Wikiomics:Exon microarrays

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[[Category:Protocol]] [[Category:In silico]] [[Category:Data analysis]]

Revision as of 06:28, 27 February 2008


Technology overview

Overview of the GeneChip® Exon and Gene Array Systems:

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:


Quality control

Affymetrix Whitepaper on exon array QA:

A Core Lab Case Study: Exon Array Challenges and Opportunities:

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.

Gene level analysis

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:

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.


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