http://www.affymetrix.com/support/technical/byproduct.affx?product=huexon-st
• http://www.affymetrix.com/support/technical/byproduct.affx?product=moexon-st
• http://www.affymetrix.com/support/technical/byproduct.affx?product=raexon-st

The Affymetrix Expression Console is avaialble to download at:

• http://www.affymetrix.com/products/software/specific/expression_console_software.affx

This page also includes a link to Affymetrix Power Tools (APT), which provides additional functionality.

Information about GeneChip compatible 3rd party software for the various applications is available at:

• http://www.affymetrix.com/products/software/compatible/index.affx

exonmap - BioConductor package to analyse Exon arrays:

• http://bioconductor.org/packages/2.0/bioc/html/exonmap.html

dChip - Exon and tiling array analysis:

• http://biosun1.harvard.edu/complab/dchip/exon.htm

Data visualization

X:MAP - is an interactive, real-time scrollable, genome browser that shows the location of individual exon probes with respect to their target genes, transcripts and exons.

http://xmap.picr.man.ac.uk/