Question

Any Alternative To David Server ?

3

Entering edit mode

13.4 years ago

Radhouane Aniba ▴ 790

Hi All,

I have a huge gene list to characterize functionnaly and I am interested in KEGG pathway enrichment, I took a look at DAVID API and there are several inconvenience using it :

Limitation in the number of queries by day (200 I think)
API not evident to use, there is an R package but also it is not well clear how to use it

So I would like to know what do you recommend for KEGG pathway enrichement tools that could be used programmatically within an automation script.

My list of genes are in Ensembl Gene IDS

Thanks

Rad

api gene kegg • 3.3k views

ADD COMMENT • link updated 13.4 years ago by Khader Shameer 18k • written 13.4 years ago by Radhouane Aniba ▴ 790

2

Entering edit mode

Do you have a special reason why the pathways need to be KEGG?

ADD REPLY • link 13.4 years ago by Chris Evelo 10k

0

Entering edit mode

Yes I am interested in kegg enriched pathways (genes)

ADD REPLY • link 13.4 years ago by Radhouane Aniba ▴ 790

0

Entering edit mode

Do you have more than 200 gene lists ?

ADD REPLY • link 13.4 years ago by Khader Shameer 18k

Ram · Answer 1 · 2011-06-27

Chris's point is very important. KEGG will not be freely available (effective from July 1 2011) for academic community. See pricing and details. At the moment the KEGG API is not affected, but how they are going to deal with third-party providers like DAVID or BioC packages are not clear.

You can use packages like SubPathwayMiner (I used it with NCBI IDs). You can use a standard ID converter to convert your Ensembl IDs. See related posts related to pathway analysis or pathway enrichment here and here.