8 GO/KEGG enrichment analysis

Performing functional enrichment analysis for given gene sets using the hypergeometric test.

8.1 Principles of over-representation enrichment analysis

1. Let’s assume there are total m genes with Gene ontology annotation in Andrographis paniculata and there are n genes in pathway A.
2. We have got a gene set G with k genes. Among them, l genes are located in pathway A.
3. Question: Would genes in gene set G be enriched in pathway A?

	User Genes	Genome
In Pathway	l	n-l
Not In Pathway	k-l	m-k-n+l

4. A statistical variable odds ratio would be computed:

\(Odds\ ratio = \frac{l * (m-k-n+l)}{(k-l) * (n-l)}\)

5. Hypothesis: Odds ratio equals 1. A Hypergeometric test would be used to check if the Odds ratio > 1.

8.2 Choose options for each required parameters step by step

Just select each parameter sequentially as labeled in the figure (or simply just click the Demo1 button).

Figure 8.1: A screenshot of the one type of selection for GO Biological process enrichment for some differentially expressed genes identified in chapter 5.

Clicking Submit, after several seconds, one bubble plot and one table are generated below.

Note

Users are allowed to choose which enriched terms to be visualized in the bubble plot.

Note

Users could check gene detail information by clicking gene names in the enrichment table.