Variability of Betweenness Centrality and Its Effect on Identifying Essential Genes

Durón, Christina; Pan, Yuan; Gutmann, David H.; Hardin, Johanna; Radunskaya, Ami

doi:10.1007/s11538-018-0526-z

Cited by 19 publications

(15 citation statements)

References 37 publications

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“…Among the 3 kinds of nodes, the degree of common genes was found to be significantly higher than other 2 gene types (Figure 1F). BC was defined as the ratio of the shortest path between a pair of nodes passing through a given node 15 . Importantly, the nodes with high BC showed bottleneck of bridges connecting different network modules.…”

Section: Resultsmentioning

confidence: 99%

“…BC was defined as the ratio of the shortest path between a pair of nodes passing through a given node. 15 Importantly, the nodes with high BC showed bottleneck of bridges connecting different network modules. BC values for common genes were found to be significantly higher as compared to the other 2 gene types (Figure 1G).…”

Section: Construction Of Ild-lmn and Topological Characteristic Analysismentioning

confidence: 99%

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Construction and comprehensive analysis of the biological network related to rheumatoid arthritis‐related interstitial lung disease

Zhou

Jia

et al. 2022

Int J of Rheum Dis

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Objective Interstitial lung disease (ILD) is a severe manifestation of rheumatoid arthritis (RA), which is characterized by low survival time post‐diagnosis. Thus, it is important to explore the role of gene regulation related with ILD. Method Constructed a RA‐ILD‐related long chain noncoding RNA – messenger RNA (lncRNA‐mRNA) network (ILD‐LMN), based on ILD‐ and RA‐related genes. We analyzed the topological properties of the resulting network. Result The results for network modularization and functional analysis showed that ILD‐LMN performed basic and specific functions in ILD pathology. Furthermore, differential expression and correlation analysis of hub nodes revealed highly correlated competitive endogenous RNA regulatory relationships with important roles in pathological regulation. Following this, statistical analysis of disease‐related single nucleotide polymorphisms (SNPs) in hub lncRNAs revealed that some of transcription factor‐related SNPs were significantly associated with the expression of lncRNA. In fact, these SNPs exhibited significant differential expression in disease and normal samples. Conclusion These results suggest that ILD‐LMN has important implications in the study of disease. Altogether, the study of RA‐ and ILD‐related lncRNA and genes on the basis of biological network would assist in providing better treatment opportunities for ILD patients. Additionally, it would promote further research on treatment of the disease.

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Section: Resultsmentioning

confidence: 99%

Section: Construction Of Ild-lmn and Topological Characteristic Analysismentioning

confidence: 99%

Construction and comprehensive analysis of the biological network related to rheumatoid arthritis‐related interstitial lung disease

Zhou

Jia

et al. 2022

Int J of Rheum Dis

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“…This measure is calculated based on the number of the shortest paths connecting all pairs of nodes in the network that go through the analyzed node. The high value of betweenness centrality means that the node is a key player or a "bridge" between different parts of a network [29]. Products of the identified genes with the highest betweenness centrality values participate in the regulation of glucose and lipid metabolism (INS, GAPDH, LEP), cell cycle and apoptosis (TP53, MAPK1, STAT3), immune and inflammatory response (IL6, TNF, MMP9), cell proliferation, differentiation, and survival (INS, LEP, EGFR, STAT3).…”

Section: Network Associated With Hyperglycemiamentioning

confidence: 99%

Gene Networks of Hyperglycemia, Diabetic Complications, and Human Proteins Targeted by SARS-CoV-2: What Is the Molecular Basis for Comorbidity?

