AthaMap

AthaMap provides a genome-wide map of putative transcription factor binding sites (TFBS) and small RNA target sites in Arabidopsis thaliana to support analyses of transcriptional and post-transcriptional gene regulation.

Key Features:

• Extensive Database Coverage: Contains over 7.4 million putative binding sites for 115 transcription factors across 16 transcription factor families.
• Positional Weight Matrices (PWMs): Identifies TFBS using positional weight matrices (PWMs) with options to select high-quality TFBS to improve specificity.
• Co-localization and Combinatorial Element Detection: Detects co-localizing cis-regulatory elements with parameters for conservation levels, spacer ranges, and combinatorial assemblies of up to four TFBSs.
• Integration with Gene Expression Data: Integrates TFBS data with microarray gene expression databases such as Genevestigator and PathoPlant to identify common cis-regulatory elements in gene sets.
• Post-Transcriptional Regulation Mapping: Maps 403,173 genomic positions of small RNAs and identifies 5772 putative post-transcriptionally regulated target genes.
• Target Gene Localization: Defines potential target genes for selected TFs within genomic regions up to 6000 base pairs.
• Genomic Positioning and Annotation: Provides positional information of TFBS relative to transcription or translation start sites and incorporates the TAIR8 genome annotation.
• Data Integration: Integrates binding site data from the TRANSFAC database and published literature.

Scientific Applications:

• Modeling Gene Expression Regulation: Supports development of models to investigate interactions governing transcriptional regulation.
• Identification of Co-Regulated Genes: Enables detection of genes sharing common cis-regulatory elements and co-localizing TFBS patterns.
• Analysis of Environmental Response Elements: Facilitates identification of enrichment of stress-responsive elements, for example drought-responsive motifs in cold-induced genes.
• Study of Post-Transcriptional Regulation: Enables analysis of small RNA target mappings to investigate post-transcriptional control of gene expression.

Methodology:

TFBS were identified using positional weight matrices (PWMs); small RNAs were mapped to genomic positions (403,173 positions) to define 5772 putative targets; TFBS positions are reported relative to transcription or translation start sites; data are integrated from TRANSFAC and published sources and annotated using the TAIR8 genome; co-localizing cis-regulatory element detection uses conservation and spacer parameters allowing combinations of up to four TFBSs and region-based target identification up to 6000 bp; integration with Genevestigator and PathoPlant supports gene-set analyses.