Question: ClusterProfiler : What is GeneRatio and BgRatio?
3
gravatar for ZheFrench
3.8 years ago by
ZheFrench300
France
ZheFrench300 wrote:

Question is in the title.

GeneRatio is like M/N where M is the number of genes from your input list that match the GO term. But I don't see what is N ?

BgRatio is like A/B where B is all genes in database but I'm not sure what A corresponds to ... Is it the number of genes specific in the database of this GO term ?

Tell me if I'm wrong. Thanks.

clusterprofiler • 12k views
ADD COMMENTlink modified 2.5 years ago by molla.linda80 • written 3.8 years ago by ZheFrench300
8
gravatar for molla.linda
2.5 years ago by
molla.linda80
United States
molla.linda80 wrote:

I will give an example to explain this that helped me understand it. I also was looking for the answer and Guangchuang link helped.

Let is suppose I have a collection of genesets called : HALLMARK Now let is suppose there is a specific geneset there called: E2F_targets

BgRatio, M/N.

M = size of the geneset (eg size of the E2F_targets); (is the number of genes within that distribution that are annotated (either directly or indirectly) to the node of interest).

N = size of all of the unique genes in the collection of genesets (example the HALLMARK collection); (is the total number of genes in the background distribution (universe)

GeneRatio is k/n.

k = size of the overlap of 'a vector of gene id' you input with the specific geneset (eg E2F_targets), only unique genes; (the number of genes within that list n, which are annotated to the node.

n = size of the overlap of 'a vector of gene id' you input with all the members of the collection of genesets (eg the HALLMARK collection),only unique genes; is the size of the list of genes of interest

ADD COMMENTlink modified 2.5 years ago • written 2.5 years ago by molla.linda80
3
gravatar for Guangchuang Yu
3.8 years ago by
Guangchuang Yu2.3k
China/Guangzhou/Southern Medical University
Guangchuang Yu2.3k wrote:

see https://bioconductor.org/packages/release/bioc/vignettes/DOSE/inst/doc/enrichmentAnalysis.html#over-representation-analysis

Corresponding to the formula, geneRatio is k/n.

ADD COMMENTlink written 3.8 years ago by Guangchuang Yu2.3k

I'm a little confused about these terms.

When I;ve used the same gene set, why do my numbers of n and N change when doing gene ontology for different categories.

For example, for the same gene list for an overrepresentation test in Biological Processes for taxis GeneRatio is 209/3770 and BGRatio is 440/12553 but for Cellular Components for the term extracellular matrix, the Gene Ratio is 162/3963 and Bg Ratio is 339/13183. Shouldn't the n and N values stay the same in different GO categories?

Cheers

ADD REPLYlink modified 14 months ago • written 14 months ago by unawaz50
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