Question: Alternative tools to DAVID pathway clustering analysis for lists of bateria genes
2
gravatar for robjohn70000
3.2 years ago by
robjohn70000110
Nigeria
robjohn70000110 wrote:

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



 

ADD COMMENTlink modified 2.1 years ago by EagleEye5.7k • written 3.2 years ago by robjohn70000110

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.

ADD REPLYlink written 3.1 years ago by dariober9.5k
1
gravatar for Gian
3.1 years ago by
Gian350
Canada
Gian350 wrote:

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

http://pantherdb.org/

ADD COMMENTlink written 3.1 years ago by Gian350

Thanks for the info
 

ADD REPLYlink written 3.0 years ago by robjohn70000110
1
gravatar for Philipp Bayer
3.1 years ago by
Philipp Bayer5.7k
Australia/Perth/UWA
Philipp Bayer5.7k wrote:

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

ADD COMMENTlink written 3.1 years ago by Philipp Bayer5.7k

Thanks for the info


 

ADD REPLYlink written 3.0 years ago by robjohn70000110
0
gravatar for diogo.pellegrina
2.1 years ago by
Universidade de São Paulo
diogo.pellegrina0 wrote:

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.

ADD COMMENTlink modified 2.1 years ago • written 2.1 years ago by diogo.pellegrina0
0
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