AthaMap: From in silico Data to Real Transcription Factor Binding Sites

• Published in: In silico biology 2006, Vol.6 (3), p.243-252
• Main Authors: Bülow, Lorenz, Steffens, Nils Ole, Galuschka, Claudia, Schindler, Martin, Hehl, Reinhard
• Format: Article
• Language: English
• Subjects: Arabidopsis - genetics; Arabidopsis Proteins - genetics; Arabidopsis Proteins - metabolism; Arabidopsis thaliana; Base Sequence; Binding Sites; Biological and medical sciences; Databases, Genetic; DNA, Plant - chemistry; DNA, Plant - genetics; Fundamental and applied biological sciences. Psychology; Genome, Plant; Molecular and cellular biology; Molecular genetics; Transcription Factors - genetics; Transcription Factors - metabolism; Transcription. Transcription factor. Splicing. Rna processing
• ISSN: 1386-6338; 1434-3207
• DOI: 10.3233/ISB-00238

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.