ATRM: Arabidopsis Transcriptional Regulatory Map

  1. Functionally confirmed transcriptional regulatory interactions in the ATRM: Excel, Cytoscape.
  2. Information content of the transcription factor (TF) binding matrices in A. thaliana: Excel.
  3. MATLAB source codes for kinetic simulations of motif 10, motif 11, and motif 12.
   Supplementary Materials:
  1. Materials and Methods, Supplementary Text, Supplementary Figures and Tables: PDF.
  2. Supplementary Table S1. Functional description of the 62 identified communities in the ATRM: Excel.
  3. Supplementary Table S5. TF numbers in each family in 28 species with genome sequences in PlantTFDB 2.0. By dating the time of emergence based on 28 plants with sequenced genomes, we classified 54 TF families present in the most recent common ancestor (MRCA) of land plants into two types: ancient and novel families. The TF families present in any of the nine green alga species were defined as ancient families (in black), and the TF families present in the MRCA of 19 land plants but absent from the nine green alga species were defined as novel families (in cyan): Excel.
  4. Supplementary Table S8. Correlation between the binding specificities of TFs and their wiring preferences in networks: Excel.