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

Question

[robjohn70000]

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

[dariober]

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.

Answer 1

[5utr]

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

http://pantherdb.org/

[robjohn70000]

Thanks for the info

Answer 2

[Philipp Bayer]

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

[robjohn70000]

Thanks for the info

Answer 3

[diogo.pellegrina]

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.

Answer 4

[EagleEye]

One more option,

Gene Set Clustering based on Functional annotation (GeneSCF)

http://genescf.kandurilab.org

A: Inconsistent numbers when using Kegg pathway analysis via DAVID?

https://www.biostars.org/local/search/page/?q=genescf