Question: Small genomic region proximity enrichment
0
gravatar for Nicolas Rosewick
4.9 years ago by
Belgium, Brussels
Nicolas Rosewick8.3k wrote:

Hi,

I've a bunch of very small genomic regions (< 1kb) that seems to be non-randomly distributed into the genome. Anyone has an idea to test wheter these regions are close together ? or some of them are clustered in specific genomic regions ?

For the first question, I was thinking to use a kolmogorov-smirnov test to test if the small regions coordinates are uniformly distributed across the genome.. any advice ?

>edit : I'm working in human ( ~ 70 regions of less than 1 kb )

Thanks

proximity genomic enrichment • 1.1k views
ADD COMMENTlink modified 4.9 years ago by Zev.Kronenberg11k • written 4.9 years ago by Nicolas Rosewick8.3k

Hi,

The following details might help us help you better:

  1. The organism you are working on
  2. Details on the genomic region data you already have

Thank you!

ADD REPLYlink written 4.9 years ago by RamRS24k

I edited the main post

ADD REPLYlink written 4.9 years ago by Nicolas Rosewick8.3k

Thank you. Could you also add details on the data - you have given us the biological premise, but not the structure of the data. What do you have - only the sequence or any mapping details (such as chromosome to which these regions map or any genes these regions are linked to). That would help too!

ADD REPLYlink written 4.9 years ago by RamRS24k

I've the sequences, and the associated alignment (blat)

ADD REPLYlink written 4.9 years ago by Nicolas Rosewick8.3k

How did you find the regions originally? The tricky part to deal with is that if this was generated by sequencing then you wouldn't expect regions to be randomly located due to various biases (GC content, mappability, etc.).

ADD REPLYlink written 4.9 years ago by Devon Ryan92k

yes my data originate from RNA-Seq data. It's a good point to take that into account

ADD REPLYlink written 4.9 years ago by Nicolas Rosewick8.3k
1
gravatar for Zev.Kronenberg
4.9 years ago by
United States
Zev.Kronenberg11k wrote:

There is a really good R package for testing these sorts of questions: http://genometricorr.sourceforge.net

ADD COMMENTlink modified 27 days ago by RamRS24k • written 4.9 years ago by Zev.Kronenberg11k
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