Correlation of expression and compartmentalization

Question

[little_more]

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?

[Sean Davis]

What cell line are you using?

[little_more]

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

[Sean Davis]

Which Liberman Aiden paper?

Answer 1

[Sean Davis]

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

[little_more]

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?

[Sean Davis]

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