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 GeneChip™ data using software packages (e.g. GeneSpring or others). To download these files see below.
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 below, 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
These are described in the October, 2001 issue of Trends in Plant Science.
Please direct all questions and suggestions to Jason Tchieu