Hi, I applied KEGG pathway enrichment analysis to multiple extracted communities from a gene network (Fisher's exact test was used to perform enrichment analysis). Which of the following three is the appropriate multiple corrections method for the p-values obtained by Fisher's exact test?

1. Adjust the p-values for all pathways of all communities.
2. Adjust the p-values of all pathways in one community. Repeat this for all communities.
3. List the pathways with the lowest p-values in each community. Adjust the p-values of the listed pathways.

For example, if there are 10 communities and each community has 20 pathways, the number of p-values to adjust would be:

1. 200 p-values
2. 20 p-values (repeat this for 10 communities)
3. 10 p-values of the listed pathways

I checked several previous studies carrying out similar analyses, but they simply stated that "the obtained p-values are adjusted for multiple testing" and did not give detailed procedures.

The third method was used in: "Castresana-Aguirre M, Guala D, Sonnhammer EL. Benefits and Challenges of Pre-clustered Network-Based Pathway Analysis. Frontiers in genetics. 2022:1168" (https://www.frontiersin.org/articles/10.3389/fgene.2022.855766/full )

Thank you.