Question: find cancer related methylation in lncRNA though online database
0
gravatar for yoman
2.4 years ago by
yoman 0
yoman 0 wrote:

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?

lncrna tool methylation • 858 views
ADD COMMENTlink modified 2.4 years ago by Charles Warden6.4k • written 2.4 years ago by yoman 0

Hi Yoman,

Please provide more information.

Cheers, Wouter

ADD REPLYlink written 2.4 years ago by WouterDeCoster37k

not sure any tool or any package can help for select the cancer-related lncRNA that is due to the hypomethylated of DNA

ADD REPLYlink written 2.4 years ago by yoman 0

I'm sorry, your posts don't make sense to me.

ADD REPLYlink written 2.4 years ago by WouterDeCoster37k

i would said i am finding Cancer-Associated Epigenetically Silenced lncRNAs in cancer , how could i achieve this

ADD REPLYlink written 2.4 years ago by yoman 0
1

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

ADD REPLYlink written 2.4 years ago by Satyajeet Khare1.3k
0
gravatar for Shicheng Guo
2.4 years ago by
Shicheng Guo7.4k
Shicheng Guo7.4k wrote:

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

ADD COMMENTlink modified 2.4 years ago • written 2.4 years ago by Shicheng Guo7.4k
0
gravatar for Charles Warden
2.4 years ago by
Charles Warden6.4k
Duarte, CA
Charles Warden6.4k wrote:

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.

ADD COMMENTlink written 2.4 years ago by Charles Warden6.4k
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