Whole genome enrichment analysis of the number of QTL/association found
on user selected chromosomes / chromosomal sub-regions
The design of this trait enrichment analysis tool aims at allowing evaluation
of all reported QTL/associations of selected traits throughout a genome, to
determine if a trait or traits are over-represented in one or more regions of
the genome. The setup of the analysis is based on an underlining assumption,
that the selected traits are related. For example the traits may belong to
a given trait type, or are from a given trait ontology path.
In this implementation we used Chi-squared analysis of the frequencies of
reported QTL/associations classified by traits and their chromosome locations.
The contingency p-values (p) are estimated to indicate the degree of
over-representations (enrichments) of QTL/associations. The false discovery
rates (FDR) is also estimated with Benjamini–Hochberg procedure. The size of
Chi-squares in each contingency class are graphically indicated with bars of
varying lengthes drawn with transformed Chi-square values.
In addition, some available trait correlation data are appended when available,
to provide additional support information for users to evaluate the results.