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Добірка наукової літератури з теми "DISEASEMETH"

Автор: Grafiati

Опубліковано: 11 вересня 2023

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Статті в журналах з теми "DISEASEMETH"

Lv, J., H. Liu, J. Su, X. Wu, H. Liu, B. Li, X. Xiao, F. Wang, Q. Wu, and Y. Zhang. "DiseaseMeth: a human disease methylation database." Nucleic Acids Research 40, no. D1 (December 1, 2011): D1030—D1035. http://dx.doi.org/10.1093/nar/gkr1169.

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Xing, Jie, Ruiyang Zhai, Cong Wang, Honghao Liu, Jiaqi Zeng, Dianshuang Zhou, Mengyan Zhang, et al. "DiseaseMeth version 3.0: a major expansion and update of the human disease methylation database." Nucleic Acids Research 50, no. D1 (November 18, 2021): D1208—D1215. http://dx.doi.org/10.1093/nar/gkab1088.

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Анотація:

Abstract DNA methylation has a growing potential for use as a biomarker because of its involvement in disease. DNA methylation data have also substantially grown in volume during the past 5 years. To facilitate access to these fragmented data, we proposed DiseaseMeth version 3.0 based on DiseaseMeth version 2.0, in which the number of diseases including increased from 88 to 162 and High-throughput profiles samples increased from 32 701 to 49 949. Experimentally confirmed associations added 448 pairs obtained by manual literature mining from 1472 papers in PubMed. The search, analyze and tools sections were updated to increase performance. In particular, the FunctionSearch now provides for the functional enrichment of genes from localized GO and KEGG annotation. We have also developed a unified analysis pipeline for identifying differentially DNA methylated genes (DMGs) from the original data stored in the database. 22 718 DMGs were found in 99 diseases. These DMGs offer application in disease evaluation using two self-developed online tools, Methylation Disease Correlation and Cancer Prognosis & Co-Methylation. All query results can be downloaded and can also be displayed through a box plot, heatmap or network module according to whichever search section is used. DiseaseMeth version 3.0 is freely available at http://diseasemeth.edbc.org/.

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Xiong, Yichun, Yanjun Wei, Yue Gu, Shumei Zhang, Jie Lyu, Bin Zhang, Chuangeng Chen, et al. "DiseaseMeth version 2.0: a major expansion and update of the human disease methylation database." Nucleic Acids Research 45, no. D1 (November 29, 2016): D888—D895. http://dx.doi.org/10.1093/nar/gkw1123.

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Zhao, Xiaorong, Wenzhuo Wang, Dandan Li, Qingjuan Li, Yuxuan Zhang, and Bo Niu. "SHCBP1: A Novel Potential Molecular Target for Pan- Cancer Therapy." Neurological Disorders and Stroke International 4, no. 1 (May 10, 2022): 1–11. http://dx.doi.org/10.25107/2641-1407-v4-id1026.

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Анотація:

Purpose: Although many experimentally validated evidence and clinical data support the link between SHCBP1 (SHC-Binding and Spindle-Associated 1) and cancer, there is no pan-cancer analysis available. Based on various databases, we analyzed the roles assumed by SHCBP1 in different cancers to provide new targets for cancer therapy. Methods: We used versatile public databases such as TIMER, Interactive Analysis of Gene Expression Profile, 2nd Edition (GEPIA), UALCAN, The Cancer Genome Atlas (TCGA), cBioPortal, Clinical Bioinformatics Assistant, DiseaseMeth, TISIDB, Human Protein Atlas (HPA), STRING and Database for Annotation, Visualization, and Integrated Discovery (DAVID) to analyze SHCBP1 expression, mutation, methylation in tumors, as well as its survival analysis, tumor-immune interactions and functional networks. Results: SHCBP1 was highly expressed in most tumors leading to poor prognosis and the degree of expression was positively correlated with the degree of infiltration by activated memory CD4+ T cells. We observed cancer-associated fibroblast infiltration in Breast Invasive Carcinoma (BRCA), Renal Clear Cell Carcinoma (KIRC) and Thyroid Cancer (THCA). Protein kinase activity and microtubules can influence gene enrichment, while "cell cycle", "oocyte meiosis" and "viral carcinogenesis" are possible pathways of SHCBP1 involvement in tumorigenesis. Conclusion: Altogether, our first pan-cancer analysis of SHCBP1 demonstrated its potential as a biomarker for tumor prognosis diagnosis or as a molecular target for immunotherapy.

