Additional file 16: of Comparative analysis of binding patterns of MADS-domain proteins in Arabidopsis thaliana

Table S8. Number of CArG-boxes with and without mutations. Note that the CArG-boxes in this table all match to the motif of AG because these CArG-boxes were used for all mutation analyses. The total number of CArG-boxes therefore differs from that in Additional file 5: Table S4. (PDF 47 kb

Additional file 2: of Comparative analysis of binding patterns of MADS-domain proteins in Arabidopsis thaliana

Table S2. Number of peaks in original analysis and after re-analysis. (PDF 45 kb

Additional file 7: of Comparative analysis of binding patterns of MADS-domain proteins in Arabidopsis thaliana

Figure S2. CArG-box like motifs in unique peaks in PI, SEP3 and SOC1 datasets. Logo representation of all matches to the motif found by MEME. Logos are from (A) PI (B) SEP3 (C) SOC1. (PDF 126 kb

Additional file 8: of Comparative analysis of binding patterns of MADS-domain proteins in Arabidopsis thaliana

Figure S3. Central enrichment of different CArG-box variants in different protein datasets. Kernel density plot of matches to the motif in peak centers relative to the peak summit. Plots are from (A) AG (B) AP1 (C) AP3 (D) FLC (E) PI (F) SEP3 (G) SOC1 (H) SVP. (PDF 251 kb

Additional file 11: of Comparative analysis of binding patterns of MADS-domain proteins in Arabidopsis thaliana

Figure S5. G-box like motifs. Logo representation of all matches to the motifs found by MEME. Datasets are from (A) AG (B) AP3 (C) PI (D) SEP3 (E) SVP. (PDF 81 kb

Additional file 3: of Comparative analysis of binding patterns of MADS-domain proteins in Arabidopsis thaliana

Figure S1. Clustering of original peak sets and peaks sets after re-analysis. Hierarchical clustering with complete linkage (function hclust in R) was performed using as distance measure between two peak sets the average distance between peaks in one set and in the other. Peaks-sets after re-analysis are indicated with name of the transcription factor, original peak sets are indicated with the suffix “orig”. (PDF 38 kb

Additional file 15: of Comparative analysis of binding patterns of MADS-domain proteins in Arabidopsis thaliana

Table S7. Top 5 most occurring extensions on the 5′ side and the 3′ side of the CArG-box and the top 5 combinations of 5′ and 3′ extensions. CArG-boxes were defined de novo by MEME-ChIP as described in the Material and Methods section. For each CArG-box like sequence, positions 1 and 10 were defined by comparing the sequence to the canonical CArG-box (CC(A/T)6GG. Position 1 was defined as the position that corresponds to the first C in the canonical CArG-box and position 10 was defined as the position that corresponds to the last G in the canonical CArG-box. Also, the strand defined by MEME-ChIP was taken to distinguish the 5′ and the 3′ sides. Subsequently, the three nucleotides on the 5′ side of position 1 and on the 3′ side of position 10 were counted for each CArG-box. The top 5 most occurring extensions and extension combinations were defined for (A) AG, (B) AP1, (C) AP3, (D) FLC, (E) PI, (F) SEP3, (G) SOC1 and (H) SVP. (PDF 95 kb

Additional file 13: of Comparative analysis of binding patterns of MADS-domain proteins in Arabidopsis thaliana

Figure S7. Central enrichment of G-boxes and TCP class I and II. Kernel density plot showing positions in peak centers relative to the peak summit of matches to the G-box (CACGTG) and the motifs for TCP class I (GGNCCCAC) and class II (GGGNCC(A/G)C) in (A) AG; (B) AP1; (C) AP3; (D) FLC; (E) PI; (F) SEP3; (G) SOC1 and (H) SVP. (PDF 232 kb

Additional file 6: of Comparative analysis of binding patterns of MADS-domain proteins in Arabidopsis thaliana

Table S5. Unique and overlapping peak centers in each dataset. A peak center is defined as the region 250 bp upstream and downstream of a peak summit. (PDF 52 kb

Additional file 10: of Comparative analysis of binding patterns of MADS-domain proteins in Arabidopsis thaliana

Figure S4. GA/CT-rich motif. Logo representation of all matches to the motifs found by MEME. Datasets are from (A) AG (B) AP1 (C) AP3 (D) PI (E) SEP3 (F) SOC1. (PDF 122 kb