Comparative analysis of aneurysm subtypes associated genes based on protein–protein interaction network

AbstractThe arterial aneurysm refers to localized dilation of blood vessel wall and is common in general population. The majority of aneurysm cases remains asymptomatic until a sudden rupture which is usually fatal and of extremely high mortality (~ 50–60%). Therefore, early diagnosis, prevention and management of aneurysm are in urgent need. Unfortunately, current understanding of disease driver genes of various aneurysm subtypes is still limited, and without appropriate biomarkers and drug targets no specialized drug has been developed for aneurysm treatment. In this research, aneurysm subtypes were analyzed based on protein–protein interaction network to better understand aneurysm pathogenesis. By measuring network-based proximity of aneurysm subtypes, we identified a relevant closest relationship between aortic aneurysm and aortic dissection. An improved random walk method was performed to prioritize candidate driver genes of each aneurysm subtype. Thereafter, transcriptomes of 6 human aneurysm subtypes were collected and differential expression genes were identified to further filter potential driver genes. Functional enrichment of above driver genes indicated a general role of ubiquitination and programmed cell death in aneurysm pathogenesis. Especially, we further observed participation of BCL-2-mediated apoptosis pathway and caspase-1 related pyroptosis in the development of cerebral aneurysm and aneurysmal subarachnoid hemorrhage in corresponding transcriptomes.

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Network Pharmacology study of Curcuma longa L.: Potential Target Proteins and their Functional Enrichment Analysis.

10.21203/rs.3.rs-31985/v2 ◽

2020 ◽

Author(s):

SANGEETA KUMARI

Keyword(s):

Signaling Pathway ◽

Mechanism Of Action ◽

Protein Interaction ◽

Protein Interaction Network ◽

Curcuma Longa ◽

Interaction Network ◽

Functional Enrichment ◽

Target Proteins ◽

Protein Protein Interaction ◽

Protein Protein Interaction Network

Abstract Objective This study’s primary goal is unraveling the mechanism of action of bioactives of Curcuma longa L. at the molecular level using protein-protein interaction network.Results We used target proteins to create protein-protein interaction network (PPIN) and identified significant node and edge attributes of PPIN. We identified the cluster of proteins in the PPIN, which were used to identify enriched pathways. . We identified closeness centrality and jaccard score as most important node and edge attribute of the PPIN respectively. The enriched pathways of various clusters were overlapped suggesting synergistic mechanism of action. The three pathways found to be common among three clusters were Gonadotropin-releasing hormone receptor pathway, Endothelin signaling pathway, and Inflammation mediated by chemokine and cytokine signaling pathway.

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Control Analysis of Protein-Protein Interaction Network Reveals Potential Regulatory Targets for MYCN

Frontiers in Oncology ◽

10.3389/fonc.2021.633579 ◽

2021 ◽

Vol 11 ◽

Author(s):

Chunyu Pan ◽

Yuyan Zhu ◽

Meng Yu ◽

Yongkang Zhao ◽

Changsheng Zhang ◽

...

Keyword(s):

Protein Interaction ◽

Protein Interaction Network ◽

Regulatory Network ◽

Interaction Network ◽

Control Analysis ◽

Potential Drug ◽

Driver Genes ◽

Protein Protein Interaction ◽

Protein Protein Interaction Network ◽

Network Controllability

BackgroundMYCN is an oncogenic transcription factor of the MYC family and plays an important role in the formation of tissues and organs during development before birth. Due to the difficulty in drugging MYCN directly, revealing the molecules in MYCN regulatory networks will help to identify effective therapeutic targets.MethodsWe utilized network controllability theory, a recent developed powerful tool, to identify the potential drug target around MYCN based on Protein-Protein interaction network of MYCN. First, we constructed a Protein-Protein interaction network of MYCN based on public databases. Second, network control analysis was applied on network to identify driver genes and indispensable genes of the MYCN regulatory network. Finally, we developed a novel integrated approach to identify potential drug targets for regulating the function of the MYCN regulatory network.ResultsWe constructed an MYCN regulatory network that has 79 genes and 129 interactions. Based on network controllability theory, we analyzed driver genes which capable to fully control the network. We found 10 indispensable genes whose alternation will significantly change the regulatory pathways of the MYCN network. We evaluated the stability and correlation analysis of these genes and found EGFR may be the potential drug target which closely associated with MYCN.ConclusionTogether, our findings indicate that EGFR plays an important role in the regulatory network and pathways of MYCN and therefore may represent an attractive therapeutic target for cancer treatment.

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Network pharmacology study of Curcuma longa L.: potential target proteins and their functional enrichment analysis

BMC Research Notes ◽

10.1186/s13104-020-05301-0 ◽

2020 ◽

Vol 13 (1) ◽

Author(s):

Sangeeta Kumari ◽

Hosahalli S. Subramanya

Keyword(s):

Signaling Pathway ◽

Mechanism Of Action ◽

Protein Interaction ◽

Protein Interaction Network ◽

Curcuma Longa ◽

Interaction Network ◽

Functional Enrichment ◽

Target Proteins ◽

Protein Protein Interaction ◽

Protein Protein Interaction Network

Abstract Objective This study’s primary goal is unraveling the mechanism of action of bioactives of Curcuma longa L. at the molecular level using protein–protein interaction network. Results We used target proteins to create protein–protein interaction network (PPIN) and identified significant node and edge attributes of PPIN. We identified the cluster of proteins in the PPIN, which were used to identify enriched pathways. We identified closeness centrality and jaccard score as most important node and edge attribute of the PPIN respectively. The enriched pathways of various clusters were overlapped suggesting synergistic mechanism of action. The three pathways found to be common among three clusters were Gonadotropin-releasing hormone receptor pathway, Endothelin signaling pathway, and Inflammation mediated by chemokine and cytokine signaling pathway.

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Network Pharmacology study of Curcuma longa L.: Potential Target Proteins and their Functional Enrichment Analysis.

10.21203/rs.3.rs-31985/v3 ◽

2020 ◽

Author(s):

SANGEETA KUMARI ◽

Hosahalli S. Subramanya

Keyword(s):

Signaling Pathway ◽

Mechanism Of Action ◽

Protein Interaction ◽

Protein Interaction Network ◽

Curcuma Longa ◽

Interaction Network ◽

Functional Enrichment ◽

Target Proteins ◽

Protein Protein Interaction ◽

Protein Protein Interaction Network

Abstract ObjectiveThis study’s primary goal is unraveling the mechanism of action of bioactives of Curcuma longa L. at the molecular level using protein-protein interaction network.ResultsWe used target proteins to create protein-protein interaction network (PPIN) and identified significant node and edge attributes of PPIN. We identified the cluster of proteins in the PPIN, which were used to identify enriched pathways. We identified closeness centrality and jaccard score as most important node and edge attribute of the PPIN respectively. The enriched pathways of various clusters were overlapped suggesting synergistic mechanism of action. The three pathways found to be common among three clusters were Gonadotropin-releasing hormone receptor pathway, Endothelin signaling pathway, and Inflammation mediated by chemokine and cytokine signaling pathway.

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