Summary
The Exon Array Analyzer (EAA) is a web server to identify alternative splicing with Affymetrix Exon Arrays by providing a user-friendly interface. The EAA implements the Splice Index algorithm to identify differential expressed exons. By using various filters, the amount of false positive results can be reduced. The result is presented with detailed annotation information and graphics to identify splice events and to facilitate biological validations.As a example we downloaded murine CEL files, available at the Affymetrix web site (www.affymetrix.com). To identify heart specific splice events, we analyzed all non-heart tissues as a group against heart. A detailed step by step manual, based on this analysis can be found in the help section. It includes screen shots of every step, detailed description about the features of the EAA and how to use the sequence information to design primer with the Primer3 tool. Also a detailed description about the filters can be found on this page.
The result of the analysis can be accessed here using the EAA interface (password="heart").
Documents
- EAA Online Manual
Step by step instructions and screen shots.
Tables
- Result of the example analysis - Heart specific spliced genes
Result is accessible by the EAA web interface including all features like genome browser and sequence informations. Password for this analysis is "heart".
The results also can be downloaded here (thresholds: Splice Index < -1 or Splice Index > 1 and p-value < 0.01). - Comparison to other tools for Exon Array analysis
Figures
- Heart specific spliced genes validated by RT-PCR
RT-PCR result of heart specific spliced genes. On the left side the according splice events are shown.