The SMART App: an interactive web application for comprehensive DNA methylation analysis and visualization

Di Ge,Yin Li,Chunlai Lu

doi:10.1186/s13072-019-0316-3

Abstract

BackgroundData 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.ResultsTo 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.ConclusionThe 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.

Highlights

All cancers arise as a result of the accumulation of somatic mutations, copy number alterations, and epigenetic modifications that alter transcription and protein expression
Home The home page first displays the number of DNA methylation samples available from The Cancer Genome Atlas (TCGA) project, colored by sample types (i.e., Normal and Tumor), for users to gain an overview of the sample size of the cancer type of interest
We previously identified that TRIM58 is a novel prognostic-related methylation-driven gene in lung squamous cell carcinoma [13]

Summary

Introduction

All cancers arise as a result of the accumulation of somatic mutations, copy number alterations, and epigenetic modifications that alter transcription and protein expression. Studies of molecular features such as DNA methylation may reveal the underlying mechanisms of carcinogenesis and progression. DNA methylation, the addition of a methyl group to DNA, plays a critical role in regulating gene expression [1]. It has been reported that DNA methylation at the promoter regions is often negatively correlated with gene expression while DNA methylation in gene bodies is often positively correlated with gene expression [2]. Abnormal DNA methylation patterns are found in every type of human cancer [3]. Existing web applications for DNA methylation analysis does not adequately address the need of experimental biologists, and many additional functions are often required

Methods

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Discussion

Conclusion