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Small genomic region proximity enrichment

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 whether 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

enrichment genomic proximity
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updated by Ram Ram • written by Nicolas Rosewick Nicolas Rosewick

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!

• 0 views • link
written by Ram Ram

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!

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written by Ram Ram

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

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updated by Ram Ram • written by Nicolas Rosewick Nicolas Rosewick

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.).

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updated by Ram Ram • written by Devon Ryan Devon Ryan

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

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updated by Ram Ram • written by Nicolas Rosewick Nicolas Rosewick

1 answer

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

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updated by Ram Ram • written by Zev.Kronenberg Zev.Kronenberg

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