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Alternative tools to DAVID pathway clustering analysis for lists of bateria genes

Hi,

In the past I have used DAVID pathway clustering tool to get enriched clusters of genes for various biological pathways using lists of genes as inputs. Recently, there is a concern that DAVID's annotation may not be up-to-date. I wonder if there is any similar tool that allows genes lists as inputs and uses specific annotation databases(e.g., kegg) for bacteria such as Salmonella and Streptococcus sp.

Thanks

transcriptome pathway rna-seq gene r
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updated by Ram Ram • written by robjohn70000 robjohn70000

I sympathize with this question even if I work with mainstream genomes. What I like of DAVID is that there is a nice interface for R (RDAVIDWebService) which generates very useful summary tables. Other packages like topGO or GOseq give an output that is much less useful.

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written by dariober dariober

4 answers

You can use PANTHER, last update may 2015, that includes Salmonella and Streptococcus.

http://pantherdb.org/

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written by 5utr 5utr

Thanks for the info

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updated by Ram Ram • written by robjohn70000 robjohn70000

If you like to use R, there's topGO. Here's the vignette going through a simple example.

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updated by Ram Ram • written by Philipp Bayer Philipp Bayer

Thanks for the info

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updated by Ram Ram • written by robjohn70000 robjohn70000

I know it's been a while since it was posted, but I've been looking for a DAVID alternative that had the option of imputing a gene background list, and few available tools (besides DAVID) have this option.

I've found this gProfiler (http://biit.cs.ut.ee/gprofiler/index.cgi) and it seems to be great, working both online, in python, and in R.

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written by diogo.pellegrina • diogo.pellegrina

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