Introduction
Materials and methods
Cell culture
Hypoxic cell culture
In vitro tube formation assay
Transfection with si-RNA
RNA isolation and genome-wide RNA-sequencing
Quantitative real-time PCR
Tube formation screening
Statistical analysis
Results
HIF-2α regulates endothelial sprouting in prolonged hypoxia
Identifying oxygen-regulated genes and pathways
All genes (834) | Upregulated genes (501) | Downregulated genes (333) |
---|---|---|
HIF-1 signaling pathway(5.7E−07)
| Cytokine–cytokine receptor interaction(3.8E−06)
| Cell cycle(5.8E−07)
|
p53 signaling pathway(9.3E−06)
| Glycolysis/gluconeogenesis(7.7E−05)
| p53 signaling pathway(1.0E−05)
|
Cytokine–cytokine receptor interaction(1.1E−04)
| HIF-1 signaling pathway(1.6E−04)
| HIF-1 signaling pathway(1.4E−03)
|
Cell cycle(3.1E−04)
| Biosynthesis of amino acids(2.3E−04)
| Glycine, serine and threonine metabolism(3.4E−03)
|
Biosynthesis of amino acids(4.1E−04)
| TNF signaling pathway(8.9E−02)
| Homologous recombination(9.0E−03)
|
Glycolysis/gluconeogenesis(5.5E−04)
| Inflammatory mediator regulation of TRP channels(1.7E−03)
| Arginine and proline metabolism(1.3E−02)
|
Inflammatory mediator regulation of TRP channels(1.2E−03)
| Carbon metabolism(2.8E−03)
| VEGF signaling pathway(1.5E−02)
|
Cysteine and methionine metabolism(2.7E−03)
| Calcium signaling pathway(2.8E−03)
| DNA replication(1.8E−02)
|
FoxO signaling pathway(2.9E−03)
| Pentose phosphate pathway(3.0E−03)
| Biosynthesis of unsaturated fatty acids(4.4E−02)
|
TNF signaling pathway(3.2E−03)
| Hedgehog signaling pathway(6.3E−03)
| |
Glycine, serine and threonine metabolism(4.0E−03)
| Fructose and mannose metabolism(6.4E−03)
| |
Proteoglycans in cancer(6.1E−03)
| FoxO signaling pathway(7.5E−03)
| |
Carbon metabolism(7.1E−03)
| Cysteine and methionine metabolism(9.8E−03)
| |
Pentose phosphate pathway(1.8E−02)
| Neuroactive ligand–receptor interaction(1.2E−02)
| |
Calcium signaling pathway(2.1E−02)
| Galactose metabolism(3.3E−02)
| |
Arginine and proline metabolism(2.5E−02)
| Proteoglycans in cancer(3.4E−02)
| |
VEGF signaling pathway(2.9E−02)
| TGF-beta signaling pathway(3.5E−02)
| |
Rap1 signaling pathway(3.3E−02)
| MAPK signaling pathway(3.6E−02)
| |
Fructose and mannose metabolism(3.6E−02)
| NOD-like receptor signaling pathway(4.3E−02)
| |
Cell adhesion molecules (CAMs)(4.4E−02)
| Glycosaminoglycan biosynthesis—keratan sulfate(4.7E−02)
| |
Hedgehog signaling pathway(4.7E−02)
| Apoptosis(4.8E−02)
| |
Protein digestion and absorption(3.8E−02)
|
Identifying HIF-2α-regulated genes and pathways
All genes (1164) | Upregulated genes (449) | Downregulated genes (715) |
---|---|---|
Carbon metabolism(5.7E−04)
| Ribosome biogenesis in eukaryotes(4.1E−03)
| Fatty acid metabolism(4.0E−05)
|
Biosynthesis of unsaturated fatty acids(8.2E−04) | Vitamin B6 metabolism (6.1E−03)
| Biosynthesis of unsaturated fatty acids(6.6E−05)
|
Fatty acid metabolism(1.3E−03)
| MAPK signaling pathway(6.6E−03)
| Metabolic pathways(9.4E−05)
|
Citrate cycle (TCA cycle)(4.1E−03)
| RNA transport(3.9E−02)
| Carbon metabolism(2.6E−04)
|
MAPK signaling pathway(4.1E−03)
| Cell cycle(4.1E−02)
| PPAR signaling pathway(2.7E−03)
|
Metabolic pathways(7.5E−03)
| Estrogen signaling pathway(4.5E−02)
| Citrate cycle (TCA cycle)(2.7E−03)
|
GnRH signaling pathway(9.5E−03)
| Regulation of actin cytoskeleton(7.3E−03)
| |
p53 signaling pathway(1.1E−02)
| p53 signaling pathway(8.6E−03)
| |
Oxytocin signaling pathway(1.2E−02)
| Axon guidance(1.2E−03)
| |
Sphingolipid metabolism(1.5E−02)
| Osteoclast differentiation(1.2E−02)
| |
cGMP-PKG signaling pathway(1.6E−02)
| Focal adhesion(1.3E−02)
| |
Axon guidance(2.1E−02)
| Ether lipid metabolism(1.3E−02)
| |
Vascular smooth muscle contraction(2.8E−02)
| Ribosome(1.6E−02)
| |
Glycerophospholipid metabolism(3.2E−02)
| Fatty acid degradation(1.7E−02)
| |
Propanoate metabolism(3.2E−02)
| Valine, leucine and isoleucine degradation(1.9E−02)
| |
Valine, leucine and isoleucine degradation(3.6E−02)
| Sphingolipid metabolism(2.4E−02)
| |
PPAR signaling pathway(3.7E−02)
| Propanoate metabolism(2.5E−02)
| |
Vitamin B6 metabolism(4.1E−02)
| Starch and sucrose metabolism(3.1E−02)
| |
Wnt signaling pathway(4.1E−02)
| GnRH signaling pathway(3.4E−02)
| |
Osteoclast differentiation(4.4E−02)
| Endocytosis(4.1E−02)
| |
VEGF signaling pathway(4.7E−02)
| Oxytocin signaling pathway(4.4E−02)
| |
Pantothenate and CoA biosynthesis(4.9E−02)
| Sulfur metabolism(4.7E−02)
| |
Ras signaling pathway(4.8E−02)
| ||
Ubiquitin-mediated proteolysis(4.8E−02)
|