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Table 4 Plant transcription factor binding sites significantly ( P <0.05) overrepresented in the promoters of HD-Zip genes belonging to each of the subfamilies

From: Comprehensive characterization and RNA-Seq profiling of the HD-Zip transcription factor family in soybean (Glycine max) during dehydration and salt stress

  Motif # 1TFBS 2Count 3Proportion 4TFBS_Dehydration 5TFBS_Salt 6TF_Class 7DE_Dehydration 8DE_Salt
HD-Zip I M00354 Dof3 33 91.7 - - Dof + +
  M00700 ROM 31 86.1 + - bZIP + +
  M01136 Dof 29 80.6 - - Dof + +
  M00353 Dof2 27 75.0 - - Dof + +
9HD-Zip II M00479 Alfin1 21 91.3 - - PHD + +
  M01136 Dof 20 87.0 - - Dof + +
  M00354 Dof3 19 82.6 - - Dof + +
  M00440 CG1 18 78.3 - - CAMTA + +
  M00506 LIM1 18 78.3 - - LIM - +
  M00502 TEIL 17 73.9 - + 10AP2-EREBP + +
  M00653 OCSBF-1 17 73.9 + + bZIP + +
  M00788 EmBP-1b 17 73.9 + + bZIP + +
  M01128 SED 17 73.9 - - DOF + +
  M00942 CPRF-1 16 69.6 + - bZIP + +
  M00948 PCF2 16 69.6 + - TCP + +
  M00443 Opaque-2 14 60.9 + + bZIP + +
  M01133 AG 14 60.9 - - MADS + +
  M00660 RITA-1 13 56.5 + + bZIP + +
  M01130 PBF 13 56.5 - - Dof + +
  M01054 bHLH66 12 52.2 + + bHLH + +
  M00503 ATHB-5 11 47.8 + - HD-Zip I + +
  M00434 PIF3 10 43.5 + + bHLH + +
HD-Zip III M00479 Alfin1 10 90.9 - - PHD + +
  M00438 ARF 9 81.8 - - ARF + +
  M01021 ID1 9 81.8 + - C2H2 - zinc + +
  M01126 BPC1 8 72.7 - - BBR/BPC - -
  M00948 PCF2 7 63.6 + - TCP + +
  11M00151 AG 7 63.6 - - MADS + +
  M00820 HAHB-4 6 54.5 - - HD-Zip I + +
  12M01061 AGL2 6 54.5 - - MADS + +
  M00392 AGL3 5 45.5 - - MADS + +
  M00949 AGL15 5 45.5 - - MADS + +
HD-Zip IV 13M00355 PBF 29 96.7 + - Dof + +
  M00438 ARF 25 83.3 - - ARF + +
  M01126 BPC1 25 83.3 - - BBR/BPC - -
  M01136 Dof 25 83.3 - - Dof + +
  M01128 SED 23 76.7 - - DOF + +
  M01021 ID1 22 73.3 + - C2H2 - zinc + +
  M00702 SPF1 20 66.7 - + 10WRKY + +
  M00654 OSBZ8 15 50.0 + + bZIP + +
  M00089 Athb-1 11 36.7 + - HD-Zip I + +
  1. 1TFBS: Transcription factor binding site (TFBS) significantly (P <0.05, motif score >5) overrepresented in the promoters of HD-Zip genes.
  2. 2Count: Number of HD-Zip genes within a subfamily that contain the TFBS significantly overrepresented in their promoters.
  3. 3Proportion: Percentage of HD-Zip genes within a subfamily that contain the TFBS overrepresented in their promoters.
  4. 4TFBS_Dehydration: " + " indicates that the respective TFBS is overrepresented in the promoters of genes that were differentially expressed under dehydration stress, and "-" represents not overrepresented.
  5. 5TFBS_Salt: " + " indicates that the respective TFBS is overrepresented in the promoters of genes that were differentially expressed under salt stress, and "-" represents not overrepresented.
  6. 6TF_Class: The membership of TFBS to a particular transcription factor (TF) class based on TRANSFAC [72] and UniprotKB [134].
  7. 7DE_Dehydration: " + " indicates members of the respective TF class are differentially expressed (DE) under dehydration stress, and “-” indicates otherwise.
  8. 8DE_Salt: " + " indicates members of the respective TF class are DE under salt stress, and “-” indicates otherwise.
  9. 9Although the HD-Zip II subfamily has 24 genes, the proportion is calculated using 23 genes. HD-Zip II gene Glyma05g23150 was excluded from the promoter analysis due to the selection criteria utilized (see methods for promoter selection criteria).
  10. 10TF class significantly (corrected P <0.05) overrepresented in the DE genes under dehydration and salt stress.
  11. 11AG TFBS has multiple motif identifiers - M00151, M01063, M01133, and M00950. Counts of AG TFBS’s irrespective of the identifier# were summed to estimate total count and proportion.
  12. 12AGL2 TFBS has two motif identifiers - M01061 and M01062. Counts of AGL2 TFBS’s irrespective of the identifier# were summed to estimate total count and proportion.
  13. 13PBF TFBS has two motif identifiers - M00355 and M01130. Counts of PBF TFBS’s irrespective of the identifier# were summed to estimate total count and proportion.