Biostar Beta. Not for public use.
Correlation of expression and compartmentalization
0
Entering edit mode
16 months ago

Hello everyone! Suppose I defined two compartments 1 and 2 and I have a number of vectors with probabilities of a chromosomal locus to be in a compartment 1 for each chromosome. How can I estimate the Spearman correlation between expression and compartmentalization for each chromosome for the known cell line? What database should be used for obtaining tracks for expression levels?

RNA-Seq R • 514 views
ADD COMMENTlink
0
Entering edit mode

What cell line are you using?

ADD REPLYlink
0
Entering edit mode

k562, for example. I'd like to compute Spearman correlation as in the Liberman-aiden paper.

ADD REPLYlink
0
Entering edit mode

Which Liberman Aiden paper?

ADD REPLYlink
0
Entering edit mode
14 months ago
National Institutes of Health, Bethesda…

https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSM922957

ADD COMMENTlink
0
Entering edit mode

Well, thank you for the link, but the question was actually about the way to estimate correlation. Moreover, how to use a .bigwig file for that?

ADD REPLYlink
0
Entering edit mode

I was replying to your question about what "database" to use for the data and your reply about using k562.

ADD REPLYlink

Login before adding your answer.

Similar Posts
Loading Similar Posts
Powered by the version 2.1