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Show animation of Hybridisation interactions in the HG-U133A Microarray (WARNING: 5Mb file)
Image generated by Tim Yates @ PICR Bioinformatics

Hybridization interactions between probesets in short oligo microarrays lead to spurious correlations. Michal J Okoniewski and Crispin J Miller BMC Bioinformatics 2006, 7:276 (journal link)

ADAPT describes the many-to-many relationships between Affymetrix™ probesets transcripts and genes, by directly mapping every probe against publicly available mRNAs/cDNA sequences from RefSeq and Ensembl.

You can search the database by Affymetrix™ Probeset ID, Transcript Accession, Gene Symbol or Gene Accession.

Currently, the ADAPT database holds information on 23 Array Types containing 255771 unique Probesets, that themselves map onto 252788 entries in both RefSeq and Ensembl.
Current RefSeq version : 'Release 27'
Current Ensembl version : 'V48'


We have a new website X:Map for visualising Affymetrix Exon Arrays on both the Human and Mouse genomes. There is also a Bioconductor package exonmap, if you wish to do your own analysis.


There is now a search plugin for Mozilla/FireFox that allows you to search ADAPT from the comfort of your own browser without ever leaving the site you're currently viewing. Just install this plugin and you'll be searching ADAPT in no time flat. (There is a problem with the plugin on Linux/Mac, please see the FAQ for a more detailed description)


Usage Guide

»  Hyperlinks take you to a detailed view of the Probeset ID, Transcript Accession, Gene Symbol or Gene Accession that you selected.

»  The mapping icon takes you to a page showing the position of every Probe and Probeset that matches the Transcript (or set of Transcripts).

»  The find icon will open a new browser which links through to an external website with detailed information on that ID or Symbol (if the data is there).

»  You can also set a filter, so that you only see probesets that are on a particular Array Type. Just click the "(edit)" link on the top right of the page to set one now!

»  There is currently a limit of 200 items per query. That is, you may only enter 200 probesets, etc. into the query form.

»  There is also a limit of 200 on the number of probesets that the system will return. Entering 200 gene symbols will only return a maximum of 200 probesets. If this is a significant problem, please email the development team who will try to assist you further.

To start using the tool, please go to either the overview search page, or the mapping search page.


Send comments to microarray@picr.man.ac.uk

 
© The Paterson Institute for Cancer Research, 2003 - 2006
When using data from ADAPT, please cite:   Hui Sun Leong, Tim Yates, Claire Wilson and Crispin J Miller (2005) "ADAPT: A Database of Affymetrix Probesets and Transcripts" Bioinformatics 2005 21(10):2552-2553   PubMed   ( journal )
Affymetrix™ and NetAffx™ are trademarks of Affymetrix. Ensembl is a trademark of the Wellcome Trust Sanger Institute.

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