a question about using Enrichr

Question

[roya.solhi]

Hi, I have a question about using Enrich r. Actually I am using Enrichr for analyzing a set of microarray data to find out the most enriched pathways considering a list of down regulated genes. However, I am not sure how to annotate the results, I mean, as you know better, the extracted results, for example by using KEGG library, will have odds ratio for each related pathway, My question is that, in case of using down regulated genes as input data, we should annotate the results in reverse form? I mean if a pathway is enriched with 12 odds ratio, it means that such pathway will be down 12 times in that specific condition? am I right?

Thanks in advance for your kind help

Answer 1

[cfos4698]

Genes in a given contrast might be downregulated in one group compared to the other, as in your case. You might then find a certain KEGG pathway is enriched based on that gene list. This means that more downregulated genes are part of that KEGG pathway than you would expect based on chance alone, given a background list of genes (normally all genes in the transcriptome of your organism).

The example of '12 odds ratio' doesn't refer to expression levels, rather that 12x more genes are assigned to a KEGG pathway than expected by chance alone.