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Table 4 The number of identified HIF-related TFBSs within a paralogous gene set and a randomly selected gene set of zebrafish species

From: Functional pathway mapping analysis for hypoxia-inducible factors

Comparison for the paralogous genes
TF ID KEGG dre30682 KEGG dre403049 KEGG dre678512 # of gene possessing the identical TFBS (0.85/0.80/0.75)
V$HIF_STKE_2005 0/0/2 0/0/0 0/0/2 0/0/2
V$HIF1_Q5 1/1/4 0/0/3 2/3/3 2/2/3
V$HIF1_Q3 1/1/4 0/0/2 2/3/5 2/2/3
V$AHRHIF_Q6 3/3/21 0/0/15 4/4/30 2/2/3
Total identified motifs 5/5/31 0/0/20 8/10/40 -
Comparison for randomly selected genes
  G1 G2 G3  
V$HIF_STKE_2005 0/0/1 0/0/0 0/0/0 0/0/1
V$HIF1_Q5 1/1/5 0/0/0 0/0/4 1/1/2
V$HIF1_Q3 1/1/9 0/0/1 0/0/3 1/1/3
V$AHRHIF_Q6 3/3/25 0/0/13 1/1/21 2/2/3
Total identified motifs 5/5/40 0/0/14 1/1/28 -
  1. Comparison of TFBS conservation of the HIF paralogous gene set and a randomly selected gene set from the zebrafish (DTR) with 3 different cut-off values. (Upper half) The paralogous genes were obtained from the “VEGF” node within the HIF pathway. These genes include ENSDARG00000034700 (KEGG: dre30682), ENSDARG00000069640 (KEGG: dre403049), and ENSDARG00000056624 (KEGG: dre678512). The selected HIF TFBS patterns are the same as those in Table 3. Each cell in the table represents the number of retrieved TFBSs using 3 different cut-off values of 0.85, 0.80, and 0.75. For example, the V$AHRHIF_Q6 for the first DTR gene (ENSDARG00000034700) is 3/3/21 which represents the total number of V$AHRHIF_Q6 motifs can be identified within the promoter region (2,000 base pairs) of the Danio rerio VEGF gene by setting cut-off values of 0.85, 0.80, and 0.75. (Lower half) A set of genes without a paralogous relationship, randomly selected from zebrafish. These genes include ENSDARG00000040535 (G1), ENSDARG00000068465 (G2), and ENSDARG00000010610 (G3). Regarding the HIF function, most of the paralogous genes from a given node in the HIF functional pathway contain the corresponding HIF TFBSs but appeared less frequently in the randomly selected genes. The rightmost columns also reflect the tendency that the total number of gene possessing identical HIF TFBSs is relatively higher within the paralogous gene set since they might retain HIF functional characteristics through the evolutionary process of gene duplication.