Question: statistical tests to show the specificity of a phenomenon (eg increase in H3K27me3 mark)
0
gravatar for Bogdan
2.8 years ago by
Bogdan580
Palo Alto, CA, USA
Bogdan580 wrote:

Dear all, 

although this may not be a question specifically for BioC, thought that I can still post it (if you do not mind), shall any packages for ChIP-seq analysis/statistical analysis be available to address it.

the question regards the statistical tests to show the specificity of phenomenon : let's consider an example - someone did a ChIP_seq for H3K27me3, and wants to show that a histone mark (eg H3K27me3 mark) increases on the genes involved in a particular biological process (eg 300 autophagy-related genes , from a total of 1000 genes with increased H3K27me3) after cell treatment .

what type of analysis would you recommend in order to show that the phenomenon (ie increase in H3K27me3) is specific to a set of genes (ie autophagy genes) :

-- taking random sets of non-autophagy genes (practically, the rest of the genes in the genome) -- and using parametric and non-parametric tests when comparing SET 1 (autophagy genes) with SET 2 (non-autophagy genes)

or

-- using hypergeometric / fisher-tests on a matrix (autophagy/no-autophagy genes vs increase/no-increase in H3K27me3) ?

thanks a lot, and happy weekend ;) !

bogdan

chip-seq • 397 views
ADD COMMENTlink modified 2.8 years ago by Wolfgang Huber13k • written 2.8 years ago by Bogdan580
Answer: statistical tests to show the specificity of a phenomenon (eg increase in H3K27m
3
gravatar for Wolfgang Huber
2.8 years ago by
EMBL European Molecular Biology Laboratory
Wolfgang Huber13k wrote:

Bogdan

The main point is: don't use a test, or the language and concepts of testing here. Rejecting a null hypothesis of non-specificity is near to uninformative (boring, besides the point, ridiculous, ...) with regard to the strength of specificity, since such a hypothesis test would confound effect size and sample size.

Instead, choose a reasonable quantitative summary statistic (e.g. odds-ratio, or other measures of enrichment) and in addition to its point estimate, get information about the associated distribution or confidence region by resampling, e.g,. bootstrap. The choice of which summary statistic to use is less a statistical question but a biological one, and presumably you can consider several.

Wolfgang
 

ADD COMMENTlink modified 2.8 years ago • written 2.8 years ago by Wolfgang Huber13k

Dear Wolfgang, greetings, very glad to hear from you, and thank you for your comments and suggestions ;)

 

ADD REPLYlink written 2.8 years ago by Bogdan580
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