I want to study the relationship between different epigenetic factors and the different types of cancer using existing records in epigenetic and / or oncological databases, but, as a bioinformatician, I have never worked with epigenetics data, so I do not know they are available in what format, they require what type of preprocessing, nor what tools I can use to analyze them.
I would really appreciate if someone gave me some basic indications of how I should start, or if someone recommended me a paper or tutorial about how to work with epigenetic data in cancer bioinformatics.
Hi Antonio,
To get an idea of the data and the tools available for epigenetic analysis, please refer the links below:
https://epigenie.com/epigenetic-tools-and-databases/
https://www.encodeproject.org/
Medvedeva, Y. A., Lennartsson, A., Ehsani, R., Kulakovskiy, I. V., Vorontsov, I. E., Panahandeh, P., Khimulya, G., Kasukawa, T., FANTOM Consortium, & Drabløs, F. (2015). EpiFactors: a comprehensive database of human epigenetic factors and complexes. Database : the journal of biological databases and curation, 2015, bav067. https://doi.org/10.1093/database/bav067
Hope this helps.
Epigenetics is very broad, so it matters what data you really want to look into.
It can be ChIP-seq, ATAC-seq, DNase-seq, WGBS/RRBS, Hi-C etc.
They may share some processing steps, however the downstream analysis is mostly different.
So it would be helpful if you are clear what kind of epigenetic assay you will work on.
Feng Yan thank you! After reviewing some articles I want to start with methylation patterns in promoters and body of genes.
Jyoti Motwani it helps so much, thank you very much!
I am glad that the links were helpful. If you are interested in methylation data of cancers, TCGA database would be a good place to explore methylation data. TCGA has cancer data for 33 cancer types (https://www.cancer.gov/about-nci/organization/ccg/research/structural-genomics/tcga) . Before exploring TCGA datasets, you can briefly visualize the TCGA data using Xena browser (https://xenabrowser.net/) or cBioportal (https://www.cbioportal.org/).
Good luck with your analysis.
If you are interested in a particular gene, UCSC genome browser HAIB Methyl RRBS Track ( http://genome.ucsc.edu/cgi-bin/hgTrackUi?hgsid=741432113_bVLYtBtfk8Z7sbbl5xrAEB9eKWTn&c=chr7&g=wgEncodeHaibMethylRrbs) is a good place, too.
Liying Yan thank you so much, it is being so useful for me!
Hi Antonio,
You can find a complete analysis pipeline from this link below:
A cross-package Bioconductor workflow for analysing methylation array data [version 3; peer review: 4 approved]
https://f1000research.com/articles/5-1281/v3
You need to install minfi package and start doing analysis following this tutorial.
http://bioconductor.org/packages/release/bioc/html/minfi.html
You also can find a lot of video tutorials at HarvardX, such as PH525.8x Case study: DNA methylation data analysis.
Also a book: http://genomicsclass.github.io/book/
One of my recent clinical study is based on methylation "Clinical impact of combined epigenetic and molecular analysis of pediatric low grade gliomas."
Please let me know if this is interesting to you,
Mamatjan
Yasin Mamatjan thank you so much! Those packages and that book can really help me with my project! I'm reading all the documentation. Thank you!
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