Functional pathway mapping analysis for hypoxia-inducible factors

BMC Systems Biology

Table 2 Identification of HRE motifs for HIF orthologous target genes

Model Species	HIF orthologous target genes (KEGG: Orthology K05448)
HSA	ENSG00000119630 GGCAGGCGTG CAGACTCA Loc:-963~-946 TGTGTCCGTG CCTGGCTA Loc:-1392~-1375 GCCCCTCGTG GGTGGGCA Loc:-628~-611	ENSG00000112715 TGAGGACGTG TGTGTCTG Loc:-517~-500 TGCATACGTG GGCTCCAA Loc:-982~-965 TGTGTGCGTG TGGGGTTG Loc:-485~-468	ENSG00000173511 CGAGATCGTG CCCCGGGG Loc:-641~-624 GGAGCGCGTG TCTGGGTC Loc:-277~-260 CTCACGCGTG CCACGGAG Loc:-1601~-1584
MMU	ENSMUSG00000004791 TGAGCACGTG TGGATCCT Loc:-542~-525 CCAATCCGTG TGTGCTCA Loc:-204~-187 ATGTCACGTG AAATGACG Loc:-122~-105	ENSMUSG00000023951 TGCATACGTG GGTTTCCA Loc:-1082~-1065 AGTCTGCGTG AGGGAGGA Loc:-1538~-1521 TGAGTGCGTG CATGCATG Loc:-1570~-1553	ENSMUSG00000024962 TCCCCTCGTG AGGCAGCG Loc:-1799~-1782 ACTACACGTG CAATAAAC Loc:-1726~-1709 GTCAAGCGTG CTGAGGCC Loc:-287~-270
GGA	ENSGALG00000010290 CCCCGACGTG CGGAGCGG Loc:-1970~-1953 TGGCACCGTG CTGGAATA Loc:-143~-126 CCCCATCGTG CAGCCCCA Loc:-208~-191	N/A	N/A
DRE	ENSDARG00000034700 CCTGTACGTG GTGATGGA Loc:-997~-980 TATCGTCGTG TTGTGATT Loc:-1106~-1089 TTAAACCGTG TGCGCTGC Loc:-55~-38	N/A	N/A
XTR	ENSXETG00000016375 TGTCTCCGTG TAATCGCG Loc:-1289~-1272 TAATCGCGTG CTGATAAC Loc:-1273~-1262	N/A	N/A
CIN	ENSCING00000014020 CAGATACGTG ATCTTGGT Loc:--1977~-1960 TTACGACGTG GACATTCC Loc:-1475~-1458 CGCCATCGTG CGAAGGCA Loc:-150~-133	N/A	N/A

The locations of HRE motifs were detected within the HIF orthologous genes for 6 model species (the PSSM pattern of V$HIF_STKR_2005 and the core segment “CGTG” pattern were required to exactly match and shown in bold and underline). The regions were identified within 2,000 base pairs upstream of the orthologous gene set of KEGG: Orthology K05448 (VEGFA_B); only the first 3 detected HREs are shown here. The Ensembl gene IDs are shown on the top of each identified HRE motif. Only 2 HRE motifs were found in XTR within the assigned promoter region. HSA, H. sapiens; MMU, M. musculus; GGA, G. gallus; DRE, D. rerio; XTR, X. tropicalis; CIN, C. intestinalis

ISSN: 1752-0509