The DOI matches its Crossref record; 5 of the 5 references it cites were found in a registry or an index.
The SMART App: an interactive web application for comprehensive DNA methylation analysis and visualization
Open accessAbstract
Background: Data mining of The Cancer Genome Atlas (TCGA) data has significantly facilitated cancer genome research and provided unprecedented opportunities for cancer researchers. However, existing web applications for DNA methylation analysis does not adequately address the need of experimental biologists, and many additional functions are often required. Results: To facilitate DNA methylation analysis, we present the SMART (Shiny Methylation Analysis Resource Tool) App, a user-friendly and easy-to-use web application for comprehensively analyzing the DNA methylation data of TCGA project. The SMART App integrates multi-omics and clinical data with DNA methylation and provides key interactive and customized functions including CpG visualization, pan-cancer methylation profile, differential methylation analysis, correlation analysis and survival analysis for users to analyze the DNA methylation in diverse cancer types in a multi-dimensional manner. Conclusion: The SMART App serves as a new approach for users, especially wet-bench scientists with no programming background, to analyze the scientific big data and facilitate data mining. The SMART App is available at http://www.bioinfo-zs.com/smartapp.
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The cancer genome atlas pan-cancer analysis project
The Cancer Genome Atlas Research Network, Weinstein, J. N., Collisson, E. A., Mills, G. B., Shaw, K. R. M., Ozenberger, B. A., Ellrott, K., Shmulevich, I., Sander, C., & Stuart, J. M. (2013) · Nature Genetics · doi:10.1038/ng.2764 · Cited by 9,092
Functions of DNA methylation: islands, start sites, gene bodies and beyond
Jones, P. A. (2012) · Nature Reviews Genetics · doi:10.1038/nrg3230 · Cited by 6,061
Du, P., Zhang, X., Huang, C.-C., Jafari, N., Kibbe, W. A., Hou, L., & Lin, S. M. (2010) · BMC Bioinformatics · doi:10.1186/1471-2105-11-587 · Cited by 2,136
IDH1 mutation is sufficient to establish the glioma hypermethylator phenotype
Turcan, S., Rohle, D., Goenka, A., Walsh, L. A., Fang, F., Yilmaz, E., Campos, C., Fabius, A. W. M., Lu, C., Ward, P. S., et al. (2012) · Nature · doi:10.1038/nature10866 · Cited by 1,974
Self-citationToil enables reproducible, open source, big biomedical data analyses
Vivian, J., Rao, A. A., Nothaft, F. A., Ketchum, C., Armstrong, J., Novak, A., Pfeil, J., Narkizian, J., Deran, A. D., Musselman-Brown, A., et al. (2017) · Nature Biotechnology · doi:10.1038/nbt.3772 · Cited by 1,365
Cited by
Wilker, S., Vukojevic, V., Schneider, A., Pfeiffer, A., Inerle, S., Pauly, M., Elbert, T., Papassotiropoulos, A., de Quervain, D., & Kolassa, I.-T. (2023) · Translational Psychiatry · doi:10.1038/s41398-023-02316-6 · Cited by 42
Fariha, F. T. J., Fuad, M., Saha, C. S., Hossen, S., & Hossain, M. J. (2025) · Scientific Reports · doi:10.1038/s41598-025-13315-6 · Cited by 1
Metadata
- Authors
- Li, Y., Ge, D., & Lu, C.
- Venue
- Epigenetics & Chromatin
- Published
- 2019-12
- Volume
- 12
- Issue
- 1
- Pages
- 71-71
- ISSN
- 1756-8935 (ISSN-L)
- OpenAlex
- W2992289032
- Cited by
- 285
- References
- 5
- FWCI
- 7.30
- Type
- journal article
- Language
- en
- Open access
- gold
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