Enrichment analysis for custom set

Question

[bharata1803]

Hello,

I want to ask if there is an API for doing enrichment analysis by submitting your own set.

For example, I have 5 gene set, Set 1, Set 2, ..., Set 5.

I have a list of gene, gene A,B,C,D.

I want to calculate the enrichment of gene A,B,C,D in the Set 1, Set 2,.., Set 5.

I know several API like enrichr, pantherdb, etc but they can only calculate our submitted gene to their internal gene set database. So, my question is, is there any API that can do this?

I don't know how to implement enrichment analysis myself and I prefer using publicly available tool.

Answer 1

[WouterDeCoster]

This is possible using GSEA.

[bharata1803]

I thought GSEA need gene list with p-value, TPM, or FPKM, right? What I want is similar with DAVID, upload a list of genes and can upload background and then do the enrichment analysis. CMIIW

[WouterDeCoster]

Somewhere in the user guide you can find

Creating Gene Sets
You can use the gene set files available on the Broad ftp site, export gene sets from the MSigDB, or create your own gene sets. To create a gene sets file:

1.       Open Excel or a text editor.

2.       Create a gene sets file using the gmx or gmt file format (see GSEA file formats).

When listing the genes in each gene set, be sure to use the appropriate gene identifiers (HUGO gene symbols or probe identifiers), as described in Consistent Feature Identifiers Across Data Files.

3.       Save the file as a tab-delimited text file with the appropriate file extension (gmx or gmt).

Note: When you create a gene sets file, the GSEA team recommends that the file name include the gene identifier format you used to list the genes; for example, setname_hgu95av2.gct.

[bharata1803]

No, I mean not the gene set definition, but the gene list that I want to calculate the enrichment. In DAVID, we just need to paste the gene symbol right, but I thought in GSEA, we need to submit gene list that contains not only the gene symbol but also the p-value or TPM or FPKM or something else.

Answer 2

[Leite]

Hey,

Similitar to DAVID, You can use PANTHER, Enrichr or yet UNIPROT

Best regards,

Leite

[WouterDeCoster]

Read the question again:

I know several API like enrichr, pantherdb, etc but they can only calculate our submitted gene to their internal gene set database. So, my question is, is there any API that can do this?

[Leite]

OMG sorry for that. I just did not see it.