I am going to do some analysis on Cancer related LncRNA , so i am going to find some target lncRNA
By access the online database , How can i select out the LncRNA that is cancer related which is due to the DNA methylation (by comparing with the normal case) what filter i should apply?
2 answers
Quite Easy:
1, Find the genomic regions of whole lncRNA in human genome.
2, Collect genome-wide DNA methylation data from Roadmap Epignomics, TCGA, BluePrint project.
3, Build statistical inference method to connect methylation and lncRNA between cancer and normal.
Done
If you really mean "in" lncRNAs (as in RNA methylation), then that may be a little harder to collect than nearby or overlapping DNA methylation.
That said, it looks like there is at least one database for m6A modifications (for mammals):
http://compgenomics.utsa.edu/methylation/
--> MeT-DB Paper
However, I have not had a chance to take a close look at this data.
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Hi Yoman,
Please provide more information.
Cheers, Wouter
not sure any tool or any package can help for select the cancer-related lncRNA that is due to the hypomethylated of DNA
I'm sorry, your posts don't make sense to me.
i would said i am finding Cancer-Associated Epigenetically Silenced lncRNAs in cancer , how could i achieve this
Yoman,
It's a project rather than a query. You need to perform transcriptome analysis to identify differentially expressed lncRNAs. Perform methylome analysis on same or similar samples and identify differentially methylated regions. Combine the two datasets to identify lncRNA expression changes that correlate with change in promoter methylation and finally perform some additional experiments to confirm that the relationship is causal.
Else, you can look for processed data in published papers and see if you can draw the relationship.
Best