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Tang, Lulu, ling Huang, and yingtao Lai. "Network pharmacology and bioinformatics analyses identify the intersection genes and mechanism of Huang Bai for recurrent aphthous stomatitis." International Journal of Immunopathology and Pharmacology 36 (January 2022): 039463202211291. http://dx.doi.org/10.1177/03946320221129134.

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Анотація:

Recurrent aphthous stomatitis (RAS) are complex inflammatory diseases caused by multi-factors, which severely impact patient quality of life. However, there is still no effective treatment method for RAS without side effects. Traditionally, Cortex Phellodendri known as “Huang Bai” was used to treat RAS for antibacterial and anti-inflammatory properties in China. Network pharmacology methods and bioinformatics analysis were utilized to search and fish incorporating target. Network analysis and silico validation were used to discover the pharmacological mechanisms of “Huang Bai” for the treatment of RAS. A total of 25 active ingredients in HB, 200 drug targets, and 578 differentially expressed genes (DEGs) between Recurrent aphthous stomatitis and normal samples were obtained. The Gene Ontology enrichment analysis revealed that the immune response was the most significantly enriched term within the DEGs. The KEGG pathway analysis identified 60 significant pathways, most of which involved in the inhibition of inflammation and regulation of immunological response. The functions are dependent on a multi-pathway, particularly the TNF signaling pathway and the HIF-1 signaling pathway. We identified six hub genes in the PPI network, most of which were validated as highly expressed in oral ulcers by DiseaseMeth databases. In addition, molecular docking displayed that the primary molecule combined well with the key targets. “Huang Bai” contains potential anti-RAS active compounds. This study reflects the multi-component multi-target multi-pathway action characteristics of “Huang Bai.” Our study provides potential biomarkers or treatment targets for further research.

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Qian, Xiang, Zhuo Chen, Sha Sha Chen, Lu Ming Liu, and Ai Qin Zhang. "Integrated Analyses Identify Immune-Related Signature Associated with Qingyihuaji Formula for Treatment of Pancreatic Ductal Adenocarcinoma Using Network Pharmacology and Weighted Gene Co-Expression Network." Journal of Immunology Research 2020 (May 20, 2020): 1–17. http://dx.doi.org/10.1155/2020/7503605.

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Анотація:

The study aimed to clarify the potential immune-related targets and mechanisms of Qingyihuaji Formula (QYHJ) against pancreatic cancer (PC) through network pharmacology and weighted gene co-expression network analysis (WGCNA). Active ingredients of herbs in QYHJ were identified by the TCMSP database. Then, the putative targets of active ingredients were predicted with SwissTargetPrediction and the STITCH databases. The expression profiles of GSE32676 were downloaded from the GEO database. WGCNA was used to identify the co-expression modules. Besides, the putative targets, immune-related targets, and the critical module genes were mapped with the specific disease to select the overlapped genes (OGEs). Functional enrichment analysis of putative targets and OGEs was conducted. The overall survival (OS) analysis of OGEs was investigated using the Kaplan-Meier plotter. The relative expression and methylation levels of OGEs were detected in UALCAN, human protein atlas (HPA), Oncomine, DiseaseMeth version 2.0 and, MEXPRESS database, respectively. Gene set enrichment analysis (GSEA) was conducted to elucidate the key pathways of highly-expressed OGEs further. OS analyses found that 12 up-regulated OGEs, including CDK1, PLD1, MET, F2RL1, XDH, NEK2, TOP2A, NQO1, CCND1, PTK6, CTSE, and ERBB2 that could be utilized as potential diagnostic indicators for PC. Further, methylation analyses suggested that the abnormal up-regulation of these OGEs probably resulted from hypomethylation, and GSEA revealed the genes markedly related to cell cycle and proliferation of PC. This study identified CDK1, PLD1, MET, F2RL1, XDH, NEK2, TOP2A, NQO1, CCND1, PTK6, CTSE, and ERBB2 might be used as reliable immune-related biomarkers for prognosis of PC, which may be essential immunotherapies targets of QYHJ.

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Qin, Sha, Gaoming Liu, Haoer Jin, Xue Chen, Jiang He, Juxiong Xiao, Yan Qin, Yitao Mao, and Luqing Zhao. "The Dysregulation of SOX Family Correlates with DNA Methylation and Immune Microenvironment Characteristics to Predict Prognosis in Hepatocellular Carcinoma." Disease Markers 2022 (April 13, 2022): 1–21. http://dx.doi.org/10.1155/2022/2676114.

