Question

Correlation of expression and compartmentalization

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6.7 years ago

little_more ▴ 70

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 • 1.4k views

ADD COMMENT • link updated 6.7 years ago by Sean Davis 27k • written 6.7 years ago by little_more ▴ 70

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What cell line are you using?

ADD REPLY • link 6.7 years ago by Sean Davis 27k

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

ADD REPLY • link 6.7 years ago by little_more ▴ 70

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Which Liberman Aiden paper?

ADD REPLY • link 6.7 years ago by Sean Davis 27k

score 0 · Answer 1 · 2018-03-17

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6.7 years ago

Sean Davis 27k

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

ADD COMMENT • link 6.7 years ago by Sean Davis 27k

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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 REPLY • link 6.1 years ago by little_more ▴ 70

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

ADD REPLY • link 6.7 years ago by Sean Davis 27k