Recommendation for pathway analysis

Question

[salman_96]

Hi I have a list of SNPs that I annotated to genes. I need some suggestions/recommendations that what kind of online tools other than can I use for pathway analysis.

Regards

Answer 1

[ATpoint]

I like https://biit.cs.ut.ee/gprofiler/gost because it allows to set a background.

Alternatively, there is https://maayanlab.cloud/Enrichr/ which does not allow background but has a richer set of annotations compared to g:profiler.

Answer 2

[c0tton]

I like fgsea for R You can pick your gene set, e.g. KEGG or GO, using msigdbr

[ATpoint]

OP seems to simply have a list of genes that have a SNP, hence the principle of fGSEA does not apply here which is comparing rank distributions of a test set and a reference (a gene set).

SNPs are binary information whereas fGSEA needs some a vector with ranked values from a comparison, e.g. genes ranked by fold change between two conditions.