which value is selected for pearson correlation for cis and trans target gene prediction ?

Question

[anisha]

I want to analyses the cis and trans target gene from the RNA-seq data. i had read several paper and it shows that either PCC or spearman's correlation is used for finding the cis and trans- target gene

which method is used for finding cis target gene ? for spearman's correlation which value is taken log2fc or p-value?

pls help me

Answer 1

[Michael]

Correlation is not causation, and neither Pearson nor Spearman correlation can give you that, and in particular it cannot give you a direction of the interaction per se. If you are interested in analysis of transcription factors (TF) from RNA-seq data however, you could look into regulatory impact factor (RIF) analysis. We have done RIF analysis, among other things, in a recent paper on our non-model organism. You could try to replicate what we did there if you have enough and suitable measurements.

[anisha]

first i want to anaylse the lncRNA from RNA-seq data after that seperating the cis and trans target gene

[Michael]

Ok, so lncRNA, that is something completely different. I cannot help you much with that. Anyway, correlation alone will not cut it.