Tools and index libraries for Arabidopsis Affymetrix chip users

["Majid Ghassemian PhD]

Tools and index libraries for Arabidopsis Affymetrix chip users

  Dear Colleagues,

             We have updated the Arabidopsis index file, provided by 
Affymetrix for the Arabidopsis chip, which will facilitate automated 
analyses of Genechip expression profiles. The Arabidopsis annotations 
file provided by Affymetrix only contains the Genbank identifiers and 
it can be time consuming to search for each gene individually in 
Genbank and to manually extract the promoter sequence from the BAC 
sequence entry.  We have updated this index file with the position of 
each element with reference to Arabidopsis chromosomes, and AGI 
identifiers for most elements. We have created files containing DNA 
sequences and protein sequences corresponding to most elements on the 
Affymetrix chip. These files will allow more rapid and automated 
analyses of Affymetrix GeneChipTM data using software packages (e.g. 
GeneSpring or others). To download these files and access the links 
please go to:

www-biology.ucsd.edu/labs/schroeder/genechip.html

Furthermore, the chromosome location function for each gene on the 
Affymetrix chip that we included can, among other uses, be helpful in 
mapping gene deletion mutations.

             We have also developed web-based tools to extract 
upstream promoter sequences using Affymetrix gene ID's and/or AGI 
identifiers. The recovered sequences are available at the same web 
site (www-biology.ucsd.edu/labs/schroeder/genechip.html) and can 
either be directly sent to a  "MEME" web site (a web based promoter 
analysis tool) for regulatory element searches or copied for export 
into other regulatory motif search and analysis tools. These tools 
will allow facilitated extraction of new promoter elements from Gene 
chip experiments.

  Majid Ghassemian, David Waner, Jason Tchieu, Michael Gribskov, 
Julian I. Schroeder