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:
- Alternative Transcript Analysis Methods for Exon Arrays v1.1 (pdf, 79 KB)]: [1]
- Exon Array Background Correction v1.0 (pdf, 78 KB): [2]
- Exon Probeset Annotations and Transcript Cluster Groupings v1.0 (pdf, 87 KB): [3]
- Exon Related Changes FAQ (pdf, 268 KB):[4]
- Gene Level Summarization on Exon Arrays (pdf, 747 KB):[5]
- Gene Signal Estimates from Exon Arrays v1.0 (pdf, 428 KB): [6]
- 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:
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
Array normalization
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/
Gene level analysis
Analysis procedure is similar to traditional gene expression arrays, i.e. summarize signals of a probe set (probes mapping to the same gene) into a whole-gene expression index [8].
Exon level analysis
Gene annotation
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:
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:
exonmap - BioConductor package to analyse Exon arrays:
dChip - Exon and tiling array analysis:
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.
