Table 2. Characteristics of the 17 SEG-MS1 clusters.
| Characteristics of the 17 SEG-MS1 clusters | |||||||
|---|---|---|---|---|---|---|---|
| Cluster | Gene loci (TAIR10) | Number of genes | Number of GOIs | Length (kb) | Atted-II P-value | Rsat k-mer motifs | Orthologous genes in cluster |
| #1 | At1g04880-920 | 5 | 3 | 19.8 | 0.946 | 0 | - |
| #2 | At1g06250-280 | 4 | 3 | 7.7 | 0.370 | 0 | - |
| #3 | At1g20120-150 | 6 | 3 | 15 | 0.977 | 0 | Yes |
| #4 | At1g22100-150 | 6 | 4 | 24 | 0.544 | 1 | - |
| #5 | At1g23510-690 | 17 | 8 | 37.3 | 0.431 | 0 | Yes |
| #6 | At1g51240-260 | 3 | 3 | 5.1 | 0.895 | 0 | Yes |
| #7 | At1g75910-940 | 4 | 3 | 12.9 | 0.388 | 0 | - |
| #8 | At2g47030-050 | 3 | 3 | 8.4 | 0.061* | 0 | Yes |
| #9 | At3g01230-270 | 5 | 4 | 8.2 | 0.598 | 0 | - |
| #10 | At3g07820-850 | 4 | 4 | 11 | 0.316 | 0 | Yes |
| #11 | At3g13220-229 | 8 | 3 | 22 | 0.952 | 0 | - |
| #12 | At3g26860-880 | 3 | 3 | 5.2 | 0.301 | 1 | - |
| #13 | At3g28780-840 | 6 | 6 | 34 | 0.079* | 0 | Yes |
| #14 | At5g07410-430 | 3 | 3 | 8.4 | 0.330 | 0 | - |
| #15 | At5g07490-560 | 8 | 7 | 21 | 0.330 | 1 | - |
| #16 | At5g45810-840 | 4 | 3 | 13 | 0.381 | 0 | - |
| #17 | At5g46940-700 | 7 | 5 | 12.1 | 0.440 | 0 | Yes |
Loci, refers to the A. thaliana accession numbers. Number of genes, number of genes in total in each cluster. Number of GOIs, number of genes-of-interest in each cluster. Length, the physical genomic distance from one end of the cluster to the other end of the cluster, measured in kilobases (kb). Atted-II P-value, the probability of finding a an average pairwise promoter similarity score equal to or larger than the observed one in the cluster (P-values are estimated from simulations), using Atted-II regulatory motifs, and where values marked with (*) indicate nominally significant at alpha <0.1. Rsat k-mer motifs, the number of overrepresented k-mer motifs present in the promoter regions of all GOIs in the cluster. Orthologous genes in cluster, whether the OrthoMCL-based gene orthology analysis revealed that orthologous genes were present in the cluster (see Supplemental Figure S3 for details). GOI, gene of interest.