Additional file 1.

Figure S1. The concepts of AtPAN. Figure S2. Output example of "TFBSs drawing tool" in AtPAN. Figure S3. Output example of "Cross Species" analysis in AtPAN. Figure S4. TFBSs of AtbZIP2, AtbZIP44, and EDF4 identified in ProDG (At3G30775.1) promoter region. The blue background indicates that the TFBSs are discovered in the conserved region between homologous gene promoters. Figure S5. Promoter and TRNs analysis results of PDF1.2 (LCR77) and PR4 (HEL) by AtPAN. (A)AtERF1 co-occur in both promoter sequences; in addition, the TFBSs are displayed. (B) co-expression TRNs of PR4 genes, both MYC2 and ERF1 are identified in the network.

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Chen et al. BMC Genomics 2012 13:85   doi:10.1186/1471-2164-13-85