Data in AthaMap is based on published transcription factor binding specificities available as
alignment matrices or experimentally determined single binding sites. Matrix- and pattern-based
screenings were performed to identify potential transcription factor binding sites
in the genome of Arabidopsis thaliana (TAIR release 8). The complete list of all transcription
factors included in AthaMap, the corresponding references, and screening results are displayed on the
documentation page. The description
pages explain all tools.
By using the search function, the sequence of a specific genomic
position or gene can be displayed in a sequence window including the potential transcription
factor binding sites. A colocalization function allows the
search for user-defined potential combinatorial elements. A set of pre-calculated known
combinatorial elements is already incorporated in AthaMap. The Gene Analysis tool enables
identification of common transcription factor binding sites in a set of user-submitted genes.
The Gene Identification tool allows the search for transcription
factor binding sites of a specific transcription factor. The Small RNA Targets tool enables
identification of small RNA target genes.
The MicroRNA Targets tool identifies
target genes of miRNAs.