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Background. Due to the molecular heterogeneity of hepatocellular carcinoma (HCC), majority of patients respond poorly among various of therapy. This study is aimed at conducting a comprehensive analysis about roles of SOX family in HCC for obtaining more therapeutic targets and biomarkers which may bring new ideas for the treatment of HCC. Methods. UALCAN, Kaplan Meier plotter, cBioPortal, STRING, WebGestalt, Metascape, TIMER 2.0, DiseaseMeth, MethSurv, HPA, CCLE database, and Cytoscape software were used to comprehensively analyze the bioinformatic data. Results. SOX2, SOX4, SOX8, SOX10, SOX11, SOX12, SOX17, and SOX18 were significantly differentially expressed in HCC and normal tissues and were valuable for the grade and survival of HCC patients. In addition, the gene alterations of SOX family happened frequently, and SOX4 and SOX17 had the highest mutation rate. The function of SOX family on HCC may be closely correlated with the regulation of angiogenesis-related signaling pathways. Moreover, SOX4, SOX8, SOX11, SOX12, SOX17, and SOX18 were correlation with 8 types of immune cells (including CD8+ T cell, CD4+ T cell, B cell, Tregs, neutrophil, macrophage, myeloid DC, and NK cell), and we found that most types of immune cells had a positive correlation with SOX family. Notably, CD4+ T cell and macrophage were positively related with all these SOX family. NK cells were negatively related with most SOX family genes. DNA methylation levels in promoter area of SOX2, SOX4, and SOX10 were lower in HCC than normal tissues, while SOX8, SOX11, SOX17, and SOX18 had higher DNA methylation levels than normal tissues. Moreover, higher DNA methylation level of SOX12 and SOX18 demonstrated worse survival rates in patients with HCC. Conclusion. SOX family genes could predict the prognosis of HCC. In addition, the regulation of angiogenesis-related signaling pathways may participate in the development of HCC. DNA methylation level and immune microenvironment characteristics (especially CD4+ T cell and macrophage immune cell infiltration) could be a novel insight for predicting prognosis in HCC.

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Peng, Lu-Shan, Sai-Li Duan, Run-Qi Li, Zi-Yuan Bai, Chun-Lin Ou, and Jun-Pu Wang. "Prognostic value of sirtuin family members and experimental verification identify SIRT5 as diagnostic biomarkers in clear cell renal cell carcinoma." PeerJ 11 (April 19, 2023): e15154. http://dx.doi.org/10.7717/peerj.15154.

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Background The sirtuins (SIRTs) family is a nicotinamide adenine dinucleotide (NAD+) family of dependent deacetylases, which includes SIRT1-7. This family is related to the development and progression of various tumors. However, a comprehensive analysis of the role of SIRTs in clear cell renal cell carcinoma (ccRCC) is still lacking, and there are few reports on the inhibitory role of SIRT5 in ccRCC. Methods We used immunohistochemical analysis, and several bioinformatic databases to perform an integrated analysis of the expression and prognostic value of SIRT5 and other SIRT family members in ccRCC along with the associated immune cell infiltration. These databases include TIMER, THPA, cell culture, UALCAN, cBioPortal, WebGestalt, Metascape, DiseaseMeth, STRING database, and Cytoscape. Results The protein expression of SIRT1, 2, 3, 6, and 7 were upregulated in ccRCC for the Human Protein Atlas database, whereas the expression of SIRT4 and SIRT5 was decreased. The expression based on tumor stage, and grade followed a similar trend. Kaplan–Meier analysis showed that high SIRT4 and SIRT5 expression was positively related to better overall survival (OS), whereas SIRT6 and SIRT7 expression was positively related to worse OS. Further, high SIRT3 expression was related to worse relapse-free survival (RFS), whereas high SIRT5 expression was related to better RFS. To explore the mechanism underlying the function of SIRTs in ccRCC, we also used several databases to perform the functional enrichment analysis and explore the relationship between infiltrating immune cells and seven SIRT family members in ccRCC. The results showed that several SIRT family members, and particularly SIRT5, are correlated with the infiltration of some important immune cells. The protein expression of SIRT5 was significantly lower in tumor tissue compared to normal tissue and was negatively related to the age of the patient ccRCC individual tumor stages, and grades. In human ccRCC samples, strong IHC staining expression of SIRT5 was displayed in adjacent normal tissue than in tumor tissues. Conclusion SIRT5 may be a prognostic marker and a novel strategy for the treatment of ccRCC.