Saik

Климонтов

2022

IJMS

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People with diabetes are more likely to have severe COVID-19 compared to the general population. Moreover, diabetes and COVID-19 demonstrate a certain parallelism in the mechanisms and organ damage. In this work, we applied bioinformatics analysis of associative molecular networks to identify key molecules and pathophysiological processes that determine SARS-CoV-2-induced disorders in patients with diabetes. Using text-mining-based approaches and ANDSystem as a bioinformatics tool, we reconstructed and matched networks related to hyperglycemia, diabetic complications, insulin resistance, and beta cell dysfunction with networks of SARS-CoV-2-targeted proteins. The latter included SARS-CoV-2 entry receptors (ACE2 and DPP4), SARS-CoV-2 entry associated proteases (TMPRSS2, CTSB, and CTSL), and 332 human intracellular proteins interacting with SARS-CoV-2. A number of genes/proteins targeted by SARS-CoV-2 (ACE2, BRD2, COMT, CTSB, CTSL, DNMT1, DPP4, ERP44, F2RL1, GDF15, GPX1, HDAC2, HMOX1, HYOU1, IDE, LOX, NUTF2, PCNT, PLAT, RAB10, RHOA, SCARB1, and SELENOS) were found in the networks of vascular diabetic complications and insulin resistance. According to the Gene Ontology enrichment analysis, the defined molecules are involved in the response to hypoxia, reactive oxygen species metabolism, immune and inflammatory response, regulation of angiogenesis, platelet degranulation, and other processes. The results expand the understanding of the molecular basis of diabetes and COVID-19 comorbidity.

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“…Firstly and commonly, we used"Degree" to evaluated the interaction between nodes [25]. Secondly,"Betweenness Centrality"was applied to determined the amount of information passing between nodes [26].Thirdly, "Closeness Centrality" re ects the closeness of a node to other nodes [27]. The higher values of this three parameters are, the more important the nodes are.…”

Section: Network Constructionmentioning

confidence: 99%

Investigating the Mechanism of Guizhi Fuling Formula in the Treatment of Primary Dysmenorrhea based on Network Pharmacology and Molecular Docking

Sun

Wang

et al. 2021

Preprint

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Background: Primary dysmenorrhea(PD)is the most common gynecologic disorder.Despite the prevalence is high, it is often underdiagnosed,undertreated and normalized even by patients themselves. Guizhi Fuling Formula (GFF) is experientially used for the treatment of PD in a long time. Therefore, the efficiency and potential mechanism are waiting to identify.Methods: We adopted network pharmacology integrated molecular docking strategy in this study.Based on published literatures, the relative compounds of GFF were selected preliminarily. Secondly, the putative targets of PD were obtained by wide-searching DisGeNET, OMIM, Drugbank and GeneCards databases.With protein-protein interaction(PPI) analysis, GO and KEGG pathway enrichment analysis and molecular docking ,we systematically evaluated the relationship of herb ingredients and disease targets.Results: The results showed that 30 ingredients of GFF and 43 hub targets made a difference.Under the further analysis,8 targets(EGFR,AKT1,PTGS2,TNF,ESR1,AHR,CTNNB1,CXCL8) were recognized as key therapeutic targets with excellent binding. The enrichment analyses indicated that the GFF had the potential to influence varieties of biological pathways, especially the pathways in cancer and steroid hormone biosynthesis, which play an important part in the pathogenesis of primary dysmenorrhea.Conclusion: GFF influenced primary dysmenorrhea through the synergistic effect of multiple components, multiple targets, and multiple pathways.This study predictedthe potential mechanism, hope that could made contribution for clinical application and scientific research.

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Variability of Betweenness Centrality and Its Effect on Identifying Essential Genes

Cited by 19 publications

References 37 publications

Construction and comprehensive analysis of the biological network related to rheumatoid arthritis‐related interstitial lung disease

Construction and comprehensive analysis of the biological network related to rheumatoid arthritis‐related interstitial lung disease

Gene Networks of Hyperglycemia, Diabetic Complications, and Human Proteins Targeted by SARS-CoV-2: What Is the Molecular Basis for Comorbidity?

Investigating the Mechanism of Guizhi Fuling Formula in the Treatment of Primary Dysmenorrhea based on Network Pharmacology and Molecular Docking

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