Boosting AthaMap Database Content with Data from Protein Binding Microarrays

Plant Cell Physiol. 2016 Jan;57(1):e4. doi: 10.1093/pcp/pcv156. Epub 2015 Nov 5.


The AthaMap database generates a map of predicted transcription factor binding sites (TFBS) and small RNA target sites for the whole Arabidopsis thaliana genome. With the advent of protein binding microarrays (PBM), the number of known TFBS for A. thaliana transcription factors (TFs) has increased dramatically. Using 113 positional weight matrices (PWMs) generated from a single PBM study and representing a total number of 68 different TFs, the number of predicted TFBS in AthaMap was now increased by about 3.8 × 10(7) to 4.9 × 10(7). The number of TFs with PWM-predicted TFBS annotated in AthaMap has increased to 126, representing a total of 29 TF families and newly including ARF, AT-Hook, YABBY, LOB/AS2 and SRS. Furthermore, links from all Arabidopsis TFs and genes to the newly established Arabidopsis Information Portal (AIP) have been implemented. With this qualitative and quantitative update, the improved AthaMap increases its value as a resource for the analysis of A. thaliana gene expression regulation at

Keywords: Arabidopsis thaliana; AthaMap; Database; Small RNAs; Transcription factors.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Arabidopsis / genetics*
  • Arabidopsis / metabolism
  • Arabidopsis Proteins / genetics
  • Arabidopsis Proteins / metabolism
  • Binding Sites
  • Computational Biology
  • Databases, Genetic*
  • Protein Array Analysis
  • Protein Binding
  • Transcription Factors / genetics
  • Transcription Factors / metabolism*


  • Arabidopsis Proteins
  • Transcription Factors