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Marques, Vastí Ferrari, Cícera Aparecida Escoura Bueno, Cleane Aparecida dos Santos, Eliane Reame, and Marjorie Samira Ferreira Bolognani. "SCHOOL DISEASEMENT: A PATHWAY OF THE MUNICIPAL EDUCATION SYSTEM OF JUNDIAÍ." International Journal of Human Sciences Research 2, no. 10 (April 18, 2022): 2–7. http://dx.doi.org/10.22533/at.ed.5582102214045.

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Stepanyan, Suren, V. M. Hakobyan, A. A. Petrosyan, H. H. Yeghiazaryan, K. T. Papazyan, H. Kh Batikyan, A. Yu Aleksanyan, H. H. Safaryan, H. H. Shmavonyan, and A. M. Babayan. "Complete versus non-complete fundoplication in surgical treatment of gastroesophageal reflux disease." NEW ARMENIAN MEDICAL JOURNAL, no. 4 (2022): 64–73. http://dx.doi.org/10.56936/18290825-2022.16.4-64.

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Анотація:

Gastroesophageal reflux disease is a common disorder accounting for approximately 75% of esophageal pathology. It seriously compromises quality of life. It develops when the reflux of gastric content causes troublesome symptoms or complications. During the last decades significant changes have occured in the role of surgery for gastroesophageal reflux disease. Initially antireflux surgery was reserved only for patients who had failed any kind of medical therapy. Now the range of indications for antireflux procedures is wide. Operations for gastroesophageal reflux disease are now well established and have good short- and long-term results, but no unique laparoscopic antireflux technique has been accepted so far, and a number of different antireflux procedures with numerous modifications have been reported. A total of 102 consecutive patients with gastroesophageal reflux disease were operated in the clinic of Republican Medical Center ‘’Armenia’’ (Yerevan, Armenia) and Mickaelyan Institute of Surgery (Yerevan, Armenia) from 2010 to 2021. In all cases the esophagogram showed hiatal hernia. Nissen, Nissen-Rossetti and Toupet fundoplications were performed as antireflux procedures. In all cases of combination of hiatal hernia and Gastroesophageal reflux diseasemesh reinforcement was performed. The results of follow-up assessment of the operated patients were compared. The results in early postoperative period were assessed with contrast X-ray examination and 24-hour pH-metry on the 5-th to 7-th days after surgery. The quality-of-life evaluation by the questionnaire showed a significant difference between the two groups, improvement of results in the laparoscopy group with complete fundoplication in comparison with not complete fundoplication. Complete fundoplication is a more reliable method of antireflux procedures for surgical treatment of gastroesophageal reflux disease. The division of short gastric vessels helps to prevent persistent dysphagia. The repair of esophageal hiatus of diaphragm is mandatory in antireflux procedures.

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Більше джерел

Дисертації з теми "DISEASEMETH"

GARG, AYUSHI. "METHCARD: A CARDIOVASCULAR DISEASES GENE METHYLATION DATABASE FOR HUMAN." Thesis, 2017. http://dspace.dtu.ac.in:8080/jspui/handle/repository/16099.

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Анотація:

DNA methylation can be elucidated as the reversible addition of methyl (CH3) group to C5 position of cytosine to form 5-methylcytosine that symbolizes an important regulatory layer associated with gene expression and regulation. It needs to be precisely regulated as any alteration in DNA methylation pattern may lead to various diseases. Recent studies have provided evidence of relation between DNA methylation and cardiovascular disease. Thus to facilitate improved diagnosis and better treatment decisions, the objective of this study is to create an efficient, effective and accurate systems to enable the extraction of the detailed information related to methylation of genes involved in cardiovascular disease development by contributing resources from various databases namely Coronary Artery Disease Gene Database (CADgene), DisGeNET, Comparative Toxicogenomics Database (CTD), DiseaseMeth, Dragon Database for Methylated Genes and Diseases (DDMGD), Database of CpG islands and Analytical Tool (DBCAT) etc. and various published literatures.

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Частини книг з теми "DISEASEMETH"

"diseasement, n." In Oxford English Dictionary. 3rd ed. Oxford University Press, 2023. http://dx.doi.org/10.1093/oed/7466259398.

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