Question: how to analyze/integrate methylation "beta value" and RNA-seq "FPKM" data from only one cell line
0
gravatar for maria2019
2 days ago by
maria2019100
maria2019100 wrote:

Hi,

I have all different kinds of sequencing data (methylation, RNA_seq, ATAC, etc) for only one cancer cell line - no control !!!!!

In fact, I only have "beta value" for methylation, "FPKM" for RNA-seq, etc and no Fold change because there is no Control data.

Is there ANY possible way to integrate or analyze these data for just one cell line and report the characteristics of the cell line? - Any paper in this regards?

ADD COMMENTlink modified 1 day ago • written 2 days ago by maria2019100
1
gravatar for Kevin Blighe
2 days ago by
Kevin Blighe61k
Kevin Blighe61k wrote:

What has your supervisor tasked you to do? - just 'analyse' the data and that's all, with no reason given?

With just a single sample for each data-type, you can simply look at the values over your genes of interest. The beta value is a measure of methylation ranging from 0 to 1, while FPKM is a decent / okay measure of expression in just a single sample. You have not mentioned the units that you have for ATAC-seq.

Some options:

  • load the data into a visualiser like UCSC Genome Browser
  • generate some side-by-side heatmaps over genes of interest
  • use GenomicRanges to programmatically find regions that fit certain filter criteria, like High Methylation Beta + Low Expression FPKM + Low ATAC-seq reads

You will think of something to do.

Kevin

ADD COMMENTlink modified 2 days ago • written 2 days ago by Kevin Blighe61k

Thank you Kevin, that would be a good start

ADD REPLYlink written 1 day ago by maria2019100
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