please make sure bedGraph, bigwig or wig file exsit on the GSM webpage in NCBI for the corresponding GSM ID.
By default, GSmPlot generates plots for CGI and Gene regions
Please select either human or mouse reference genome correctly. References for the same species can be lifted over but is time consuming.
If GsmPlot could not be opened, please try "clear history" in the browser.
GsmPlot is a web service to automatically download, analyze and visualize epigenetics data(ChIP-Seq, ATAC-Seq, Bis-Seq),public from NCBI or private from you.
Motivation: Epigenetic regulation is essential for cell differentiation, development and diseases. Many high-throughput sequencing technologies have been widely used to study the epigenetic modifications such as histone modification, transcription factor binding sites, DNA methylation or hydroxylation, chromatin accessibility , and etc. A large scale of epigenetic data for various species, cell types, diseases and experimental conditions are stored in NCBI Gene Expression Omnibus (GEO). This public data repository is utilized by all the investigators worldwide. However, for researchers who do not specialize in bioinformatics skills, it is very hard to reanalyze and utilize such publicly available data.
Results: GsmPlot web server allows quick visualization and efficient exploration of any NCBI epigenetic data in any genomic region without need of bioinformatics skills or special computing resources. GsmPlot can simply accept GSM ID to automatically download NCBI data or can accept user’s private bigwig files as input to plot the interested data on promoters, exons or any other 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.
Contact: The package is developed by Jia Li, Yue Yin and Deqiang Sun. Please post any questions, suggestions or problems to the Discussion google group or send email to Deqiang Sun at email@example.com
Cite our paper: Li, J., Yin, Y., Zhang, M., Cui, J., Zhang, Z., Zhang, Z. and Sun, D., 2020. GsmPlot: a web server to visualize epigenome data in NCBI. BMC bioinformatics, 21(1), pp.1-7.
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