Question: Pathway Analysis Of Bacteria Seq Data
2
gravatar for kanwarjag
6.0 years ago by
kanwarjag950
United States
kanwarjag950 wrote:

I have an RNA-seq expression data where I have identified a a set of signature genes which can be associated with treatment of particular drug. In general with human genes, I have used, GSEA, DAVID or even IPA to find out a pathways that can be affected with these genes. Is there and such tool where I can upload gene ids of bacteria and can give something close to getting GO terms or functional pathways.

Thanks

pathway rna-seq go • 4.8k views
ADD COMMENTlink modified 6.0 years ago by sarahhunter600 • written 6.0 years ago by kanwarjag950
2
gravatar for Manu Prestat
6.0 years ago by
Manu Prestat3.9k
Marseille, France
Manu Prestat3.9k wrote:

You can use MEGAN (this works with refseq gene IDs). It's for metagenomics mainly, but you might find it useful anyway. Also, take a look at Voronto. This is a new visualization tool which can generate interactive Voronoi maps with cell areas which grow with the number of total annotations (as far as I understood). It works with several built'in ontologies, and you can use your own.

ADD COMMENTlink modified 6.0 years ago • written 6.0 years ago by Manu Prestat3.9k
1
gravatar for Raygozak
6.0 years ago by
Raygozak1.3k
State College, PA, Penn State
Raygozak1.3k wrote:

The only solution i can find for you is to use the sigPathway package of bioconductor, most web tools seem to be tailored to eukaryotes.

ADD COMMENTlink written 6.0 years ago by Raygozak1.3k
1
gravatar for sarahhunter
6.0 years ago by
sarahhunter600
Cambridge, UK
sarahhunter600 wrote:

You can also use InterProScan (v5) to scan your sequences against the InterPro database. InterProScan5 has the options to include both GO terms and Pathways (e.g. from KEGG) associated with your protein by virtue of the InterPro models (aka "protein signatures") that they match.

As an example, InterPro entry IPR011284 incorporates a predictive signature from TIGRFAMs for the enzyme family 3-oxoacyl-(acyl-carrier-protein) reductase. You can see this family has been associated with the GO terms GO:0006633 (fatty acid biosynthetic process) and GO:0055114 (oxidation-reduction process) as well as being implicated in pathways represented in KEGG, MetaCyc and UniPathway (see the "pathways and interactions" sub-page). So, if you search your sequence against InterPro using InterProScan, and this signature matched to it, InterProScan would also show the associations with the GO terms and Pathways in the output.

Hope this helps!

Sarah

ADD COMMENTlink written 6.0 years ago by sarahhunter600
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