Interaction network analysis revealed biomarkers in myocardial infarction

Zhang, Tong; Zhao, Lili; Zhang, Zhuoran; Fu, Pei-De; Su, Zhendong; Qi, Lichun; Li, Xueqi; Yan, Dong

doi:10.1007/s11033-014-3366-4

Cited by 4 publications

(3 citation statements)

References 33 publications

Supporting

Mentioning

Contrasting

Order By: Relevance

“…Protein-protein interaction (PPI) analysis was done by STRING ( https://cn.string-db.org/ ) using a confidence score of > 0.4 to identify PPI pairs [ 27 ]. Then, Graphed with R's “igraph”package [ 28 ]. The network of proteins was subjected to a cluster analysis using the MCODE plug-in of Cytoscape.…”

Section: Methodsmentioning

confidence: 99%

B2M is a Biomarker Associated With Immune Infiltration In High Altitude Pulmonary Edema

Zhan

Xing

et al. 2024

CCHTS

View full text Add to dashboard Cite

Background: High altitude pulmonary edema (HAPE) is a serious mountain sickness with certain mortality. Its early diagnosis is very important. However, the mechanism of its onset and progression is still controversial. Purpose: This study aimed to analyze the HAPE occurrence and development mechanism and search for prospective biomarkers in peripheral blood. Methods: The difference genes (DEGs) of the Control group and the HAPE group were enriched by gene ontology (GO), Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment analysis, and then GSEA analysis was performed. After identifying the immune-related hub genes, QPCR was used to verify and analyze the hub gene function and diagnostic value with single-gene GSEA and ROC curves, and the drugs that acted on the hub gene was found in the CTD database. Immune infiltration and its association with the hub genes were analyzed using CIBERSORT. Finally, WGCNA was employed to investigate immune invasion cells' significantly related gene modules, following enrichment analysis of their GO and KEGG. Results: The dataset enrichment analysis, immune invasion analysis and WGCNA analysis showed that the occurrence and early progression of HAPE were unrelated to inflammation. The hub genes associated with immunity obtained with MCODE algorithm of Cytoscape were JAK2 and B2M. RT-qPCR and ROC curves confirmed that the hub gene B2M was a specific biomarker of HAPE and had diagnostic value, and single-gene GSEA analysis confirmed that it participated in MHC I molecule-mediated antigen presentation ability decreased, resulting in reduced immunity. Conclusion: Occurrence and early progression of high altitude pulmonary edema may not be related to inflammation. B2M may be a new clinical potential biomarker for HAPE for early diagnosis and therapeutic evaluation as well as therapeutic targets, and its decrease may be related to reduced immunity due to reduced ability of MCH I to participate in antigen submission.

show abstract

Section: Methodsmentioning

confidence: 99%

B2M is a Biomarker Associated With Immune Infiltration In High Altitude Pulmonary Edema

Zhan

Xing

et al. 2024

CCHTS

View full text Add to dashboard Cite

show abstract

“…Gene sets with an expression of Log 2 FC (Fold Change) > 1.5 and FDR (False Discovery Rate) < 0.05 were filtered for and collected. The collected GEO data were marked as T GEO (Barrett et al, 2007; Cappuzzello et al, 2009; Song et al, 2013; Steudemann et al, 2013; Gray et al, 2014; Liu et al, 2014, 2015, 2017; Zhang et al, 2014a,b; Peterson et al, 2015; Wang et al, 2015; Andersen et al, 2017; Gupta et al, 2017; Wu et al, 2017; Fang et al, 2018; Gunawan et al, 2018; Murugesan and Premkumar, 2018; Sabrkhany et al, 2018).…”

Section: Methodsmentioning

confidence: 99%

Analysis of Effect of Schisandra in the Treatment of Myocardial Infarction Based on Three-Mode Gene Ontology Network

Zuo

et al. 2019

Front. Pharmacol.

View full text Add to dashboard Cite

Schisandra chinensis is a commonly used traditional Chinese medicine, which has been widely used in the treatment of acute myocardial infarction in China. However, it has been difficult to systematically clarify the major pharmacological effect of Schisandra, due to its multi-component complex mechanism. In order to solve this problem, a comprehensive network analysis method was established based-on “component–gene ontology–effect” interactions. Through the network analysis, reduction of cardiac preload and myocardial contractility was shown to be the major effect of Schisandra components, which was further experimentally validated. In addition, the expression of NCOR2 and NFAT in myocyte were experimentally confirmed to be associated with Schisandra in the treatment of AMI, which may be responsible for the preservation effect of myocardial contractility. In conclusion, the three-mode gene ontology network can be an effective network analysis workflow to evaluate the pharmacological effects of a multi-drug complex system.

show abstract

“…Thus, exploring the biological pathways relying on systems biology techniques can provide extensive insights into the components of pathways, thereby aiding in developing novel targets for diseases. However, previous studies have mainly focused on the single dysregulated pathways based on the pre-defined threshold (13,14). Pathways having significant P-values did not have biological meaning, but several pathways possessing non-significant P-values are statistically significant and biological meaningful (15).…”

Section: Introductionmentioning

confidence: 99%

Constructing differential co‑expression network to predict key pathways for myocardial infarction

Guo

Liu

2019

Exp Ther Med

View full text Add to dashboard Cite

New thoughts are warranted to develop efficient diagnosis and optimal therapeutics to combat unstable angina (UA)/myocardial infarction (MI). Therefore, the gene data of patients with UA or MI were used in this study to identify the optimal pathways which can provide comprehensive information for UA/MI development. Differentially expressed genes (DEGs) between UA and MI were detected using LIMMA package, and pathway enrichment analysis was conducted for the DEGs, based on the DAVID tool, to detect the significant pathways. Then, differential co-expression network (DCN) and sub-DCN for the DEGs were constructed. Subsequently, informative pathways were extracted using guilt-by-association (GBA) principle relying on the area under the curve (AUC), and the pathway categories with AUC >0.8 were defined as the informative pathways. Finally, we selected the optimal pathways based on the traditional pathway analysis and the sub-DCN-based-GBA pathway prediction method. A total of 203 and 266 DEGs were identified from the expression profile of blood of MI samples comparing with UAs in the time-point 1 and time-point 2 groups. Moreover, 7 and 10 informative pathway terms were identified based on AUC>0.8. Significantly, cytokine-cytokine receptor interaction, as well as MAPK signaling pathway were the common optimal pathways in the two groups. Calcium signaling pathway was unique to the whole blood of patients with acute coronary syndrome (ACS) taken at 30 days post-ACS. In conclusion, the optimal pathways (MAPK signaling pathway, cytokine-cytokine receptor interaction, and calcium signaling pathway) might play important roles in the progression of UA/MI.

show abstract

Interaction network analysis revealed biomarkers in myocardial infarction

Cited by 4 publications

References 33 publications

B2M is a Biomarker Associated With Immune Infiltration In High Altitude Pulmonary Edema

B2M is a Biomarker Associated With Immune Infiltration In High Altitude Pulmonary Edema

Analysis of Effect of Schisandra in the Treatment of Myocardial Infarction Based on Three-Mode Gene Ontology Network

Constructing differential co‑expression network to predict key pathways for myocardial infarction

Contact Info

Product

Resources

About