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Table 3 The number of identified HIF-related TFBSs within an orthologous gene set and a randomly selected gene set

From: Functional pathway mapping analysis for hypoxia-inducible factors

Comparison for HIF orthologous gene set
TF ID HSA MMU GGA CIN DRE XTR # of species possessing the identical TFBS (0.85/0.80/0.75)
V$HIF_STKE_2005 0/0/2 1/1/3 1/1/3 0/0/1 0/0/2 0/0/0 2/2/5
V$HIF1_Q5 1/3/7 2/2/12 1/3/10 2/2/6 1/1/4 0/1/4 5/6/6
V$HIF1_Q3 1/3/10 2/2/12 1/4/9 2/3/7 1/1/4 0/0/11 5/5/6
V$AHRHIF_Q6 5/5/29 3/3/24 5/5/22 6/6/23 3/3/21 2/2/18 6/6/6
Total identified motifs 7/11/48 8/8/51 8/13/44 8/11/37 5/5/31 2/3/33 -
Comparison for a randomly selected gene set
V$HIF_STKE_2005 0/0/1 0/0/0 1/1/4 0/1/2 1/1/2 0/0/0 2/3/4
V$HIF1_Q5 0/0/3 0/0/3 4/5/6 2/2/8 2/3/13 0/1/4 3/4/6
V$HIF1_Q3 0/0/4 0/0/1 4/4/6 2/3/14 2/2/7 0/0/11 3/3/6
V$AHRHIF_Q6 1/1/21 0/0/21 5/5/20 5/5/16 7/7/27 2/2/18 5/5/6
Total identified motifs 1/1/29 0/0/25 14/15/36 9/11/40 12/13/49 2/3/33 -
  1. Comparison of TFBS conservation of the HIF orthologous gene set and a randomly selected gene set with 3 different cut-off values. (Upper half) The orthologous genes were obtained from 6 model species at the “VEGF” node within the HIF pathway (KEGG: Orthology K05448). These genes include ENSG00000119630 (HSA), ENSMUSG00000004791 (MMU), ENSGALG00000010290 (GGA), ENSCING00000014020 (CIN), ENSDARG00000034700 (DRE), and ENSXETG00000016375 (XTR). Three HIF-related TFBSs selected from the TRANSFAC library (V$HIF1_Q3, V$HIF1_Q5, and V$AHRHIF1_Q6) and 1 customized HRE motif (V$HIF_STKE_2005) were employed for scanning through all of the selected genes. Each cell in the table represents the numbers of retrieved TFBSs using 3 different cut-off values of 0.85, 0.80, and 0.75. For example, the V$AHRHIF_Q6 for HSA is 5/5/29, which represents the total number of V$AHRHIF_Q6 motifs that can be identified within the promoter region of the Homo sapiens VEGF gene by setting cut-off values at 0.85, 0.80, and 0.75. (Lower half) A set of genes without an orthologous relationship, randomly selected from 6 species. These genes include ENSG00000001460 (HSA), ENSMUSG00000073489 (MMU), ENSGALG00000000002 (GGA), ENSCING00000002344 (CIN), ENSDARG00000000086 (DRE), and ENSXETG00000016375 (XTR). Regarding the HIF function, most of the orthologous genes from various species indeed contain HIF TFBSs; however, they are sparsely distributed within the randomly selected genes. The rightmost columns also reflect the fact that the total number of species possessing identical HIF TFBSs is relatively higher within the orthologous gene set, since they are expected to retain HIF functional characteristics through the evolutionary process of speciation. HSA, H. sapiens; MMU, M. musculus; GGA, G. gallus; DRE, D. rerio; XTR, X. tropicalis; CIN, C. intestinalis