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Multi-omics data is difficult to interpret due to the heterogeneity of information by the volume of data, the complexity of characteristics of each data, and the diversity of omics platforms. There is not yet a system for interpreting to visualize research data on environmental diseases concerning environmental harmful substances. We provide MEE, a web-based visualization tool, to comprehensively explore the complexity of data due to the interconnected characteristics of high-dimensional data sets according to exposure to various environmental harmful substances. MEE visualizes omics data of correlation between omics data, subjects and samples by keyword searches of meta data, multi-omics data, and harmful substances. MEE has been demonstrated the versatility by two examples. We confirmed the correlation between smoking and asthma with RNA-seq and Methylation-Chip data, it was visualized that genes (PHACTR3, PXDN, QZMB, SOCS3 etc.) significantly related to autoimmune or inflammatory diseases. To visualize the correlation between atopic dermatitis and heavy metals, we selected 32 genes related immune response by integrated analysis of multi-omics data. However, it did not show a significant correlation between mercury in blood and atopic dermatitis. In the future, should continuously collect an appropriate level of multi-omics data in MEE system, will obtain data to analyze environmental substances and diseases.
Multi-omics data is difficult to interpret due to the heterogeneity of information by the volume of data, the complexity of characteristics of each data, and the diversity of omics platforms. There is not yet a system for interpreting to visualize research data on environmental diseases concerning environmental harmful substances. We provide MEE, a web-based visualization tool, to comprehensively explore the complexity of data due to the interconnected characteristics of high-dimensional data sets according to exposure to various environmental harmful substances. MEE visualizes omics data of correlation between omics data, subjects and samples by keyword searches of meta data, multi-omics data, and harmful substances. MEE has been demonstrated the versatility by two examples. We confirmed the correlation between smoking and asthma with RNA-seq and Methylation-Chip data, it was visualized that genes (PHACTR3, PXDN, QZMB, SOCS3 etc.) significantly related to autoimmune or inflammatory diseases. To visualize the correlation between atopic dermatitis and heavy metals, we selected 32 genes related immune response by integrated analysis of multi-omics data. However, it did not show a significant correlation between mercury in blood and atopic dermatitis. In the future, should continuously collect an appropriate level of multi-omics data in MEE system, will obtain data to analyze environmental substances and diseases.번호 | 참고문헌 | 국회도서관 소장유무 |
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9 | R. Hernández-de-Diego, S. Tarazona, C. Martínez-Mira, L. Balzano-Nogueira, P. Furió-Tarí, G.J. Pappas et al., “PaintOmics3: a Web Resource for the Pathway Analysis and Visualization of Multi-omics Data,” Nucleic Acids Research. Vol. 46, pp. W503-W509, 2018. | 미소장 |
10 | J. Gao, B.A. Aksoy, U. Dogrusoz, G. Dresdner, B. Gross, S.O. Sumer et al., “Integrative Analysis of Complex Cancer Genomics and Cinical Profiles Using the cBioPortal,” Science Signaling. Vol. 6, p. pl1, 2013. | 미소장 |
11 | M.J. Goldman, B, Craft, M. Hastie, K. Repečka, F. McDade, A. Kamath et al., “Visualizing and Interpreting Cancer Genomics Data via the Xena Platform,” Nature Biotechnology. Vol. 38, pp. 675-678, 2020. | 미소장 |
12 | S.V. Vasaikar, P. Straub, J. Wang, and B. Zhang, “LinkedOmics: Analyzing Multi-Omics Data within and across 32 Cancer Types,”Nucleic Acids Research. Vol. 46, pp. D956-D963, 2018. | 미소장 |
13 | R. Ihaka and R. Gentleman, “R: a Language for Data Analysis and Graphics,” Journal of Computational and Graphical Statistics, Vol. 5, No. 3, pp. 299-314, 1996. | 미소장 |
14 | E. Bonnet, L. Calzone, and T. Michoel, “Integrative Multi-Omics Module Network Inference with Lemon-Tree,” PLoS Computational Biology, Vol. 11, No. 2, pp. e1003983, 2015. | 미소장 |
15 | R. Argelaguet, B. Velten, D. Arnol, S. Dietrich, T. Zenz, J.C. Marioni et al., “Multi-Omics Factor Analysis—a Framework for Unsupervised Integration of Multi-Omics Data Sets,”Molecular Systems Biology, Vol. 14, No. 6, pp. 8124, 2018. | 미소장 |
16 | J. Nicodemus-Johnson, R.A. Myers, N.J. Sakabe, D.R. Sobreira, D.K. Hogarth, E.T. Naureckas et al., “DNA Methylation in Lung Cells is Associated with Asthma Endotypes and Genetic Risk,” The Journal of Clinical Investigation Insight, Vol. 1, No. 20, pp. 90151, 2016. | 미소장 |
17 | Y. Park and Y. Lee, “A Study on Countermeasure for Privacy in Mobile Office,” Journal of Korea Multimedia Society, Vol. 18, No. 2, pp. 178-188, 2015. | 미소장 |
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