Introducing Serine as Cardiovascular Disease Biomarker Candidate via Pathway Analysis

Tavirani, Mostafa Rezaei; Azodi, Mona Zamanian; Rostami‐Nejad, Mohammad; Morravej, Hamideh; Razzaghi, Zahra; Okhovatian, Farshad; Rezaei-Tavirani, Majid

doi:10.31661/gmj.v9i0.1696

Cited by 3 publications

(4 citation statements)

References 24 publications

(19 reference statements)

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“…Pathway analysis is a common way to detect the molecular mechanism of diseases. 20 Pathway analysis revealed the differences between both methods in signaling pathway activation. Five groups of pathways were identified as the related biological terms for the 148 queried genes.…”

Section: Discussionmentioning

confidence: 99%

Gene Ontology Assessment of Indirect Cold Physical Plasma and UV-Radiation Molecular Mechanism at the Cellular Level

et al. 2023

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Introduction: The development of therapeutic methods implies an understanding of the molecular mechanism of the applied methods. Due to the widespread use of UV radiation and cold physical plasma in medicine, the molecular mechanism of these two methods is compared via gene ontology. Methods: Data were derived from Gene Expression Omnibus (GEO). The differentially expressed genes (DEGs) which discriminate the cells treated with UV radiation versus indirect cold physical plasma were analyzed via gen ontology enrichment. The related biochemical pathways were extracted from the "Kyoto Encyclopedia of Genes and Genomes" (KEGG). Results: Among the 152 queried DEGs, 18 critical genes including SOC1, LDLR, ALO5, PTGS2, TNF, JUNB, TNFRSF1A, CD40, SMAD7, ID1, SMAD6, SERPINE1, PMAIP1, MDM2, CREB5, GADD45A, E2F3, and ETV5 were highlighted as the genes that victimize the two methods. Conclusion: NOTCH1 and TNF as the main genes plus SEREPINE1, KLF, and BDNF were introduced as the significant genes that are involved in the processes which discriminate cold physical plasma administration and UV-radiation as the two evaluated therapeutic methods.

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Section: Discussionmentioning

confidence: 99%

Gene Ontology Assessment of Indirect Cold Physical Plasma and UV-Radiation Molecular Mechanism at the Cellular Level

et al. 2023

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“…Metabolites and lipids with a p < 0.05 in two-tailed Mann–Whitney U tests were applied for the pathway analysis, and biomarkers with no matched HMDB ID were removed. The correlation network analysis has significant advantages of interconnection discovery and biomarker selection . The Pearson correlation network of biomarkers was visualized by cytoscape software.…”

Section: Methodsmentioning

confidence: 99%

“…The correlation network analysis has significant advantages of interconnection discovery and biomarker selection. 30 The Pearson correlation network of biomarkers was visualized by cytoscape software. The pathwayrelated network was processed by Metscape and MetDisease, plugins of Cytoscape software for pathway network visualization and metabolite annotation.…”

Section: Data Processing and Statistical Analysismentioning

confidence: 99%

Integrated Metabolomics and Lipidomics Approach for the Study of Metabolic Network and Early Diagnosis in Cerebral Infarction

Zhu

Chen

et al. 2022

J. Proteome Res.

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Cerebral infarction (CI) remains a major cause of high mortality and long-term disability worldwide. The exploration of biomarkers and pathogenesis is crucial for the early diagnosis of CI. Although the understanding of metabolic perturbations underlying CI has increased in recent years, the relationship between altered metabolites and disease pathogenesis has only been partially elucidated and requires further investigation. In this study, we performed an integrated metabolomics and lipidomics analysis on 59 healthy subjects and 47 CI patients. Ultimately, 49 metabolite and 68 lipid biomarkers were identified and enriched in 24 disturbed pathways. The metabolic network revealed a significant interaction between altered lipids and other metabolites. Using receiver operating characteristic curve (ROC) analysis, a panel of three polar metabolites and seven lipids was optimized in the training set, which included taurine,

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“…The genes with the highest degree and betweenness, which are called hubs and bottlenecks, were determined. 18 Hub-bottlenecks which are common between both hubs and bottlenecks were identified.…”

Section: Methodsmentioning

confidence: 99%

Assessment of the Microbiome Role in Skin Protection Against UV Irradiation Via Network Analysis

et al. 2020

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Introduction: Diverse microbiotas which have some contributions to gene expression reside in human skin. To identify the protective role of the skin microbiome against UV exposure, proteinprotein interaction (PPI) network analysis is used to assessment gene expression alteration. Methods: A microarray dataset, GEO accession number GSE117359, was considered in this respect. Differential expressed genes (DEGs) in the germ-free (GF) and specific pathogen-free (SPF) groups are analyzed by GEO2R. The top significant DEGs were assigned for network analysis via Cytoscape 3.7.2 and its applications. Results: A total of 28 genes were identified as significant DEGs and the centrality analysis of the network indicated that only one of the seven hub-bottlenecks was from queried genes. The gene ontology analysis of Il6, Cxcl2, Cxcl1, TNF, Il10, Cxcl10, and Mmp9 showed that the crucial genes were highly enriched in the immune system. Conclusion: The skin microbiome plays a significant role in the protection of skin against UV irradiation and the role of TNF and IL6 is prominent in this regard.

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Introducing Serine as Cardiovascular Disease Biomarker Candidate via Pathway Analysis

Cited by 3 publications

References 24 publications

Gene Ontology Assessment of Indirect Cold Physical Plasma and UV-Radiation Molecular Mechanism at the Cellular Level

Gene Ontology Assessment of Indirect Cold Physical Plasma and UV-Radiation Molecular Mechanism at the Cellular Level

Integrated Metabolomics and Lipidomics Approach for the Study of Metabolic Network and Early Diagnosis in Cerebral Infarction

Assessment of the Microbiome Role in Skin Protection Against UV Irradiation Via Network Analysis

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