Abstract: AthaMap generates a map for cis-regulatory sequences for the
whole Arabidopsis thaliana genome. AthaMap was initially developed by
matrix-based detection of putative transcription factor binding sites (TFBS)
mostly determined from random binding site selection experiments. Now, also
experimentally verified TFBS have been included for 48 different
Arabidopsis thaliana transcription factors (TF). Based on these sequences,
89,416 very similar putative TFBS were determined within the genome of A.
thaliana and annotated to AthaMap. Matrix- and single sequence-based binding
sites can be included in colocalization analysis for the identification of
combinatorial cis-regulatory elements. As an example, putative target
genes of the WRKY18 transcription factor that is involved in plant-pathogen
interaction were determined. New functions of AthaMap include descriptions for
all annotated Arabidopsis thaliana genes and direct links to TAIR, TIGR
and MIPS. Transcription factors used in the binding site determination are
linked to TAIR and TRANSFAC® databases.
AthaMap is freely available at http://www.athamap.de.