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. 2021 May 14;20:100097. doi: 10.1016/j.mcpro.2021.100097

Table 3.

Cis-acting regulatory element analysis of upstream 1500-bp promoter region of genes encoding differentially accumulated proteins in Ay-integrated lines

Element name No. of cluster 1
 No. of cluster 2
 No. of background
 p-value (Fisher’s exact test)
 Function category
Total Mean Total Mean Total Mean Cluster 1 versus background 1 Cluster 2 versus background 1 Cluster 1 versus cluster 2
Cluster 1 enriched cis-element sites
 TATA-box 1504 15.67 2274 15.79 12,265 13.72 0 0 0.129 Promoter-related elements
 WUN-motif 35 0.36 30 0.21 186 0.21 0.006 0.921 0.043 Environmental stress–related elements
 G-box 308 3.21 336 2.33 2410 2.7 0.013 0.024 0 Light-responsive elements
 G-Box 117 1.22 121 0.84 852 0.95 0.027 0.281 0.012 Light-responsive elements
 Box 4 73 0.76 69 0.48 457 0.51 0.004 0.751 0.013 Light-responsive elements
 GATT-motif 5 0.05 1 0.01 9 0.01 0.009 1 0.045 Light-responsive elements
 ABRE 454 4.73 400 2.78 3109 3.48 0 0 0 Hormone-responsive elements
 P-box 37 0.39 37 0.26 225 0.25 0.029 0.857 0.124 Hormone-responsive elements
Cluster 2 enriched cis-element sites
 CAAT-box 1823 18.99 2888 20.06 16,178 18.1 0.263 0 0 Promoter-related elements
 AT-rich element 7 0.07 16 0.11 55 0.06 0.67 0.037 0.397 Site binding–related elements
 GT1-motif 45 0.47 91 0.63 445 0.5 0.649 0.032 0.066 Light-responsive elements
 Pc-CMA2c 1 0.01 5 0.03 6 0.01 0.518 0.011 0.411 Light-responsive elements
 AuxRR-core 10 0.1 27 0.19 104 0.12 0.875 0.029 0.095 Hormone-responsive elements
Non-DAPs enriched cis-element sites
 Motif I 9 0.09 1 0.01 46 0.05 0.113 0.017 0.002 Development-related elements
 Circadian 6 0.06 4 0.03 111 0.12 0.088 0.001 0.335 Development-related elements
 MBS 72 0.75 68 0.47 579 0.65 0.323 0.018 0.012 Environmental stress–related elements
 GC motif 58 0.6 75 0.52 673 0.75 0.081 0.003 0.537 Environmental stress–related elements
 Sp1 70 0.73 105 0.73 1107 1.24 0 0 0.817 Light-responsive elements
 3-AF1 binding site 0 0 4 0.03 34 0.04 0.045 0.813 0.15 Light-responsive elements
 A-box 63 0.66 113 0.78 875 0.98 0.001 0.041 0.167 Hormone-responsive elements

Fisher’s exact test was applied for statistical analysis, and only those known functions and significantly changed sites are included in this table. The detailed cis-element information of each gene and full summary table are listed in supplemental Table S6.