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. 2010 Dec 21:2010:baq034.
doi: 10.1093/database/baq034. Print 2010.

AthaMap-assisted transcription factor target gene identification in Arabidopsis thaliana

Lorenz Bülow  1 , Yuri Brill, Reinhard Hehl
Affiliations

AthaMap-assisted transcription factor target gene identification in Arabidopsis thaliana

Lorenz Bülow et al. Database (Oxford). .

Abstract

The AthaMap database generates a map of potential transcription factor binding sites (TFBS) and small RNA target sites in the Arabidopsis thaliana genome. The database contains sites for 115 different transcription factors (TFs). TFBS were identified with positional weight matrices (PWMs) or with single binding sites. With the new web tool 'Gene Identification', it is possible to identify potential target genes for selected TFs. For these analyses, the user can define a region of interest of up to 6000 bp in all annotated genes. For TFBS determined with PWMs, the search can be restricted to high-quality TFBS. The results are displayed in tables that identify the gene, position of the TFBS and, if applicable, individual score of the TFBS. In addition, data files can be downloaded that harbour positional information of TFBS of all TFs in a region between -2000 and +2000 bp relative to the transcription or translation start site. Also, data content of AthaMap was increased and the database was updated to the TAIR8 genome release. Database URL: http://www.athamap.de/gene_ident.php.

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Figures

Figure 1.
Figure 1.
Schematic representation of the ‘Gene Identification’ function. The first level (red) shows user-selected parameters, the second level (yellow) shows results and the third level (green) shows further options for data analysis.
Figure 2.
Figure 2.
The web interface of the AthaMap ‘Gene Identification’ function. The result obtained with TF ABF1 is partially shown.
See this image and copyright information in PMC

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