A genomic position can be submitted and results in a sequence window showing the transcription factor binding sites. AthaMap provides two different search modes for the user. One can either enter a genomic location on a specific chromosome manually, and the 500 bp upstream and downstream of the submitted position are displayed. Alternatively, one can enter an Arabidopsis genome identification number as provided by TAIR (AGI, format: AtxGnnnnn), and 500 bp upstream and downstream of the transcription or translation start site will be displayed. The navigation buttons in the lower corners of the sequence window allow scrolling the displayed genomic region 500 bp in either direction.
For the identification of highly conserved TF binding sites determined by matrix-based screening, a function was implemented which enables the user to select a particular quality of the TFBS displayed in AthaMap. For this, a percentage (0-100) can be provided by the user in the text field 'restriction' on the search page. This number reflects the percentage between maximum score and threshold that the individual score of a binding site must exceed in order to be displayed.
For example, if a matrix for a TF has a max. score of 10, a threshold of 5, and the user defines the restriction to 20% by entering a "20" in the text field 'restriction', only TFBS for that factor with a score of 6 or greater will be displayed since 5 + (5 * 0.2) = 6. If a "50" was entered in that text field, only TFBS with a score greater than or equal to 5 + (0.5 * (10 - 5)) = 7.5 will be displayed in AthaMap. As a higher score means a higher sequence conservation, this feature enables the user to exclude TFBS with low sequence conservation from the display in AthaMap.
In the sequence window displayed after the search, sequences of genes and their features like exons, introns, CDS, and UTRs are coloured according to the TAIR annotation. A short description of the function of the gene product is provided at the bottom of the page as well as links to the respective records in TAIR and MIPS for additional information.
Potential transcription factor binding sites are indicated as arrows above the sequence. The arrow indicates the extension and orientation of the binding site. The arrow type is dependent on the type of binding site. Arrows -----> symbolize matrix-based, arrow heads >>>>>> pattern-based binding sites, and double lines ====== symbolize combinatorial elements. By moving the mouse pointer over the arrow, information about the particular binding site is displayed. The individual position is given, and in the case of matrix-based binding sites, the score of that particular site, the threshold and the maximum possible score are indicated as determined by the search program Patser (Hertz and Stormo, 1999). The score of the site can be compared with the maximum score displayed in the same window. A high score close to the maximum score represents a highly conserved binding site. A low score close to the threshold represents a less conserved binding site. These values enable the user to judge the quality of a match or putative binding site by comparing the particular score of a site with the threshold and maximum score determined by Patser. The name of the binding transcription factor is indicated adjacent to the arrow. Selecting the factor's name will open a new window with general information on the transcription factor like the corresponding factor family, species, and reference as well as screening parameters, the matrix or screening sequence, respectively, and additional links to external databases.
Transcription start sites (TSS) are also annotated to AthaMap and are symbolized with an asterisk (*TSS). The positions were derived from TAIR annotation data. The factors TBP and CBF constitute special cases since functional binding sites for these factors are defined by their position relative to gene start sites. Hence, only binding sites for TBP and CBF in proximity of gene start sites are annotated to AthaMap.
To identify potential target genes of small RNAs, sequences from small transcriptome screenings were annotated to AthaMap and are symbolized as xxxxx>. Selecting the name adjacent to this symbol will open a new window giving additional information on the small RNA like the exact sequence and other corresponding target sites of this sequence. MicroRNA target sites were determined by a genome-wide screening of miRNA sequences from miRBase using psRNATarget. MicroRNAs are symbolized as XXXXX>.