PMID- 33868803
OWN - NLM
STAT- PubMed-not-MEDLINE
LR  - 20220422
IS  - 2167-8359 (Print)
IS  - 2167-8359 (Electronic)
IS  - 2167-8359 (Linking)
VI  - 9
DP  - 2021
TI  - A structural analysis of the hypoxia response network.
PG  - e10985
LID - 10.7717/peerj.10985 [doi]
LID - e10985
AB  - BACKGROUND: The hypoxia-inducible factor-1 (HIF-1) signaling pathway is an 
      important topic in high-altitude medicine. Network analysis is a novel method for 
      integrating information on different aspects and levels of biological networks. 
      However, this method has not been used in research on the HIF-1 signaling pathway 
      network. To introduce this method into HIF-1-related research fields and verify 
      its feasibility and effectiveness, we used a network analytical method to explore 
      the structural attributes of the HIF-1 signaling pathway network. METHODS: First, 
      we analyzed the overall network of the HIF-1 signaling pathway using information 
      retrieved from the Kyoto Encyclopedia of Genes and Genomes (KEGG). We performed 
      topology analysis, centrality analysis, and subgroup analysis of the network. 
      Then, we analyzed the core network based on the overall network analysis. We 
      analyzed the properties of the topology, the bow-tie structure, and the 
      structural complexity of the core network. RESULTS: We obtained topological 
      structure diagrams and quantitative indicators of the overall and core networks 
      of the HIF-1 signaling pathway. For the structure diagrams, we generated topology 
      diagrams of the network and the bow-tie structure of the core network. As 
      quantitative indicators, we identified topology, centrality, subgroups, the 
      bow-tie structure, and structural complexity. The topology indicators were the 
      number of nodes, the number of lines, the network diameter, and the network 
      density. The centrality indicators were the degree, closeness, and betweenness. 
      The cohesive subgroup indicator was the components of the network. The bow-tie 
      structure indicators included the core, input, and tendril-like structures. The 
      structural complexity indicators included a power-law fitting model and its scale 
      parameter. CONCLUSIONS: The core network could be extracted based on the subgroup 
      analysis of the overall network of the HIF-1 signaling pathway. The critical 
      elements of the network could be identified in the centrality analysis. The 
      results of the study show the feasibility and effectiveness of the network 
      analytical method used to explore the network properties of the HIF-1 signaling 
      pathway and provide support for further research.
CI  - (c)2021 Li et al.
FAU - Li, Jianjie
AU  - Li J
AD  - Department of Health Service, Army Medical University, Chongqing, Shapingba, 
      China.
FAU - Gao, Yuqi
AU  - Gao Y
AD  - Institute of Medicine and Hygienic Equipment for High Altitude Region, Army 
      Medical University, Chongqing, Shapingba, China.
FAU - Yu, Xuan
AU  - Yu X
AD  - Department of Health Service, Army Medical University, Chongqing, Shapingba, 
      China.
LA  - eng
PT  - Journal Article
DEP - 20210406
PL  - United States
TA  - PeerJ
JT  - PeerJ
JID - 101603425
PMC - PMC8034363
OTO - NOTNLM
OT  - Bow-tie structure
OT  - Complex networks
OT  - Network topology
OT  - Structural complexity
OT  - Hypoxia response network
COIS- The authors declare there are no competing interests.
EDAT- 2021/04/20 06:00
MHDA- 2021/04/20 06:01
PMCR- 2021/04/06
CRDT- 2021/04/19 06:29
PHST- 2020/06/26 00:00 [received]
PHST- 2021/01/31 00:00 [accepted]
PHST- 2021/04/19 06:29 [entrez]
PHST- 2021/04/20 06:00 [pubmed]
PHST- 2021/04/20 06:01 [medline]
PHST- 2021/04/06 00:00 [pmc-release]
AID - 10985 [pii]
AID - 10.7717/peerj.10985 [doi]
PST - epublish
SO  - PeerJ. 2021 Apr 6;9:e10985. doi: 10.7717/peerj.10985. eCollection 2021.