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BioinformaticsFMRP / TCGAbiolinks

TCGAbiolinks
http://bioconductor.org/packages/devel/bioc/vignettes/TCGAbiolinks/inst/doc/index.html
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Integration of miRNA expression and methylation data. #57

Open cloudred20 opened 7 years ago

cloudred20 commented 7 years ago

The vignette allows integration of mRNA expression and methylation data. Can a similar strategy be employed for miRNA expression and methylation integration????

labrazil commented 7 years ago

It could, but we never tried.

torongs82 commented 7 years ago

hi @megha20 thank you again for your interest in TCGAbiolinks.

When you speak about integration of mRNA expression (DEGs) and methylation data (DMRs) were you interested in showing together in a plot by means of TCGAvisualize_starburst ? It was introduced by Noushmehr et. al @labrazil in 2010 [https://www.ncbi.nlm.nih.gov/pubmed/20399149]. I agree with you to follow a similar strategy using TCGAvisualize_starburst to combine and visualize results from TCGAanalyze_DEA (using mRNA's data or miRNA's data) and TCGAanalyze_DMR (using DNA methylaiton's data). So if it is fine for you my suggestion could be to add some code in TCGAvisualize_starburst that can take in input miRNA DEGs (output from DEA) and input of DMRs or in the same time miRNA DEGs (output from DEA) and mRNA DEGs. @tiagochst can we work on it? In particular considering Biological Integromics Expected proposed by Cava et. al @claudiacava in [http://bmcsystbiol.biomedcentral.com/articles/10.1186/s12918-015-0211-x] miRNA down - mRNA Up - DNA amplification - Hypomethylation - protein up can be significantly associated to miRNA Up - mRNA down- DNA deletion - Hypermethylation - protein down. So lets say that @megha20 can be interested in showing combination of two by two of above conditions, do you agree? If you have any suggestions please you can write us. Best, Antonio.

cloudred20 commented 7 years ago

Ya, it will be helpful if a code can be included such that miRNA DEGs can be used along with DMRs input and a starburst plot can be generated for the same.

labrazil commented 7 years ago

Thinking more about it, it might not be so trivial since the CpG probes were designed to target known TSS. You'll have to hope that the CpG probe is near a known miRNA, but I assume you may be able to find some.

jacorvar commented 4 years ago

Dear all,

has it already been implemented? I've just tried to integrate miRNA expression and methylation data by means of TCGAvisualize_starburst function but it struggles with miRNA IDs and prompts an error.

Thanks