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Question: Correct for Gene Length bias in GO analysis of retrotransposition
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gravatar for mujupas
8 months ago by
mujupas0
mujupas0 wrote:

Hi,

in my lab we have captured and sequenced L1 and ALU retrotransposons form many tissue samples from different donors/conditions.

We're now running GOstats using the list of detected somatic insertions withing Refseq genes +/- 1Kb in order to look for tissue-specific and condition-specific patterns for somatic retrotransposition events.  

A known issue in the field is that since neuronal related genes on average longer that other annotated protein-coding genes, neuronal-related GO terms will show up as the most enriched in any case, no matter the tissue in examination, unless a proper background noise filtering is applied. This can be easily verified by generating a list of random bedtools intervals to simulate a set of insertions from a real experiment, intersecting the intervals with Refseq genes coordinates and running a GO analysis on the intersection, as explained and illustrated in a nice review by Thomas C.A. et al. (http://www.ncbi.nlm.nih.gov/pubmed/23057747, Fig.1).

What is in your opinion the best way to correct for this bias in this kind of analyses?

Thank you in advance.

ADD COMMENTlink modified 8 months ago by Gordon Smyth32k • written 8 months ago by mujupas0
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gravatar for Gordon Smyth
8 months ago by
Gordon Smyth32k
Walter and Eliza Hall Institute of Medical Research, Melbourne, Australia
Gordon Smyth32k wrote:

The goseq package is specifically designed to do a GO analysis adjusting for gene length.

ADD COMMENTlink written 8 months ago by Gordon Smyth32k
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