GsmPlot: a web server to visualize epigenome data in NCBI

BMC Bioinformatics

Zhenhai Zhang¹  Jia Li²  Yue Yin²  Mutian Zhang²  Deqiang Sun²  Jie Cui³  Zhiyong Zhang⁴ 

[1] Center for Bioinformatics, School of Basic Medical Sciences, Southern Medical University;Center for Epigenetics & Disease Prevention, Institute of Biosciences and Technology, Texas A&M University College of Medicine;Key Laboratory of Special Pathogens and Biosafety, Wuhan Institute of Virology, Chinese Academy of Sciences;The Third Affiliated Hospital of Guangzhou Medical University;

关键词: GsmPlot;    Epigenetics;    Webserver;    NCBI;    Visualization;   

DOI  :  10.1186/s12859-020-3386-0

来源: DOAJ

【 摘 要 】

Abstract Background Epigenetic regulation is essential in regulating gene expression across a variety of biological processes. Many high-throughput sequencing technologies have been widely used to generate epigenetic data, such as histone modification, transcription factor binding sites, DNA modifications, chromatin accessibility, and etc. A large scale of epigenetic data is stored in NCBI Gene Expression Omnibus (GEO). However, it is a great challenge to reanalyze these large scale and complex data, especially for researchers who do not specialize in bioinformatics skills or do not have access to expensive computational infrastructure. Results GsmPlot can simply accept GSM IDs to automatically download NCBI data or can accept user’s private bigwig files as input to plot the concerned data on promoters, exons or any other user-defined genome locations and generate UCSC visualization tracks. By linking public data repository and private data, GsmPlot can spark data-driven ideas and hence promote the epigenetic research. Conclusions GsmPlot web server allows convenient visualization and efficient exploration of any NCBI epigenetic data in any genomic region without need of any bioinformatics skills or special computing resources. GsmPlot is freely available at https://gsmplot.deqiangsun.org/.

【 授权许可】

Unknown