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Any Alternative To David Server ?

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 :

  1. Limitation in the number of queries by day (200 I think)
  2. 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
• 4,000 views • link
updated by Khader Shameer Khader Shameer • written by Radhouane Aniba Radhouane Aniba

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

• 0 views • link
written by Chris Evelo Chris Evelo

Yes I am interested in kegg enriched pathways (genes)

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written by Radhouane Aniba Radhouane Aniba

Do you have more than 200 gene lists ?

• 0 views • link
written by Khader Shameer Khader Shameer

1 answer

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.

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updated by Ram Ram • written by Khader Shameer Khader Shameer

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